update to Gradle 8.5

build.gradle

@@ -1,10 +1,12 @@
+
 plugins {
-    id "de.marcphilipp.nexus-publish" version "0.4.0"
+    id 'maven-publish'
-    id "io.codearte.nexus-staging" version "0.21.1"
+    id 'signing'
+    id "io.github.gradle-nexus.publish-plugin" version "2.0.0-rc-1"
 }
 
 wrapper {
-    gradleVersion = "${project.property('gradle.wrapper.version')}"
+    gradleVersion = libs.versions.gradle.get()
     distributionType = Wrapper.DistributionType.ALL
 }
 
@@ -25,9 +27,9 @@ ext {
 
 subprojects {
     apply plugin: 'java-library'
-    apply from: rootProject.file('gradle/ide/idea.gradle')
     apply from: rootProject.file('gradle/compile/java.gradle')
     apply from: rootProject.file('gradle/test/junit5.gradle')
-    apply from: rootProject.file('gradle/publishing/publication.gradle')
+    apply from: rootProject.file('gradle/publish/maven.gradle')
 }
-apply from: rootProject.file('gradle/publishing/sonatype.gradle')
+apply from: rootProject.file('gradle/publish/sonatype.gradle')
+apply from: rootProject.file('gradle/publish/forgejo.gradle')

gradle.properties

@@ -1,5 +1,3 @@
 group = org.xbib
 name = archive
-version = 1.0.0
+version = 4.0.0
-
-gradle.wrapper.version = 6.4.1

gradle/compile/java.gradle

@@ -2,17 +2,12 @@
 apply plugin: 'java-library'
 
 java {
+    toolchain {
+        languageVersion = JavaLanguageVersion.of(21)
+    }
     modularity.inferModulePath.set(true)
-}
+    withSourcesJar()
-
+    withJavadocJar()
-compileJava {
-    sourceCompatibility = JavaVersion.VERSION_11
-    targetCompatibility = JavaVersion.VERSION_11
-}
-
-compileTestJava {
-    sourceCompatibility = JavaVersion.VERSION_11
-    targetCompatibility = JavaVersion.VERSION_11
 }
 
 jar {
@@ -21,15 +16,14 @@ jar {
     }
 }
 
-task sourcesJar(type: Jar, dependsOn: classes) {
+tasks.withType(JavaCompile) {
-    classifier 'sources'
+    options.fork = true
-    from sourceSets.main.allSource
+    options.forkOptions.jvmArgs += ['-Duser.language=en','-Duser.country=US']
+    options.compilerArgs << '-Xlint:all,-fallthrough'
+    options.encoding = 'UTF-8'
 }
 
-task javadocJar(type: Jar, dependsOn: javadoc) {
+javadoc {
-    classifier 'javadoc'
+    options.addStringOption('Xdoclint:none', '-quiet')
-}
+    options.encoding = 'UTF-8'
-
-artifacts {
-    archives sourcesJar, javadocJar
 }

gradle/publish/forgejo.gradle

@@ -0,0 +1,16 @@
+if (project.hasProperty('forgeJoToken')) {
+    publishing {
+        repositories {
+            maven {
+                url 'https://xbib.org/api/packages/joerg/maven'
+                credentials(HttpHeaderCredentials) {
+                    name = "Authorization"
+                    value = "token ${project.property('forgeJoToken')}"
+                }
+                authentication {
+                    header(HttpHeaderAuthentication)
+                }
+            }
+        }
+    }
+}

gradle/publish/ivy.gradle

@@ -0,0 +1,27 @@
+apply plugin: 'ivy-publish'
+
+publishing {
+    repositories {
+        ivy {
+            url = "https://xbib.org/repo"
+        }
+    }
+    publications {
+        ivy(IvyPublication) {
+            from components.java
+            descriptor {
+                license {
+                    name = 'The Apache License, Version 2.0'
+                    url = 'http://www.apache.org/licenses/LICENSE-2.0.txt'
+                }
+                author {
+                    name = 'Jörg Prante'
+                    url = 'http://example.com/users/jane'
+                }
+                descriptor.description {
+                    text = rootProject.ext.description
+                }
+            }
+        }
+    }
+}

gradle/publish/maven.gradle

@@ -1,13 +1,10 @@
 
-apply plugin: "de.marcphilipp.nexus-publish"
-
 publishing {
     publications {
-        mavenJava(MavenPublication) {
+        "${project.name}"(MavenPublication) {
             from components.java
-            artifact sourcesJar
-            artifact javadocJar
             pom {
+                artifactId = project.name
                 name = project.name
                 description = rootProject.ext.description
                 url = rootProject.ext.url
@@ -49,16 +46,6 @@ publishing {
 if (project.hasProperty("signing.keyId")) {
     apply plugin: 'signing'
     signing {
-        sign publishing.publications.mavenJava
+        sign publishing.publications."${project.name}"
-    }
-}
-
-nexusPublishing {
-    repositories {
-        sonatype {
-            username = project.property('ossrhUsername')
-            password = project.property('ossrhPassword')
-            packageGroup = "org.xbib"
-        }
     }
 }

gradle/publish/sonatype.gradle

@@ -0,0 +1,11 @@
+if (project.hasProperty('ossrhUsername') && project.hasProperty('ossrhPassword')) {
+    nexusPublishing {
+        repositories {
+            sonatype {
+                username = project.property('ossrhUsername')
+                password = project.property('ossrhPassword')
+                packageGroup = "org.xbib"
+            }
+        }
+    }
+}

gradle/publishing/sonatype.gradle

@@ -1,11 +0,0 @@
-
-if (project.hasProperty('ossrhUsername') && project.hasProperty('ossrhPassword')) {
-
-    apply plugin: 'io.codearte.nexus-staging'
-
-    nexusStaging {
-        username = project.property('ossrhUsername')
-        password = project.property('ossrhPassword')
-        packageGroup = "org.xbib"
-    }
-}

gradle/test/junit5.gradle

@@ -1,12 +1,10 @@
 
-def junitVersion = project.hasProperty('junit.version')?project.property('junit.version'):'5.6.2'
-def hamcrestVersion = project.hasProperty('hamcrest.version')?project.property('hamcrest.version'):'2.2'
-
 dependencies {
-    testImplementation "org.junit.jupiter:junit-jupiter-api:${junitVersion}"
+    testImplementation testLibs.junit.jupiter.api
-    testImplementation "org.junit.jupiter:junit-jupiter-params:${junitVersion}"
+    testImplementation testLibs.junit.jupiter.params
-    testImplementation "org.hamcrest:hamcrest-library:${hamcrestVersion}"
+    testImplementation testLibs.hamcrest
-    testRuntimeOnly "org.junit.jupiter:junit-jupiter-engine:${junitVersion}"
+    testRuntimeOnly testLibs.junit.jupiter.engine
+    testRuntimeOnly testLibs.junit.jupiter.platform.launcher
 }
 
 test {

gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,7 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-6.4.1-all.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.5-all.zip
+networkTimeout=10000
+validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

gradlew

@@ -1,7 +1,7 @@
-#!/usr/bin/env sh
+#!/bin/sh
 
 #
-# Copyright 2015 the original author or authors.
+# Copyright © 2015-2021 the original authors.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -17,67 +17,99 @@
 #
 
 ##############################################################################
-##
+#
-##  Gradle start up script for UN*X
+#   Gradle start up script for POSIX generated by Gradle.
-##
+#
+#   Important for running:
+#
+#   (1) You need a POSIX-compliant shell to run this script. If your /bin/sh is
+#       noncompliant, but you have some other compliant shell such as ksh or
+#       bash, then to run this script, type that shell name before the whole
+#       command line, like:
+#
+#           ksh Gradle
+#
+#       Busybox and similar reduced shells will NOT work, because this script
+#       requires all of these POSIX shell features:
+#         * functions;
+#         * expansions «$var», «${var}», «${var:-default}», «${var+SET}»,
+#           «${var#prefix}», «${var%suffix}», and «$( cmd )»;
+#         * compound commands having a testable exit status, especially «case»;
+#         * various built-in commands including «command», «set», and «ulimit».
+#
+#   Important for patching:
+#
+#   (2) This script targets any POSIX shell, so it avoids extensions provided
+#       by Bash, Ksh, etc; in particular arrays are avoided.
+#
+#       The "traditional" practice of packing multiple parameters into a
+#       space-separated string is a well documented source of bugs and security
+#       problems, so this is (mostly) avoided, by progressively accumulating
+#       options in "$@", and eventually passing that to Java.
+#
+#       Where the inherited environment variables (DEFAULT_JVM_OPTS, JAVA_OPTS,
+#       and GRADLE_OPTS) rely on word-splitting, this is performed explicitly;
+#       see the in-line comments for details.
+#
+#       There are tweaks for specific operating systems such as AIX, CygWin,
+#       Darwin, MinGW, and NonStop.
+#
+#   (3) This script is generated from the Groovy template
+#       https://github.com/gradle/gradle/blob/HEAD/subprojects/plugins/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt
+#       within the Gradle project.
+#
+#       You can find Gradle at https://github.com/gradle/gradle/.
+#
 ##############################################################################
 
 # Attempt to set APP_HOME
+
 # Resolve links: $0 may be a link
-PRG="$0"
+app_path=$0
-# Need this for relative symlinks.
+
-while [ -h "$PRG" ] ; do
+# Need this for daisy-chained symlinks.
-    ls=`ls -ld "$PRG"`
+while
-    link=`expr "$ls" : '.*-> \(.*\)$'`
+    APP_HOME=${app_path%"${app_path##*/}"}  # leaves a trailing /; empty if no leading path
-    if expr "$link" : '/.*' > /dev/null; then
+    [ -h "$app_path" ]
-        PRG="$link"
+do
-    else
+    ls=$( ls -ld "$app_path" )
-        PRG=`dirname "$PRG"`"/$link"
+    link=${ls#*' -> '}
-    fi
+    case $link in             #(
+      /*)   app_path=$link ;; #(
+      *)    app_path=$APP_HOME$link ;;
+    esac
 done
-SAVED="`pwd`"
-cd "`dirname \"$PRG\"`/" >/dev/null
-APP_HOME="`pwd -P`"
-cd "$SAVED" >/dev/null
 
-APP_NAME="Gradle"
+# This is normally unused
-APP_BASE_NAME=`basename "$0"`
+# shellcheck disable=SC2034
-
+APP_BASE_NAME=${0##*/}
-# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+# Discard cd standard output in case $CDPATH is set (https://github.com/gradle/gradle/issues/25036)
-DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
+APP_HOME=$( cd "${APP_HOME:-./}" > /dev/null && pwd -P ) || exit
 
 # Use the maximum available, or set MAX_FD != -1 to use that value.
-MAX_FD="maximum"
+MAX_FD=maximum
 
 warn () {
     echo "$*"
-}
+} >&2
 
 die () {
     echo
     echo "$*"
     echo
     exit 1
-}
+} >&2
 
 # OS specific support (must be 'true' or 'false').
 cygwin=false
 msys=false
 darwin=false
 nonstop=false
-case "`uname`" in
+case "$( uname )" in                #(
-  CYGWIN* )
+  CYGWIN* )         cygwin=true  ;; #(
-    cygwin=true
+  Darwin* )         darwin=true  ;; #(
-    ;;
+  MSYS* | MINGW* )  msys=true    ;; #(
-  Darwin* )
+  NONSTOP* )        nonstop=true ;;
-    darwin=true
-    ;;
-  MINGW* )
-    msys=true
-    ;;
-  NONSTOP* )
-    nonstop=true
-    ;;
 esac
 
 CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
@@ -87,9 +119,9 @@ CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
 if [ -n "$JAVA_HOME" ] ; then
     if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
         # IBM's JDK on AIX uses strange locations for the executables
-        JAVACMD="$JAVA_HOME/jre/sh/java"
+        JAVACMD=$JAVA_HOME/jre/sh/java
     else
-        JAVACMD="$JAVA_HOME/bin/java"
+        JAVACMD=$JAVA_HOME/bin/java
     fi
     if [ ! -x "$JAVACMD" ] ; then
         die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME
@@ -98,88 +130,120 @@ Please set the JAVA_HOME variable in your environment to match the
 location of your Java installation."
     fi
 else
-    JAVACMD="java"
+    JAVACMD=java
-    which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+    if ! command -v java >/dev/null 2>&1
+    then
+        die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
 
 Please set the JAVA_HOME variable in your environment to match the
 location of your Java installation."
+    fi
 fi
 
 # Increase the maximum file descriptors if we can.
-if [ "$cygwin" = "false" -a "$darwin" = "false" -a "$nonstop" = "false" ] ; then
+if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then
-    MAX_FD_LIMIT=`ulimit -H -n`
+    case $MAX_FD in #(
-    if [ $? -eq 0 ] ; then
+      max*)
-        if [ "$MAX_FD" = "maximum" -o "$MAX_FD" = "max" ] ; then
+        # In POSIX sh, ulimit -H is undefined. That's why the result is checked to see if it worked.
-            MAX_FD="$MAX_FD_LIMIT"
+        # shellcheck disable=SC2039,SC3045
-        fi
+        MAX_FD=$( ulimit -H -n ) ||
-        ulimit -n $MAX_FD
+            warn "Could not query maximum file descriptor limit"
-        if [ $? -ne 0 ] ; then
+    esac
-            warn "Could not set maximum file descriptor limit: $MAX_FD"
+    case $MAX_FD in  #(
-        fi
+      '' | soft) :;; #(
-    else
+      *)
-        warn "Could not query maximum file descriptor limit: $MAX_FD_LIMIT"
+        # In POSIX sh, ulimit -n is undefined. That's why the result is checked to see if it worked.
-    fi
+        # shellcheck disable=SC2039,SC3045
-fi
+        ulimit -n "$MAX_FD" ||
-
+            warn "Could not set maximum file descriptor limit to $MAX_FD"
-# For Darwin, add options to specify how the application appears in the dock
-if $darwin; then
-    GRADLE_OPTS="$GRADLE_OPTS \"-Xdock:name=$APP_NAME\" \"-Xdock:icon=$APP_HOME/media/gradle.icns\""
-fi
-
-# For Cygwin or MSYS, switch paths to Windows format before running java
-if [ "$cygwin" = "true" -o "$msys" = "true" ] ; then
-    APP_HOME=`cygpath --path --mixed "$APP_HOME"`
-    CLASSPATH=`cygpath --path --mixed "$CLASSPATH"`
-    
-    JAVACMD=`cygpath --unix "$JAVACMD"`
-
-    # We build the pattern for arguments to be converted via cygpath
-    ROOTDIRSRAW=`find -L / -maxdepth 1 -mindepth 1 -type d 2>/dev/null`
-    SEP=""
-    for dir in $ROOTDIRSRAW ; do
-        ROOTDIRS="$ROOTDIRS$SEP$dir"
-        SEP="|"
-    done
-    OURCYGPATTERN="(^($ROOTDIRS))"
-    # Add a user-defined pattern to the cygpath arguments
-    if [ "$GRADLE_CYGPATTERN" != "" ] ; then
-        OURCYGPATTERN="$OURCYGPATTERN|($GRADLE_CYGPATTERN)"
-    fi
-    # Now convert the arguments - kludge to limit ourselves to /bin/sh
-    i=0
-    for arg in "$@" ; do
-        CHECK=`echo "$arg"|egrep -c "$OURCYGPATTERN" -`
-        CHECK2=`echo "$arg"|egrep -c "^-"`                                 ### Determine if an option
-
-        if [ $CHECK -ne 0 ] && [ $CHECK2 -eq 0 ] ; then                    ### Added a condition
-            eval `echo args$i`=`cygpath --path --ignore --mixed "$arg"`
-        else
-            eval `echo args$i`="\"$arg\""
-        fi
-        i=`expr $i + 1`
-    done
-    case $i in
-        0) set -- ;;
-        1) set -- "$args0" ;;
-        2) set -- "$args0" "$args1" ;;
-        3) set -- "$args0" "$args1" "$args2" ;;
-        4) set -- "$args0" "$args1" "$args2" "$args3" ;;
-        5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;;
-        6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;;
-        7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;;
-        8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;;
-        9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;;
     esac
 fi
 
-# Escape application args
+# Collect all arguments for the java command, stacking in reverse order:
-save () {
+#   * args from the command line
-    for i do printf %s\\n "$i" | sed "s/'/'\\\\''/g;1s/^/'/;\$s/\$/' \\\\/" ; done
+#   * the main class name
-    echo " "
+#   * -classpath
-}
+#   * -D...appname settings
-APP_ARGS=`save "$@"`
+#   * --module-path (only if needed)
+#   * DEFAULT_JVM_OPTS, JAVA_OPTS, and GRADLE_OPTS environment variables.
 
-# Collect all arguments for the java command, following the shell quoting and substitution rules
+# For Cygwin or MSYS, switch paths to Windows format before running java
-eval set -- $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS "\"-Dorg.gradle.appname=$APP_BASE_NAME\"" -classpath "\"$CLASSPATH\"" org.gradle.wrapper.GradleWrapperMain "$APP_ARGS"
+if "$cygwin" || "$msys" ; then
+    APP_HOME=$( cygpath --path --mixed "$APP_HOME" )
+    CLASSPATH=$( cygpath --path --mixed "$CLASSPATH" )
+
+    JAVACMD=$( cygpath --unix "$JAVACMD" )
+
+    # Now convert the arguments - kludge to limit ourselves to /bin/sh
+    for arg do
+        if
+            case $arg in                                #(
+              -*)   false ;;                            # don't mess with options #(
+              /?*)  t=${arg#/} t=/${t%%/*}              # looks like a POSIX filepath
+                    [ -e "$t" ] ;;                      #(
+              *)    false ;;
+            esac
+        then
+            arg=$( cygpath --path --ignore --mixed "$arg" )
+        fi
+        # Roll the args list around exactly as many times as the number of
+        # args, so each arg winds up back in the position where it started, but
+        # possibly modified.
+        #
+        # NB: a `for` loop captures its iteration list before it begins, so
+        # changing the positional parameters here affects neither the number of
+        # iterations, nor the values presented in `arg`.
+        shift                   # remove old arg
+        set -- "$@" "$arg"      # push replacement arg
+    done
+fi
+
+
+# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
+
+# Collect all arguments for the java command:
+#   * DEFAULT_JVM_OPTS, JAVA_OPTS, JAVA_OPTS, and optsEnvironmentVar are not allowed to contain shell fragments,
+#     and any embedded shellness will be escaped.
+#   * For example: A user cannot expect ${Hostname} to be expanded, as it is an environment variable and will be
+#     treated as '${Hostname}' itself on the command line.
+
+set -- \
+        "-Dorg.gradle.appname=$APP_BASE_NAME" \
+        -classpath "$CLASSPATH" \
+        org.gradle.wrapper.GradleWrapperMain \
+        "$@"
+
+# Stop when "xargs" is not available.
+if ! command -v xargs >/dev/null 2>&1
+then
+    die "xargs is not available"
+fi
+
+# Use "xargs" to parse quoted args.
+#
+# With -n1 it outputs one arg per line, with the quotes and backslashes removed.
+#
+# In Bash we could simply go:
+#
+#   readarray ARGS < <( xargs -n1 <<<"$var" ) &&
+#   set -- "${ARGS[@]}" "$@"
+#
+# but POSIX shell has neither arrays nor command substitution, so instead we
+# post-process each arg (as a line of input to sed) to backslash-escape any
+# character that might be a shell metacharacter, then use eval to reverse
+# that process (while maintaining the separation between arguments), and wrap
+# the whole thing up as a single "set" statement.
+#
+# This will of course break if any of these variables contains a newline or
+# an unmatched quote.
+#
+
+eval "set -- $(
+        printf '%s\n' "$DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS" |
+        xargs -n1 |
+        sed ' s~[^-[:alnum:]+,./:=@_]~\\&~g; ' |
+        tr '\n' ' '
+    )" '"$@"'
 
 exec "$JAVACMD" "$@"

gradlew.bat

@@ -14,7 +14,7 @@
 @rem limitations under the License.
 @rem
 
-@if "%DEBUG%" == "" @echo off
+@if "%DEBUG%"=="" @echo off
 @rem ##########################################################################
 @rem
 @rem  Gradle startup script for Windows
@@ -25,7 +25,8 @@
 if "%OS%"=="Windows_NT" setlocal
 
 set DIRNAME=%~dp0
-if "%DIRNAME%" == "" set DIRNAME=.
+if "%DIRNAME%"=="" set DIRNAME=.
+@rem This is normally unused
 set APP_BASE_NAME=%~n0
 set APP_HOME=%DIRNAME%
 
@@ -40,7 +41,7 @@ if defined JAVA_HOME goto findJavaFromJavaHome
 
 set JAVA_EXE=java.exe
 %JAVA_EXE% -version >NUL 2>&1
-if "%ERRORLEVEL%" == "0" goto init
+if %ERRORLEVEL% equ 0 goto execute
 
 echo.
 echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
@@ -54,7 +55,7 @@ goto fail
 set JAVA_HOME=%JAVA_HOME:"=%
 set JAVA_EXE=%JAVA_HOME%/bin/java.exe
 
-if exist "%JAVA_EXE%" goto init
+if exist "%JAVA_EXE%" goto execute
 
 echo.
 echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME%
@@ -64,21 +65,6 @@ echo location of your Java installation.
 
 goto fail
 
-:init
-@rem Get command-line arguments, handling Windows variants
-
-if not "%OS%" == "Windows_NT" goto win9xME_args
-
-:win9xME_args
-@rem Slurp the command line arguments.
-set CMD_LINE_ARGS=
-set _SKIP=2
-
-:win9xME_args_slurp
-if "x%~1" == "x" goto execute
-
-set CMD_LINE_ARGS=%*
-
 :execute
 @rem Setup the command line
 
@@ -86,17 +72,19 @@ set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar
 
 
 @rem Execute Gradle
-"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %CMD_LINE_ARGS%
+"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %*
 
 :end
 @rem End local scope for the variables with windows NT shell
-if "%ERRORLEVEL%"=="0" goto mainEnd
+if %ERRORLEVEL% equ 0 goto mainEnd
 
 :fail
 rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of
 rem the _cmd.exe /c_ return code!
-if  not "" == "%GRADLE_EXIT_CONSOLE%" exit 1
+set EXIT_CODE=%ERRORLEVEL%
-exit /b 1
+if %EXIT_CODE% equ 0 set EXIT_CODE=1
+if not ""=="%GRADLE_EXIT_CONSOLE%" exit %EXIT_CODE%
+exit /b %EXIT_CODE%
 
 :mainEnd
 if "%OS%"=="Windows_NT" endlocal

io-archive-ar/src/main/java/module-info.java

@@ -1,4 +1,4 @@
 module org.xbib.io.archive.ar {
     exports org.xbib.io.archive.ar;
-    requires org.xbib.io.archive;
+    requires transitive org.xbib.io.archive;
 }

io-archive-ar/src/main/java/org/xbib/io/archive/ar/ArArchiveEntry.java

@@ -24,7 +24,6 @@ import java.util.Date;
  * can read but not write the GNU variant and doesn't support
  * the BSD variant at all.
  *
- * <a href="http://www.freebsd.org/cgi/man.cgi?query=ar&sektion=5">ar man page</a>
  */
 public class ArArchiveEntry implements ArchiveEntry {
 

io-archive-cpio/src/main/java/module-info.java

@@ -1,4 +1,4 @@
 module org.xbib.io.archive.cpio {
     exports org.xbib.io.archive.cpio;
-    requires org.xbib.io.archive;
+    requires transitive org.xbib.io.archive;
 }

io-archive-cpio/src/main/java/org/xbib/io/archive/cpio/CpioArchiveInputStream.java

@@ -1,6 +1,5 @@
 package org.xbib.io.archive.cpio;
 
-import org.xbib.io.archive.entry.ArchiveEntry;
 import org.xbib.io.archive.stream.ArchiveInputStream;
 import org.xbib.io.archive.util.ArchiveUtils;
 
@@ -33,7 +32,7 @@ import java.io.InputStream;
  * Note: This implementation should be compatible to cpio 2.5
  */
 
-public class CpioArchiveInputStream extends ArchiveInputStream implements CpioConstants {
+public class CpioArchiveInputStream extends ArchiveInputStream<CpioArchiveEntry> implements CpioConstants {
 
     private boolean closed = false;
 
@@ -380,7 +379,7 @@ public class CpioArchiveInputStream extends ArchiveInputStream implements CpioCo
     }
 
     @Override
-    public ArchiveEntry getNextEntry() throws IOException {
+    public CpioArchiveEntry getNextEntry() throws IOException {
         return getNextCPIOEntry();
     }
 

io-archive-dump/src/main/java/module-info.java

@@ -1,4 +1,4 @@
 module org.xbib.io.archive.dump {
     exports org.xbib.io.archive.dump;
-    requires org.xbib.io.archive;
+    requires transitive org.xbib.io.archive;
 }

io-archive-dump/src/main/java/org/xbib/io/archive/dump/DumpArchiveException.java

@@ -2,10 +2,10 @@ package org.xbib.io.archive.dump;
 
 import java.io.IOException;
 
-
 /**
  * Dump Archive Exception
  */
+@SuppressWarnings("serial")
 public class DumpArchiveException extends IOException {
 
     public DumpArchiveException(String msg) {

io-archive-dump/src/main/java/org/xbib/io/archive/dump/DumpArchiveInputStream.java

@@ -19,9 +19,9 @@ import java.util.Stack;
  * the archive, and the read each entry as a normal input stream
  * using read().
  */
-public class DumpArchiveInputStream extends ArchiveInputStream {
+public class DumpArchiveInputStream extends ArchiveInputStream<DumpArchiveEntry> {
 
-    private DumpArchiveSummary summary;
+    private final DumpArchiveSummary summary;
 
     private DumpArchiveEntry active;
 
@@ -35,7 +35,7 @@ public class DumpArchiveInputStream extends ArchiveInputStream {
 
     private int readIdx;
 
-    private byte[] readBuf = new byte[DumpArchiveConstants.TP_SIZE];
+    private final byte[] readBuf = new byte[DumpArchiveConstants.TP_SIZE];
 
     private byte[] blockBuffer;
 
@@ -46,13 +46,13 @@ public class DumpArchiveInputStream extends ArchiveInputStream {
     protected TapeInputStream raw;
 
     // map of ino -> dirent entry. We can use this to reconstruct full paths.
-    private Map<Integer, Dirent> names = new HashMap<Integer, Dirent>();
+    private final Map<Integer, Dirent> names = new HashMap<Integer, Dirent>();
 
     // map of ino -> (directory) entry when we're missing one or more elements in the path.
-    private Map<Integer, DumpArchiveEntry> pending = new HashMap<Integer, DumpArchiveEntry>();
+    private final Map<Integer, DumpArchiveEntry> pending = new HashMap<Integer, DumpArchiveEntry>();
 
     // queue of (directory) entries where we now have the full path.
-    private Queue<DumpArchiveEntry> queue;
+    private final Queue<DumpArchiveEntry> queue;
 
     /**
      * Constructor.

io-archive-dump/src/main/java/org/xbib/io/archive/dump/InvalidFormatException.java

@@ -1,11 +1,10 @@
-
 package org.xbib.io.archive.dump;
 
-
 /**
  * Invalid Format Exception. There was an error decoding a
  * tape segment header.
  */
+@SuppressWarnings("serial")
 public class InvalidFormatException extends DumpArchiveException {
 
     protected long offset;

io-archive-dump/src/main/java/org/xbib/io/archive/dump/TapeInputStream.java

@@ -8,18 +8,24 @@ import java.util.Arrays;
 import java.util.zip.DataFormatException;
 import java.util.zip.Inflater;
 
-
 /**
  * Filter stream that mimics a physical tape drive capable of compressing
  * the data stream
  */
-class TapeInputStream extends FilterInputStream {
+public class TapeInputStream extends FilterInputStream {
+
     private byte[] blockBuffer = new byte[DumpArchiveConstants.TP_SIZE];
+
     private int currBlkIdx = -1;
+
     private int blockSize = DumpArchiveConstants.TP_SIZE;
+
     private int recordSize = DumpArchiveConstants.TP_SIZE;
+
     private int readOffset = DumpArchiveConstants.TP_SIZE;
+
     private boolean isCompressed = false;
+
     private long bytesRead = 0;
 
     /**

io-archive-jar/src/main/java/module-info.java

@@ -1,5 +1,4 @@
 module org.xbib.io.archive.jar {
     exports org.xbib.io.archive.jar;
-    requires org.xbib.io.archive;
+    requires transitive org.xbib.io.archive.zip;
-    requires org.xbib.io.archive.zip;
 }

io-archive-jar/src/main/java/org/xbib/io/archive/jar/JarArchiveInputStream.java

@@ -1,7 +1,6 @@
 
 package org.xbib.io.archive.jar;
 
-import org.xbib.io.archive.entry.ArchiveEntry;
 import org.xbib.io.archive.zip.ZipArchiveEntry;
 import org.xbib.io.archive.zip.ZipArchiveInputStream;
 
@@ -11,7 +10,7 @@ import java.io.InputStream;
 /**
  * Implements an input stream that can read entries from jar files.
  */
-public class JarArchiveInputStream extends ZipArchiveInputStream {
+public class JarArchiveInputStream extends ZipArchiveInputStream<JarArchiveEntry> {
 
     public JarArchiveInputStream(final InputStream inputStream) {
         super(inputStream);
@@ -23,7 +22,7 @@ public class JarArchiveInputStream extends ZipArchiveInputStream {
     }
 
     @Override
-    public ArchiveEntry getNextEntry() throws IOException {
+    public JarArchiveEntry getNextEntry() throws IOException {
         return getNextJarEntry();
     }
 

io-archive-tar/src/main/java/module-info.java

@@ -1,4 +1,4 @@
 module org.xbib.io.archive.tar {
     exports org.xbib.io.archive.tar;
-    requires org.xbib.io.archive;
+    requires transitive org.xbib.io.archive;
 }

io-archive-tar/src/main/java/org/xbib/io/archive/tar/TarArchiveEntry.java

@@ -546,6 +546,207 @@ public class TarArchiveEntry implements TarConstants, ArchiveEntry {
         parseTarHeader(header, encoding, false);
     }
 
+
+    /**
+     * Write an entry's header information to a header buffer.
+     *
+     * @param outbuf   The tar entry header buffer to fill in.
+     * @param encoding encoding to use when writing the file name.
+     * @param starMode whether to use the star/GNU tar/BSD tar
+     *                 extension for numeric fields if their value doesn't fit in the
+     *                 maximum size of standard tar archives
+     */
+    public void writeEntryHeader(byte[] outbuf, ArchiveEntryEncoding encoding, boolean starMode) throws IOException {
+        int offset = 0;
+        offset = ArchiveUtils.formatNameBytes(name, outbuf, offset, NAMELEN, encoding);
+        offset = writeEntryHeaderField(mode, outbuf, offset, MODELEN, starMode);
+        offset = writeEntryHeaderField(userId, outbuf, offset, UIDLEN, starMode);
+        offset = writeEntryHeaderField(groupId, outbuf, offset, GIDLEN, starMode);
+        offset = writeEntryHeaderField(size, outbuf, offset, SIZELEN, starMode);
+        offset = writeEntryHeaderField(modTime, outbuf, offset, MODTIMELEN, starMode);
+        int csOffset = offset;
+        for (int c = 0; c < CHKSUMLEN; ++c) {
+            outbuf[offset++] = (byte) ' ';
+        }
+        outbuf[offset++] = linkFlag;
+        offset = ArchiveUtils.formatNameBytes(linkName, outbuf, offset, NAMELEN, encoding);
+        offset = ArchiveUtils.formatNameBytes(MAGIC_POSIX, outbuf, offset, MAGICLEN);
+        offset = ArchiveUtils.formatNameBytes(version, outbuf, offset, VERSIONLEN);
+        offset = ArchiveUtils.formatNameBytes(userName, outbuf, offset, UNAMELEN, encoding);
+        offset = ArchiveUtils.formatNameBytes(groupName, outbuf, offset, GNAMELEN, encoding);
+        offset = writeEntryHeaderField(devMajor, outbuf, offset, DEVLEN, starMode);
+        offset = writeEntryHeaderField(devMinor, outbuf, offset, DEVLEN, starMode);
+        while (offset < outbuf.length) {
+            outbuf[offset++] = 0;
+        }
+        long chk = computeCheckSum(outbuf);
+        formatCheckSumOctalBytes(chk, outbuf, csOffset, CHKSUMLEN);
+    }
+
+    private int writeEntryHeaderField(long value, byte[] outbuf, int offset, int length, boolean starMode) {
+        if (!starMode && (value < 0
+                || value >= (1l << (3 * (length - 1))))) {
+            // value doesn't fit into field when written as octal
+            // number, will be written to PAX header or causes an
+            // error
+            return formatLongOctalBytes(0, outbuf, offset, length);
+        }
+        return formatLongOctalOrBinaryBytes(value, outbuf, offset, length);
+    }
+
+
+    /**
+     * Write an long integer into a buffer as an octal string if this
+     * will fit, or as a binary number otherwise.
+     * <p/>
+     * Uses {@link #formatUnsignedOctalString} to format
+     * the value as an octal string with leading zeros.
+     * The converted number is followed by a space.
+     *
+     * @param value  The value to write into the buffer.
+     * @param buf    The destination buffer.
+     * @param offset The starting offset into the buffer.
+     * @param length The length of the buffer.
+     * @return The updated offset.
+     * @throws IllegalArgumentException if the value (and trailer)
+     *                                  will not fit in the buffer.
+     */
+    private int formatLongOctalOrBinaryBytes(final long value, byte[] buf, final int offset, final int length) {
+        // Check whether we are dealing with UID/GID or SIZE field
+        final long maxAsOctalChar = length == UIDLEN ? MAXID : MAXSIZE;
+        final boolean negative = value < 0;
+        if (!negative && value <= maxAsOctalChar) { // OK to store as octal chars
+            return formatLongOctalBytes(value, buf, offset, length);
+        }
+        if (length < 9) {
+            formatLongBinary(value, buf, offset, length, negative);
+        }
+        formatBigIntegerBinary(value, buf, offset, length, negative);
+        buf[offset] = (byte) (negative ? 0xff : 0x80);
+        return offset + length;
+    }
+
+    private void formatLongBinary(final long value, byte[] buf, final int offset, final int length, final boolean negative) {
+        final int bits = (length - 1) * 8;
+        final long max = 1l << bits;
+        long val = Math.abs(value);
+        if (val >= max) {
+            throw new IllegalArgumentException("Value " + value +
+                    " is too large for " + length + " byte field.");
+        }
+        if (negative) {
+            val ^= max - 1;
+            val |= 0xff << bits;
+            val++;
+        }
+        for (int i = offset + length - 1; i >= offset; i--) {
+            buf[i] = (byte) val;
+            val >>= 8;
+        }
+    }
+
+    private void formatBigIntegerBinary(final long value, byte[] buf,
+                                        final int offset,
+                                        final int length,
+                                        final boolean negative) {
+        BigInteger val = BigInteger.valueOf(value);
+        final byte[] b = val.toByteArray();
+        final int len = b.length;
+        final int off = offset + length - len;
+        System.arraycopy(b, 0, buf, off, len);
+        final byte fill = (byte) (negative ? 0xff : 0);
+        for (int i = offset + 1; i < off; i++) {
+            buf[i] = fill;
+        }
+    }
+
+    /**
+     * Writes an octal value into a buffer.
+     * <p/>
+     * Uses {@link #formatUnsignedOctalString} to format
+     * the value as an octal string with leading zeros.
+     * The converted number is followed by NUL and then space.
+     *
+     * @param value  The value to convert
+     * @param buf    The destination buffer
+     * @param offset The starting offset into the buffer.
+     * @param length The size of the buffer.
+     * @return The updated value of offset, i.e. offset+length
+     * @throws IllegalArgumentException if the value (and trailer) will not fit in the buffer
+     */
+    private int formatCheckSumOctalBytes(final long value, byte[] buf, final int offset, final int length) {
+        int idx = length - 2;
+        formatUnsignedOctalString(value, buf, offset, idx);
+        buf[offset + idx++] = 0;
+        buf[offset + idx] = (byte) ' ';
+        return offset + length;
+    }
+
+    /**
+     * Write an octal long integer into a buffer.
+     * <p/>
+     * Uses {@link #formatUnsignedOctalString} to format
+     * the value as an octal string with leading zeros.
+     * The converted number is followed by a space.
+     *
+     * @param value  The value to write as octal
+     * @param buf    The destinationbuffer.
+     * @param offset The starting offset into the buffer.
+     * @param length The length of the buffer
+     * @return The updated offset
+     * @throws IllegalArgumentException if the value (and trailer) will not fit in the buffer
+     */
+    private int formatLongOctalBytes(final long value, byte[] buf, final int offset, final int length) {
+        int idx = length - 1; // For space
+        formatUnsignedOctalString(value, buf, offset, idx);
+        buf[offset + idx] = (byte) ' '; // Trailing space
+        return offset + length;
+    }
+
+    /**
+     * Fill buffer with unsigned octal number, padded with leading zeroes.
+     *
+     * @param value  number to convert to octal - treated as unsigned
+     * @param buffer destination buffer
+     * @param offset starting offset in buffer
+     * @param length length of buffer to fill
+     * @throws IllegalArgumentException if the value will not fit in the buffer
+     */
+    private void formatUnsignedOctalString(final long value, byte[] buffer, final int offset, final int length) {
+        int remaining = length;
+        remaining--;
+        if (value == 0) {
+            buffer[offset + remaining--] = (byte) '0';
+        } else {
+            long val = value;
+            for (; remaining >= 0 && val != 0; --remaining) {
+                buffer[offset + remaining] = (byte) ((byte) '0' + (byte) (val & 7));
+                val = val >>> 3;
+            }
+            if (val != 0) {
+                throw new IllegalArgumentException(value + "=" + Long.toOctalString(value) + " will not fit in octal number buffer of length " + length);
+            }
+        }
+
+        for (; remaining >= 0; --remaining) { // leading zeros
+            buffer[offset + remaining] = (byte) '0';
+        }
+    }
+
+    /**
+     * Compute the checksum of a tar entry header.
+     *
+     * @param buf The tar entry's header buffer.
+     * @return The computed checksum.
+     */
+    private long computeCheckSum(final byte[] buf) {
+        long sum = 0;
+        for (byte aBuf : buf) {
+            sum += 255 & aBuf;
+        }
+        return sum;
+    }
+
     private void parseTarHeader(byte[] header, ArchiveEntryEncoding encoding, final boolean oldStyle)
             throws IOException {
         int offset = 0;

io-archive-tar/src/main/java/org/xbib/io/archive/tar/TarArchiveOutputEntry.java

@@ -10,7 +10,7 @@ import java.math.BigInteger;
 import java.util.Date;
 
 /**
- * This class represents an entry in a Tar archive for output
+ * This class represents an entry in a Tar archive for output.
  */
 public class TarArchiveOutputEntry implements TarConstants, ArchiveEntry {
 

io-archive-tar/src/main/java/org/xbib/io/archive/tar/TarArchiveOutputStream.java

@@ -7,7 +7,7 @@ import org.xbib.io.archive.entry.ArchiveEntryEncodingHelper;
 import java.io.IOException;
 import java.io.OutputStream;
 import java.io.StringWriter;
-import java.nio.charset.Charset;
+import java.nio.charset.StandardCharsets;
 import java.util.Arrays;
 import java.util.HashMap;
 import java.util.Map;
@@ -15,7 +15,7 @@ import java.util.Map;
 /**
  * The TarOutputStream writes a UNIX tar archive as an output stream
  */
-public class TarArchiveOutputStream extends ArchiveOutputStream<TarArchiveOutputEntry> implements TarConstants {
+public class TarArchiveOutputStream extends ArchiveOutputStream<TarArchiveEntry> implements TarConstants {
 
     private static final ArchiveEntryEncoding ASCII = ArchiveEntryEncodingHelper.getEncoding("ASCII");
 
@@ -239,8 +239,8 @@ public class TarArchiveOutputStream extends ArchiveOutputStream<TarArchiveOutput
     }
 
     @Override
-    public TarArchiveOutputEntry newArchiveEntry() {
+    public TarArchiveEntry newArchiveEntry() {
-        return new TarArchiveOutputEntry();
+        return new TarArchiveEntry();
     }
 
     /**
@@ -257,7 +257,7 @@ public class TarArchiveOutputStream extends ArchiveOutputStream<TarArchiveOutput
      * @throws ClassCastException  if archiveEntry is not an instance of TarArchiveEntry
      */
     @Override
-    public void putArchiveEntry(TarArchiveOutputEntry archiveEntry) throws IOException {
+    public void putArchiveEntry(TarArchiveEntry archiveEntry) throws IOException {
         if (finished) {
             throw new IOException("Stream has already been finished");
         }
@@ -272,7 +272,7 @@ public class TarArchiveOutputStream extends ArchiveOutputStream<TarArchiveOutput
             } else if (longFileMode == LONGFILE_GNU) {
                 // create a TarEntry for the LongLink, the contents
                 // of which are the entry's name
-                TarArchiveOutputEntry longLinkEntry = new TarArchiveOutputEntry(GNU_LONGLINK, LF_GNUTYPE_LONGNAME);
+                TarArchiveEntry longLinkEntry = new TarArchiveEntry(GNU_LONGLINK, LF_GNUTYPE_LONGNAME);
                 longLinkEntry.setEntrySize(nameBytes.length + 1); // +1 for NUL
                 putArchiveEntry(longLinkEntry);
                 write(nameBytes);
@@ -440,7 +440,7 @@ public class TarArchiveOutputStream extends ArchiveOutputStream<TarArchiveOutput
         if (name.length() >= NAMELEN) {
             name = name.substring(0, NAMELEN - 1);
         }
-        TarArchiveOutputEntry pex = new TarArchiveOutputEntry(name, LF_PAX_EXTENDED_HEADER_LC);
+        TarArchiveEntry pex = new TarArchiveEntry(name, LF_PAX_EXTENDED_HEADER_LC);
         StringWriter w = new StringWriter();
         for (Map.Entry<String, String> h : headers.entrySet()) {
             String key = h.getKey();
@@ -449,7 +449,7 @@ public class TarArchiveOutputStream extends ArchiveOutputStream<TarArchiveOutput
                     + 3 /* blank, equals and newline */
                     + 2 /* guess 9 < actual length < 100 */;
             String line = len + " " + key + "=" + value + "\n";
-            int actualLength = line.getBytes(Charset.forName("UTF-8")).length;
+            int actualLength = line.getBytes(StandardCharsets.UTF_8).length;
             while (len != actualLength) {
                 // Adjust for cases where length < 10 or > 100
                 // or where UTF-8 encoding isn't a single octet
@@ -458,11 +458,11 @@ public class TarArchiveOutputStream extends ArchiveOutputStream<TarArchiveOutput
                 // first pass so we'd need a second.
                 len = actualLength;
                 line = len + " " + key + "=" + value + "\n";
-                actualLength = line.getBytes(Charset.forName("UTF-8")).length;
+                actualLength = line.getBytes(StandardCharsets.UTF_8).length;
             }
             w.write(line);
         }
-        byte[] data = w.toString().getBytes(Charset.forName("UTF-8"));
+        byte[] data = w.toString().getBytes(StandardCharsets.UTF_8);
         pex.setEntrySize(data.length);
         putArchiveEntry(pex);
         write(data);
@@ -499,7 +499,7 @@ public class TarArchiveOutputStream extends ArchiveOutputStream<TarArchiveOutput
     }
 
     private void addPaxHeadersForBigNumbers(Map<String, String> paxHeaders,
-                                            TarArchiveOutputEntry entry) {
+                                            TarArchiveEntry entry) {
         addPaxHeaderForBigNumber(paxHeaders, "size", entry.getEntrySize(), MAXSIZE);
         addPaxHeaderForBigNumber(paxHeaders, "gid", entry.getGroupId(), MAXID);
         addPaxHeaderForBigNumber(paxHeaders, "mtime", entry.getLastModified().getTime() / 1000, MAXSIZE);
@@ -519,7 +519,7 @@ public class TarArchiveOutputStream extends ArchiveOutputStream<TarArchiveOutput
         }
     }
 
-    private void failForBigNumbers(TarArchiveOutputEntry entry) {
+    private void failForBigNumbers(TarArchiveEntry entry) {
         failForBigNumber("entry size", entry.getEntrySize(), MAXSIZE);
         failForBigNumber("group id", entry.getGroupId(), MAXID);
         failForBigNumber("last modification time", entry.getLastModified().getTime() / 1000, MAXSIZE);

io-archive-tar/src/test/java/org/xbib/io/archive/tar/TarTest.java

@@ -9,7 +9,7 @@ import org.junit.jupiter.api.Test;
 public class TarTest {
 
     @Test
-    public void testTar() throws IOException {
+    public void testReadTar() throws IOException {
         InputStream in = getClass().getResourceAsStream("test.tar");
         TarArchiveInputStream tarArchiveInputStream = new TarArchiveInputStream(in);
         byte[] buffer = new byte[1024];

io-archive-zip/src/main/java/module-info.java

@@ -1,4 +1,4 @@
 module org.xbib.io.archive.zip {
     exports org.xbib.io.archive.zip;
-    requires org.xbib.io.archive;
+    requires transitive org.xbib.io.archive;
 }

io-archive-zip/src/main/java/org/xbib/io/archive/zip/ExtraFieldUtils.java

@@ -1,4 +1,3 @@
-
 package org.xbib.io.archive.zip;
 
 import java.util.ArrayList;
@@ -20,7 +19,7 @@ public class ExtraFieldUtils {
     private static final Map<ZipShort, Class<?>> implementations;
 
     static {
-        implementations = new HashMap<ZipShort, Class<?>>();
+        implementations = new HashMap<>();
         register(AsiExtraField.class);
         register(JarMarker.class);
         register(UnicodePathExtraField.class);
@@ -37,14 +36,10 @@ public class ExtraFieldUtils {
      */
     public static void register(Class<?> c) {
         try {
-            ZipExtraField ze = (ZipExtraField) c.newInstance();
+            ZipExtraField ze = (ZipExtraField) c.getDeclaredConstructor().newInstance();
             implementations.put(ze.getHeaderId(), c);
-        } catch (ClassCastException cc) {
+        } catch (Exception e) {
-            throw new RuntimeException(c + " doesn\'t implement ZipExtraField");
+            throw new RuntimeException(e);
-        } catch (InstantiationException ie) {
-            throw new RuntimeException(c + " is not a concrete class");
-        } catch (IllegalAccessException ie) {
-            throw new RuntimeException(c + "\'s no-arg constructor is not public");
         }
     }
 
@@ -54,14 +49,13 @@ public class ExtraFieldUtils {
      *
      * @param headerId the header identifier
      * @return an instance of the appropiate ExtraField
-     * @throws InstantiationException if unable to instantiate the class
+     * @throws Exception if unable to instantiate the class
-     * @throws IllegalAccessException if not allowed to instatiate the class
      */
     public static ZipExtraField createExtraField(ZipShort headerId)
-            throws InstantiationException, IllegalAccessException {
+            throws Exception {
         Class<?> c = implementations.get(headerId);
         if (c != null) {
-            return (ZipExtraField) c.newInstance();
+            return (ZipExtraField) c.getDeclaredConstructor().newInstance();
         }
         UnrecognizedExtraField u = new UnrecognizedExtraField();
         u.setHeaderId(headerId);
@@ -157,7 +151,7 @@ public class ExtraFieldUtils {
                             length);
                 }
                 v.add(ze);
-            } catch (InstantiationException | IllegalAccessException ie) {
+            } catch (Exception ie) {
                 throw new ZipException(ie.getMessage());
             }
             start += (length + WORD);

io-archive-zip/src/main/java/org/xbib/io/archive/zip/UnsupportedZipFeatureException.java

@@ -7,6 +7,7 @@ import java.util.zip.ZipException;
  * Exception thrown when attempting to read or write data for a zip
  * entry that uses ZIP features not supported by this library.
  */
+@SuppressWarnings("serial")
 public class UnsupportedZipFeatureException extends ZipException {
 
     private final Feature reason;

io-archive-zip/src/main/java/org/xbib/io/archive/zip/Zip64RequiredException.java

@@ -8,6 +8,7 @@ import java.util.zip.ZipException;
  * support to an archive and {@link ZipArchiveOutputStream#setUseZip64
  * UseZip64} has been set to {@link Zip64Mode#Never Never}.
  */
+@SuppressWarnings("serial")
 public class Zip64RequiredException extends ZipException {
 
     /**

io-archive-zip/src/main/java/org/xbib/io/archive/zip/ZipArchiveInputStream.java

@@ -1,6 +1,5 @@
 package org.xbib.io.archive.zip;
 
-import org.xbib.io.archive.entry.ArchiveEntry;
 import org.xbib.io.archive.stream.ArchiveInputStream;
 import org.xbib.io.archive.entry.ArchiveEntryEncoding;
 import org.xbib.io.archive.entry.ArchiveEntryEncodingHelper;
@@ -34,7 +33,7 @@ import static org.xbib.io.archive.zip.ZipConstants.ZIP64_MAGIC;
  *
  * @see ZipFile
  */
-public class ZipArchiveInputStream extends ArchiveInputStream {
+public class ZipArchiveInputStream<E extends ZipArchiveEntry> extends ArchiveInputStream<E> {
 
     /**
      * The zip encoding to use for filenames and the file comment.
@@ -252,9 +251,10 @@ public class ZipArchiveInputStream extends ArchiveInputStream {
         }
     }
 
+    @SuppressWarnings("unchecked")
     @Override
-    public ArchiveEntry getNextEntry() throws IOException {
+    public E getNextEntry() throws IOException {
-        return getNextZipEntry();
+        return (E) getNextZipEntry();
     }
 
     @Override

io-archive-zip/src/main/java/org/xbib/io/archive/zip/ZipArchiveOutputStream.java

@@ -562,9 +562,10 @@ public class ZipArchiveOutputStream<E extends ZipArchiveEntry> extends ArchiveOu
         raf.seek(save);
     }
 
+    @SuppressWarnings("unchecked")
     @Override
     public E newArchiveEntry() {
-        return (E)new ZipArchiveEntry();
+        return (E) new ZipArchiveEntry();
     }
 
     /**

io-archive-zip/src/main/java/org/xbib/io/archive/zip/ZipFile.java

@@ -316,23 +316,6 @@ public class ZipFile {
         }
     }
 
-    /**
-     * Ensures that the close method of this zipfile is called when
-     * there are no more references to it.
-     *
-     * @see #close()
-     */
-    @Override
-    protected void finalize() throws Throwable {
-        try {
-            if (!closed) {
-                close();
-            }
-        } finally {
-            super.finalize();
-        }
-    }
-
     /**
      * Length of a "central directory" entry structure without file
      * name, extra fields or comment.
@@ -370,8 +353,7 @@ public class ZipFile {
      */
     private Map<ZipArchiveEntry, NameAndComment> populateFromCentralDirectory()
             throws IOException {
-        HashMap<ZipArchiveEntry, NameAndComment> noUTF8Flag =
+        HashMap<ZipArchiveEntry, NameAndComment> noUTF8Flag = new HashMap<>();
-                new HashMap<ZipArchiveEntry, NameAndComment>();
 
         positionAtCentralDirectory();
 

io-archive-zip/src/test/java/org/xbib/io/archive/zip/ZipTest.java

@@ -9,7 +9,7 @@ public class ZipTest {
     @Test
     public void testZip() throws Exception {
         InputStream in = getClass().getResourceAsStream("test.zip");
-        ZipArchiveInputStream z = new ZipArchiveInputStream(in);
+        ZipArchiveInputStream<ZipArchiveEntry> z = new ZipArchiveInputStream<>(in);
         byte[] buffer = new byte[1024];
         long total = 0L;
         while ((z.getNextEntry()) != null) {

io-codec/build.gradle

@@ -1,5 +1,6 @@
 dependencies {
     api project(':io-archive')
+    implementation project(':io-compress-bgzf')
     implementation project(':io-compress-bzip2')
     implementation project(':io-compress-lzf')
     implementation project(':io-compress-xz')

io-codec/src/main/java/module-info.java

@@ -1,20 +1,22 @@
 module org.xbib.io.codec {
+    uses org.xbib.io.codec.StreamCodec;
     exports org.xbib.io.codec;
     exports org.xbib.io.codec.ar;
+    exports org.xbib.io.codec.bgzf;
     exports org.xbib.io.codec.cpio;
     exports org.xbib.io.codec.file;
     exports org.xbib.io.codec.jar;
     exports org.xbib.io.codec.tar;
     exports org.xbib.io.codec.zip;
+    requires transitive org.xbib.io.compress.bgzf;
     requires org.xbib.io.compress.bzip;
     requires org.xbib.io.compress.lzf;
     requires org.xbib.io.compress.xz;
     requires org.xbib.io.compress.zlib;
-    requires org.xbib.io.archive;
+    requires transitive org.xbib.io.archive.ar;
-    requires org.xbib.io.archive.ar;
+    requires transitive org.xbib.io.archive.cpio;
-    requires org.xbib.io.archive.cpio;
+    requires transitive org.xbib.io.archive.dump;
-    requires org.xbib.io.archive.dump;
+    requires transitive org.xbib.io.archive.jar;
-    requires org.xbib.io.archive.jar;
+    requires transitive org.xbib.io.archive.tar;
-    requires org.xbib.io.archive.tar;
+    requires transitive org.xbib.io.archive.zip;
-    requires org.xbib.io.archive.zip;
 }

io-codec/src/main/java/org/xbib/io/codec/ArchiveCodec.java

@@ -1,5 +1,6 @@
 package org.xbib.io.codec;
 
+import org.xbib.io.archive.entry.ArchiveEntry;
 import org.xbib.io.archive.stream.ArchiveInputStream;
 import org.xbib.io.archive.stream.ArchiveOutputStream;
 import java.io.IOException;
@@ -14,7 +15,7 @@ import java.io.OutputStream;
  * @param <I> the archive input stream type
  * @param <O> the archive output type
  */
-public interface ArchiveCodec<S extends ArchiveSession, I extends ArchiveInputStream, O extends ArchiveOutputStream> {
+public interface ArchiveCodec<E extends ArchiveEntry, I extends ArchiveInputStream<E>, O extends ArchiveOutputStream<E>, S extends ArchiveSession<E, I, O>> {
 
     /**
      * Returns the name of this archive codec ("cpio", "tar", "zip")
@@ -23,14 +24,6 @@ public interface ArchiveCodec<S extends ArchiveSession, I extends ArchiveInputSt
      */
     String getName();
 
-    /**
-     * Creates a new archive session with a progress watcher.
-     *
-     * @param watcher the progress watcher
-     * @return the new archive session
-     */
-    S newSession(BytesProgressWatcher watcher);
-
     /**
      * Creates a new archive input stream
      *
@@ -49,4 +42,11 @@ public interface ArchiveCodec<S extends ArchiveSession, I extends ArchiveInputSt
      */
     O createArchiveOutputStream(OutputStream out) throws IOException;
 
+    /**
+     * Creates a new archive session with a progress watcher.
+     *
+     * @param watcher the progress watcher
+     * @return the new archive session
+     */
+    S newSession(BytesProgressWatcher watcher);
 }

io-codec/src/main/java/org/xbib/io/codec/ArchiveSession.java

@@ -1,34 +1,3 @@
-/*
- * Licensed to Jörg Prante and xbib under one or more contributor
- * license agreements. See the NOTICE.txt file distributed with this work
- * for additional information regarding copyright ownership.
- *
- * Copyright (C) 2012 Jörg Prante and xbib
- *
- * This program is free software; you can redistribute it and/or modify
- * it under the terms of the GNU Affero General Public License as published
- * by the Free Software Foundation; either version 3 of the License, or
- * (at your option) any later version.
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU Affero General Public License for more details.
- *
- * You should have received a copy of the GNU Affero General Public License
- * along with this program; if not, see http://www.gnu.org/licenses
- * or write to the Free Software Foundation, Inc., 51 Franklin Street,
- * Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * The interactive user interfaces in modified source and object code
- * versions of this program must display Appropriate Legal Notices,
- * as required under Section 5 of the GNU Affero General Public License.
- *
- * In accordance with Section 7(b) of the GNU Affero General Public
- * License, these Appropriate Legal Notices must retain the display of the
- * "Powered by xbib" logo. If the display of the logo is not reasonably
- * feasible for technical reasons, the Appropriate Legal Notices must display
- * the words "Powered by xbib".
- */
 package org.xbib.io.codec;
 
 import org.xbib.io.archive.entry.ArchiveEntry;
@@ -45,13 +14,11 @@ import java.util.Date;
 import java.util.Set;
 
 /**
- * Archive session
+ * Archive session.
  */
-public abstract class ArchiveSession<I extends ArchiveInputStream, O extends ArchiveOutputStream>
+public abstract class ArchiveSession<E extends ArchiveEntry, I extends ArchiveInputStream<E>, O extends ArchiveOutputStream<E>>
         implements Session<StringPacket> {
 
-    private final static StreamCodecService codecFactory = StreamCodecService.getInstance();
-
     private final static int DEFAULT_INPUT_BUFSIZE = 65536;
 
     protected int bufferSize = DEFAULT_INPUT_BUFSIZE;
@@ -65,15 +32,13 @@ public abstract class ArchiveSession<I extends ArchiveInputStream, O extends Arc
     protected ArchiveSession() {
     }
 
-    public ArchiveSession setPath(Path path, OpenOption option) {
+    public void setPath(Path path, OpenOption option) {
         this.path = path;
         this.option = option;
-        return this;
     }
 
-    public ArchiveSession setBufferSize(int bufferSize) {
+    public void setBufferSize(int bufferSize) {
         this.bufferSize = bufferSize;
-        return this;
     }
 
     @Override
@@ -138,7 +103,7 @@ public abstract class ArchiveSession<I extends ArchiveInputStream, O extends Arc
         byte[] buf = packet.toString().getBytes();
         if (buf.length > 0) {
             String name = packet.name();
-            ArchiveEntry entry = getOutputStream().newArchiveEntry();
+            E entry = getOutputStream().newArchiveEntry();
             entry.setName(name);
             entry.setLastModified(new Date());
             entry.setEntrySize(buf.length);

io-codec/src/main/java/org/xbib/io/codec/Session.java

@@ -7,11 +7,11 @@ import java.io.IOException;
  * operations, and being closed. Sessions must be opened before the first
  * operation and closed after the last operation.
  */
-public interface Session<P extends Packet> {
+public interface Session<P extends StringPacket> {
 
     enum Mode {
 
-        READ, WRITE, APPEND,CONTROL, DELETE;
+        READ, WRITE, APPEND, CONTROL, DELETE;
     }
 
     /**

io-codec/src/main/java/org/xbib/io/codec/StreamCodecService.java

@@ -1,5 +1,7 @@
 package org.xbib.io.codec;
 
+import java.io.InputStream;
+import java.io.OutputStream;
 import java.util.Map;
 import java.util.ServiceLoader;
 import java.util.Set;
@@ -10,13 +12,14 @@ import java.util.WeakHashMap;
  */
 public class StreamCodecService {
 
-    private final static Map<String, StreamCodec> codecs = new WeakHashMap<>();
+    private final static Map<String, StreamCodec<InputStream, OutputStream>> codecs = new WeakHashMap<>();
 
     private final static StreamCodecService instance = new StreamCodecService();
 
+    @SuppressWarnings({"rawtypes","unchecked"})
     private StreamCodecService() {
         ServiceLoader<StreamCodec> loader = ServiceLoader.load(StreamCodec.class);
-        for (StreamCodec codec : loader) {
+        for (StreamCodec<InputStream, OutputStream> codec : loader) {
             if (!codecs.containsKey(codec.getName())) {
                 codecs.put(codec.getName(), codec);
             }
@@ -27,7 +30,7 @@ public class StreamCodecService {
         return instance;
     }
 
-    public StreamCodec getCodec(String suffix) {
+    public StreamCodec<InputStream, OutputStream> getCodec(String suffix) {
         if (codecs.containsKey(suffix)) {
             return codecs.get(suffix);
         }

io-codec/src/main/java/org/xbib/io/codec/ar/ArConnection.java

@@ -27,6 +27,7 @@ public class ArConnection extends URLConnection implements Connection<ArSession>
      * the object referenced by the URL is not created.
      *
      * @param url the specified URL.
+     * @throws URISyntaxException if URI is invalid
      */
     public ArConnection(URL url) throws URISyntaxException {
         super(url);

io-codec/src/main/java/org/xbib/io/codec/ar/ArSession.java

@@ -1,9 +1,9 @@
 package org.xbib.io.codec.ar;
 
+import org.xbib.io.archive.ar.ArArchiveEntry;
 import org.xbib.io.codec.ArchiveSession;
 import org.xbib.io.archive.ar.ArArchiveInputStream;
 import org.xbib.io.archive.ar.ArArchiveOutputStream;
-import org.xbib.io.codec.Packet;
 import org.xbib.io.codec.Session;
 import org.xbib.io.codec.StringPacket;
 import java.io.InputStream;
@@ -12,7 +12,7 @@ import java.io.OutputStream;
 /**
  * Ar Session
  */
-public class ArSession extends ArchiveSession<ArArchiveInputStream, ArArchiveOutputStream>
+public class ArSession extends ArchiveSession<ArArchiveEntry, ArArchiveInputStream, ArArchiveOutputStream>
         implements Session<StringPacket> {
 
     private final static String SUFFIX = "ar";

io-codec/src/main/java/org/xbib/io/codec/bgzf/BzgfStreamCodec.java

@@ -0,0 +1,37 @@
+package org.xbib.io.codec.bgzf;
+
+import org.xbib.io.codec.StreamCodec;
+import org.xbib.io.compress.bgzf.BlockCompressedInputStream;
+import org.xbib.io.compress.bgzf.BlockCompressedOutputStream;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
+
+public class BzgfStreamCodec implements StreamCodec<BlockCompressedInputStream, BlockCompressedOutputStream> {
+
+    @Override
+    public String getName() {
+        return "bgzf";
+    }
+
+    @Override
+    public BlockCompressedInputStream decode(InputStream in) throws IOException {
+        return new BlockCompressedInputStream(in);
+    }
+
+    @Override
+    public BlockCompressedInputStream decode(InputStream in, int bufsize) throws IOException {
+        return new BlockCompressedInputStream(in);
+    }
+
+    @Override
+    public BlockCompressedOutputStream encode(OutputStream out) throws IOException {
+        return new BlockCompressedOutputStream(out);
+    }
+
+    @Override
+    public BlockCompressedOutputStream encode(OutputStream out, int bufsize) throws IOException {
+        return new BlockCompressedOutputStream(out);
+    }
+}

io-codec/src/main/java/org/xbib/io/codec/cpio/CpioSession.java

@@ -1,5 +1,6 @@
 package org.xbib.io.codec.cpio;
 
+import org.xbib.io.archive.cpio.CpioArchiveEntry;
 import org.xbib.io.codec.ArchiveSession;
 import org.xbib.io.archive.cpio.CpioArchiveInputStream;
 import org.xbib.io.archive.cpio.CpioArchiveOutputStream;
@@ -9,7 +10,7 @@ import java.io.OutputStream;
 /**
  * Cpio Session
  */
-public class CpioSession extends ArchiveSession<CpioArchiveInputStream, CpioArchiveOutputStream> {
+public class CpioSession extends ArchiveSession<CpioArchiveEntry, CpioArchiveInputStream, CpioArchiveOutputStream> {
 
     private final static String SUFFIX = "cpio";
 

io-codec/src/main/java/org/xbib/io/codec/jar/JarSession.java

@@ -1,12 +1,13 @@
 package org.xbib.io.codec.jar;
 
+import org.xbib.io.archive.jar.JarArchiveEntry;
 import org.xbib.io.codec.ArchiveSession;
 import org.xbib.io.archive.jar.JarArchiveInputStream;
 import org.xbib.io.archive.jar.JarArchiveOutputStream;
 import java.io.InputStream;
 import java.io.OutputStream;
 
-public class JarSession extends ArchiveSession<JarArchiveInputStream, JarArchiveOutputStream> {
+public class JarSession extends ArchiveSession<JarArchiveEntry, JarArchiveInputStream, JarArchiveOutputStream> {
 
     private final static String SUFFIX = "jar";
 

io-codec/src/main/java/org/xbib/io/codec/tar/TarSession.java

@@ -31,6 +31,7 @@
  */
 package org.xbib.io.codec.tar;
 
+import org.xbib.io.archive.tar.TarArchiveEntry;
 import org.xbib.io.codec.ArchiveSession;
 import org.xbib.io.archive.tar.TarArchiveInputStream;
 import org.xbib.io.archive.tar.TarArchiveOutputStream;
@@ -38,7 +39,7 @@ import java.io.IOException;
 import java.io.InputStream;
 import java.io.OutputStream;
 
-public class TarSession extends ArchiveSession<TarArchiveInputStream, TarArchiveOutputStream> {
+public class TarSession extends ArchiveSession<TarArchiveEntry, TarArchiveInputStream, TarArchiveOutputStream> {
 
     private final static String SUFFIX = "tar";
 

io-codec/src/main/java/org/xbib/io/codec/zip/ZipSession.java

@@ -1,37 +1,37 @@
 package org.xbib.io.codec.zip;
 
+import org.xbib.io.archive.zip.ZipArchiveEntry;
 import org.xbib.io.codec.ArchiveSession;
 import org.xbib.io.archive.zip.ZipArchiveInputStream;
 import org.xbib.io.archive.zip.ZipArchiveOutputStream;
 import java.io.InputStream;
 import java.io.OutputStream;
 
-public class ZipSession extends ArchiveSession<ZipArchiveInputStream, ZipArchiveOutputStream> {
+public class ZipSession extends ArchiveSession<ZipArchiveEntry, ZipArchiveInputStream<ZipArchiveEntry>, ZipArchiveOutputStream<ZipArchiveEntry>> {
 
     private final static String SUFFIX = "zip";
 
-    private ZipArchiveInputStream in;
+    private ZipArchiveInputStream<ZipArchiveEntry> in;
 
-    private ZipArchiveOutputStream out;
+    private ZipArchiveOutputStream<ZipArchiveEntry> out;
 
     protected String getSuffix() {
         return SUFFIX;
     }
 
     protected void open(InputStream in) {
-        this.in = new ZipArchiveInputStream(in);
+        this.in = new ZipArchiveInputStream<>(in);
     }
 
     protected void open(OutputStream out) {
-        this.out = new ZipArchiveOutputStream(out);
+        this.out = new ZipArchiveOutputStream<>(out);
     }
 
-    public ZipArchiveInputStream getInputStream() {
+    public ZipArchiveInputStream<ZipArchiveEntry> getInputStream() {
         return in;
     }
 
-    public ZipArchiveOutputStream getOutputStream() {
+    public ZipArchiveOutputStream<ZipArchiveEntry> getOutputStream() {
         return out;
     }
-
 }

io-compress-bgzf/LICENSE.txt

@@ -0,0 +1,21 @@
+/*
+ * The MIT License
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ * THE SOFTWARE.
+ */

io-compress-bgzf/src/main/java/module-info.java

@@ -0,0 +1,3 @@
+module org.xbib.io.compress.bgzf {
+    exports org.xbib.io.compress.bgzf;
+}

io-compress-bgzf/src/main/java/org/xbib/io/compress/bgzf/BGZFException.java

@@ -0,0 +1,19 @@
+package org.xbib.io.compress.bgzf;
+
+@SuppressWarnings("serial")
+public class BGZFException extends RuntimeException {
+
+    public BGZFException() {}
+
+    public BGZFException(final String s) {
+        super(s);
+    }
+
+    public BGZFException(final String s, final Throwable throwable) {
+        super(s, throwable);
+    }
+
+    public BGZFException(final Throwable throwable) {
+        super(throwable);
+    }
+}

io-compress-bgzf/src/main/java/org/xbib/io/compress/bgzf/BGZFFilePointerUtil.java

@@ -0,0 +1,67 @@
+
+package org.xbib.io.compress.bgzf;
+
+public class BGZFFilePointerUtil {
+
+    private static final int SHIFT_AMOUNT = 16;
+    private static final int OFFSET_MASK = 0xffff;
+    private static final long ADDRESS_MASK = 0xFFFFFFFFFFFFL;
+
+    public static final long MAX_BLOCK_ADDRESS = ADDRESS_MASK;
+    public static final int MAX_OFFSET = OFFSET_MASK;
+
+    public static int compare(final long vfp1, final long vfp2) {
+        if (vfp1 == vfp2) return 0;
+        // When treating as unsigned, negative number is > positive.
+        if (vfp1 < 0 && vfp2 >= 0) return 1;
+        if (vfp1 >= 0 && vfp2 < 0) return -1;
+        // Either both negative or both non-negative, so regular comparison works.
+        if (vfp1 < vfp2) return -1;
+        return 1; // vfp1 > vfp2
+    }
+
+    /**
+     * @return true if vfp2 points to somewhere in the same BGZF block, or the one immediately
+     *         following vfp1's BGZF block.
+     */
+    public static boolean areInSameOrAdjacentBlocks(final long vfp1, final long vfp2) {
+        final long block1 = getBlockAddress(vfp1);
+        final long block2 = getBlockAddress(vfp2);
+        return (block1 == block2 || block1 + 1 == block2);
+    }
+
+    /**
+     * @param blockAddress File offset of start of BGZF block.
+     * @param blockOffset Offset into uncompressed block.
+     * @return Virtual file pointer that embodies the input parameters.
+     */
+    static long makeFilePointer(final long blockAddress, final int blockOffset) {
+        if (blockOffset < 0) {
+            throw new IllegalArgumentException("Negative blockOffset " + blockOffset
+                + " not allowed.");
+        }
+        if (blockAddress < 0) {
+            throw new IllegalArgumentException("Negative blockAddress " + blockAddress
+                + " not allowed.");
+        }
+        if (blockOffset > MAX_OFFSET) {
+            throw new IllegalArgumentException("blockOffset " + blockOffset + " too large.");
+        }
+        if (blockAddress > MAX_BLOCK_ADDRESS) {
+            throw new IllegalArgumentException("blockAddress " + blockAddress + " too large.");
+        }
+        return blockAddress << SHIFT_AMOUNT | blockOffset;
+    }
+
+    public static long getBlockAddress(final long virtualFilePointer) {
+        return (virtualFilePointer >> SHIFT_AMOUNT) & ADDRESS_MASK;
+    }
+
+    public static int getBlockOffset(final long virtualFilePointer) {
+        return (int)(virtualFilePointer & OFFSET_MASK);
+    }
+
+    public static String asString(final long vfp) {
+        return String.format("%d(0x%x): (block address: %d, offset: %d)", vfp, vfp, getBlockAddress(vfp), getBlockOffset(vfp));
+    }
+}

io-compress-bgzf/src/main/java/org/xbib/io/compress/bgzf/BGZFFormatException.java

@@ -0,0 +1,19 @@
+package org.xbib.io.compress.bgzf;
+
+@SuppressWarnings("serial")
+public class BGZFFormatException extends BGZFException {
+
+    public BGZFFormatException() {}
+
+    public BGZFFormatException(final String s) {
+        super(s);
+    }
+
+    public BGZFFormatException(final String s, final Throwable throwable) {
+        super(s, throwable);
+    }
+
+    public BGZFFormatException(final Throwable throwable) {
+        super(throwable);
+    }
+}

io-compress-bgzf/src/main/java/org/xbib/io/compress/bgzf/BGZFStreamConstants.java

@@ -0,0 +1,95 @@
+package org.xbib.io.compress.bgzf;
+
+/**
+ * Constants shared by BlockCompressed{Input,Output}Stream classes
+ */
+public class BGZFStreamConstants {
+
+    // Number of bytes in the gzip block before the deflated data.
+    // This is not the standard header size, because we include one optional subfield,
+    // but it is the standard for us.
+    public static final int BLOCK_HEADER_LENGTH = 18;
+
+    // Location in the gzip block of the total block size (actually total block size - 1)
+    public static final int BLOCK_LENGTH_OFFSET = 16;
+
+    // Number of bytes that follow the deflated data
+    public static final int BLOCK_FOOTER_LENGTH = 8;
+
+    // We require that a compressed block (including header and footer, be <= this)
+    public static final int MAX_COMPRESSED_BLOCK_SIZE = 64 * 1024;
+
+    // Gzip overhead is the header, the footer, and the block size (encoded as a short).
+    public static final int GZIP_OVERHEAD = BLOCK_HEADER_LENGTH + BLOCK_FOOTER_LENGTH + 2;
+
+    // If Deflater has compression level == NO_COMPRESSION, 10 bytes of overhead (determined experimentally).
+    public static final int NO_COMPRESSION_OVERHEAD = 10;
+
+    // Push out a gzip block when this many uncompressed bytes have been accumulated.
+    // This size is selected so that if data is not compressible,  if Deflater is given
+    // compression level == NO_COMPRESSION, compressed size is guaranteed to be <= MAX_COMPRESSED_BLOCK_SIZE.
+    public static final int DEFAULT_UNCOMPRESSED_BLOCK_SIZE = 64 * 1024 - (GZIP_OVERHEAD + NO_COMPRESSION_OVERHEAD);
+
+    // Magic numbers
+    public static final byte GZIP_ID1 = 31;
+    public static final int GZIP_ID2 = 139;
+
+    // FEXTRA flag means there are optional fields
+    public static final int GZIP_FLG = 4;
+
+    // extra flags
+    public static final int GZIP_XFL = 0;
+
+    // length of extra subfield
+    public static final short GZIP_XLEN = 6;
+
+    // The deflate compression, which is customarily used by gzip
+    public static final byte GZIP_CM_DEFLATE = 8;
+
+    public static final int DEFAULT_COMPRESSION_LEVEL = 5;
+
+    // We don't care about OS because we're not doing line terminator translation
+    public static final int GZIP_OS_UNKNOWN = 255;
+
+    // The subfield ID
+    public static final byte BGZF_ID1 = 66;
+    public static final byte BGZF_ID2 = 67;
+
+    // subfield length in bytes
+    public static final byte BGZF_LEN = 2;
+
+    public static final byte[] EMPTY_GZIP_BLOCK = {
+            BGZFStreamConstants.GZIP_ID1,
+            (byte)BGZFStreamConstants.GZIP_ID2,
+            BGZFStreamConstants.GZIP_CM_DEFLATE,
+            BGZFStreamConstants.GZIP_FLG,
+            0, 0, 0, 0, // Modification time
+            BGZFStreamConstants.GZIP_XFL,
+            (byte)BGZFStreamConstants.GZIP_OS_UNKNOWN,
+            BGZFStreamConstants.GZIP_XLEN, 0, // Little-endian short
+            BGZFStreamConstants.BGZF_ID1,
+            BGZFStreamConstants.BGZF_ID2,
+            BGZFStreamConstants.BGZF_LEN, 0, // Little-endian short
+            // Total block size - 1
+            BGZFStreamConstants.BLOCK_HEADER_LENGTH +
+                    BGZFStreamConstants.BLOCK_FOOTER_LENGTH - 1 + 2, 0, // Little-endian short
+            // Dummy payload?
+            3, 0,
+            0, 0, 0, 0, // crc
+            0, 0, 0, 0, // uncompressedSize
+    };
+
+    public static final byte[] GZIP_BLOCK_PREAMBLE = {
+            BGZFStreamConstants.GZIP_ID1,
+            (byte)BGZFStreamConstants.GZIP_ID2,
+            BGZFStreamConstants.GZIP_CM_DEFLATE,
+            BGZFStreamConstants.GZIP_FLG,
+            0, 0, 0, 0, // Modification time
+            BGZFStreamConstants.GZIP_XFL,
+            (byte)BGZFStreamConstants.GZIP_OS_UNKNOWN,
+            BGZFStreamConstants.GZIP_XLEN, 0, // Little-endian short
+            BGZFStreamConstants.BGZF_ID1,
+            BGZFStreamConstants.BGZF_ID2,
+            BGZFStreamConstants.BGZF_LEN, 0, // Little-endian short
+    };
+}

io-compress-bgzf/src/main/java/org/xbib/io/compress/bgzf/BinaryCodec.java

@@ -0,0 +1,666 @@
+package org.xbib.io.compress.bgzf;
+
+import java.io.ByteArrayInputStream;
+import java.io.EOFException;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
+import java.io.SyncFailedException;
+import java.nio.ByteBuffer;
+import java.nio.ByteOrder;
+
+/**
+ * Encapsulates file representation of various primitive data types. Forces little-endian disk
+ * representation. Note that this class is currently not very efficient. There are plans to increase
+ * the size of the ByteBuffer, and move data between the ByteBuffer and the underlying input or
+ * output stream in larger chunks.
+ *
+ * All the read methods throw EOFException if the input stream is exhausted before the
+ * required number of bytes are read.
+ */
+public class BinaryCodec {
+
+    // Outstream to write to
+    private OutputStream outputStream;
+    // If a file or filename was given it will be stored here. Used for error reporting.
+    private String outputFileName;
+
+    // Input stream to read from
+    private InputStream inputStream;
+    // If a file or filename was give to read from it will be stored here. Used for error reporting.
+    private String inputFileName;
+
+    /*
+     * Mode that the BinaryCodec is in. It is either writing to a binary file or reading from. This
+     * is set to true if it is writing to a binary file Right now we don't support reading and
+     * writing to the same file with the same BinaryCodec instance
+     */
+    private boolean isWriting;
+
+    /**
+     * For byte swapping.
+     */
+    private ByteBuffer byteBuffer;
+
+    /**
+     * For reading Strings of known length, this can reduce object creation
+     */
+    private final byte[] scratchBuffer = new byte[16];
+
+    // Byte order used in BAM files.
+    private static final ByteOrder LITTLE_ENDIAN = ByteOrder.LITTLE_ENDIAN;
+    private static final byte[] NULL_BYTE = {0};
+
+    private static final long MAX_UBYTE = (Byte.MAX_VALUE * 2) + 1;
+    private static final long MAX_USHORT = (Short.MAX_VALUE * 2) + 1;
+    private static final long MAX_UINT = ((long)Integer.MAX_VALUE * 2) + 1;
+
+    // We never serialize more than this much at a time (except for Strings)
+    private static final int MAX_BYTE_BUFFER = 8;
+    /**
+     * Constructs BinaryCodec from a file and set it's mode to writing or not
+     *
+     * @param file file to be written to or read from
+     * @param writing whether the file is being written to
+     * @throws FileNotFoundException
+     */
+    public BinaryCodec(final File file, final boolean writing) throws FileNotFoundException {
+        this();
+
+        this.isWriting = writing;
+        if (this.isWriting) {
+            this.outputStream = new FileOutputStream(file);
+            this.outputFileName = file.getName();
+        } else {
+            this.inputStream = new FileInputStream(file);
+            this.inputFileName = file.getName();
+        }
+    }
+
+    /**
+     * Constructs BinaryCodec from a file name and set it's mode to writing or not
+     *
+     * @param fileName name of the file to be written to or read from
+     * @param writing writing whether the file is being written to
+     * @throws FileNotFoundException
+     */
+    public BinaryCodec(final String fileName, final boolean writing) throws FileNotFoundException {
+        this(new File(fileName), writing);
+    }
+
+    /**
+     * Constructs BinaryCodec from an output stream
+     *
+     * @param outputStream Stream to write to, since it's an output stream we know that isWriting
+     *        should be set to true
+     */
+    public BinaryCodec(final OutputStream outputStream) {
+        this();
+        setOutputStream(outputStream);
+    }
+
+    /**
+     * Constructs BinaryCodec from an input stream
+     *
+     * @param inputStream Stream to read from, since we are reading isWriting is set to false
+     */
+    public BinaryCodec(final InputStream inputStream) {
+        this();
+        setInputStream(inputStream);
+    }
+
+    /**
+     * Ambiguous whether reading or writing until set{In,Out}putStream is called
+     */
+    public BinaryCodec() {
+        initByteBuffer();
+    }
+
+    /**
+     * Shared among ctors. Note that if endianness is changed, all the unsigned methods must also be
+     * changed.
+     */
+    private void initByteBuffer() {
+        byteBuffer = ByteBuffer.allocate(MAX_BYTE_BUFFER);
+        byteBuffer.order(LITTLE_ENDIAN);
+    }
+
+
+    /**
+     * Write whatever has been put into the byte buffer
+     *
+     * @param numBytes -- how much to write. Note that in case of writing an unsigned value, more
+     *        bytes were put into the ByteBuffer than will get written out.
+     * @throws IOException
+     */
+    private void writeByteBuffer(final int numBytes) throws IOException {
+        assert (numBytes <= byteBuffer.limit());
+        writeBytes(byteBuffer.array(), 0, numBytes);
+    }
+
+    /**
+     * Writes a byte to the output buffer
+     *
+     * @param bite byte array to write
+     * @throws IOException
+     */
+    public void writeByte(final byte bite) throws IOException {
+        byteBuffer.clear();
+        byteBuffer.put(bite);
+        writeByteBuffer(1);
+    }
+
+    public void writeByte(final int b) throws IOException {
+        writeByte((byte)b);
+    }
+
+    /**
+     * Writes a byte array to the output buffer
+     *
+     * @param bytes value to write
+     * @throws IOException
+     */
+    public void writeBytes(final byte[] bytes) throws IOException {
+        writeBytes(bytes, 0, bytes.length);
+    }
+
+    public void writeBytes(final byte[] bytes, final int startOffset, final int numBytes) throws IOException {
+        if (!isWriting) {
+            throw new IllegalStateException("Calling write method on BinaryCodec open for read.");
+        }
+
+        outputStream.write(bytes, startOffset, numBytes);
+    }
+
+    /**
+     * Write a 32-bit int to the output stream
+     *
+     * @param value int to write
+     * @throws IOException
+     */
+    public void writeInt(final int value) throws IOException {
+        byteBuffer.clear();
+        byteBuffer.putInt(value);
+        writeByteBuffer(4);
+    }
+
+    /**
+     * Write a double (8 bytes) to the output stream
+     *
+     * @param value double to write
+     * @throws IOException
+     */
+    public void writeDouble(final double value) throws IOException {
+        byteBuffer.clear();
+        byteBuffer.putDouble(value);
+        writeByteBuffer(8);
+    }
+
+    /**
+     * Write a 64-bit long to the output stream
+     *
+     * @param value long to write
+     * @throws IOException
+     */
+    public void writeLong(final long value) throws IOException {
+        byteBuffer.clear();
+        byteBuffer.putLong(value);
+        writeByteBuffer(8);
+    }
+
+
+    /**
+     * Write a 16-bit short to output stream
+     *
+     * @throws IOException
+     */
+    public void writeShort(final short value) throws IOException {
+        byteBuffer.clear();
+        byteBuffer.putShort(value);
+        writeByteBuffer(2);
+    }
+
+    /**
+     * Write a float (4 bytes) to the output stream
+     *
+     * @param value float to write
+     * @throws IOException
+     */
+    public void writeFloat(final float value) throws IOException {
+        byteBuffer.clear();
+        byteBuffer.putFloat(value);
+        writeByteBuffer(4);
+    }
+
+    /**
+     * Writes a boolean (1 byte) to the output buffer
+     *
+     * @param value boolean to write
+     * @throws IOException
+     */
+    public void writeBoolean(final boolean value) throws IOException {
+        byteBuffer.clear();
+        byteBuffer.put(value ? (byte)1 : (byte)0);
+        writeByteBuffer(1);
+    }
+
+    /**
+     * Writes a string to the buffer as ASCII bytes
+     *
+     * @param value string to write to buffer
+     * @param writeLength prefix the string with the length as a 32-bit int
+     * @param appendNull add a null byte to the end of the string
+     * @throws IOException
+     */
+    public void writeString(final String value, final boolean writeLength, final boolean appendNull) throws IOException {
+        if (writeLength) {
+            int lengthToWrite = value.length();
+            if (appendNull) lengthToWrite++;
+            writeInt(lengthToWrite);
+        }
+
+        // Actually writes the string to a buffer
+        writeString(value);
+
+        if (appendNull) writeBytes(NULL_BYTE);
+
+    }
+
+
+    /**
+     * Write a string to the buffer as ASCII bytes
+     *
+     * @param value string to write
+     * @throws IOException
+     */
+    private void writeString(final String value) throws IOException {
+        final byte[] byteBuffer = new byte[value.length()];
+        final char[] charBuffer = value.toCharArray();
+        for (int i = 0; i < charBuffer.length; ++i) {
+            byteBuffer[i] = (byte)(charBuffer[i] & 0xff);
+        }
+        writeBytes(byteBuffer);
+    }
+
+    /**
+     * Write an 8-bit unsigned byte. NOTE: This method will break if we change to big-endian.
+     *
+     * @throws IOException
+     */
+    public void writeUByte(final short val) throws IOException {
+        if (val < 0) {
+            throw new IllegalArgumentException("Negative value (" + val
+                + ") passed to unsigned writing method.");
+        }
+        if (val > MAX_UBYTE) {
+            throw new IllegalArgumentException("Value (" + val
+                + ") to large to be written as ubyte.");
+        }
+        byteBuffer.clear();
+        byteBuffer.putShort(val);
+        writeByteBuffer(1);
+    }
+
+    /**
+     * Write a 16-bit unsigned short. NOTE: This method will break if we change to big-endian.
+     *
+     * @throws IOException
+     */
+    public void writeUShort(final int val) throws IOException {
+        if (val < 0) {
+            throw new IllegalArgumentException("Negative value (" + val
+                + ") passed to unsigned writing method.");
+        }
+        if (val > MAX_USHORT) {
+            throw new IllegalArgumentException("Value (" + val
+                + ") to large to be written as ushort.");
+        }
+        byteBuffer.clear();
+        byteBuffer.putInt(val);
+        writeByteBuffer(2);
+    }
+
+    /**
+     * Write a 32-bit unsigned int. NOTE: This method will break if we change to big-endian.
+     *
+     * @throws IOException
+     */
+    public void writeUInt(final long val) throws IOException {
+        if (val < 0) {
+            throw new IllegalArgumentException("Negative value (" + val
+                + ") passed to unsigned writing method.");
+        }
+        if (val > MAX_UINT) {
+            throw new IllegalArgumentException("Value (" + val
+                + ") to large to be written as uint.");
+        }
+        byteBuffer.clear();
+        byteBuffer.putLong(val);
+        writeByteBuffer(4);
+    }
+
+    /**
+     * Read a byte array from the input stream.
+     *
+     * @throws IOException
+     */
+    public void readBytes(final byte[] buffer) throws IOException {
+        readBytes(buffer, 0, buffer.length);
+    }
+
+    /**
+     * Read a byte array from the input stream
+     *
+     * @param buffer where to put bytes read
+     * @param offset offset to start putting bytes into buffer
+     * @param length number of bytes to read
+     * @throws IOException
+     */
+    public void readBytes(final byte[] buffer, final int offset, final int length) throws IOException {
+        int totalNumRead = 0;
+        do {
+            final int numRead =
+                readBytesOrFewer(buffer, offset + totalNumRead, length - totalNumRead);
+            if (numRead < 0) {
+                throw new EOFException(constructErrorMessage("Premature EOF"));
+            } else {
+                totalNumRead += numRead;
+            }
+        } while (totalNumRead < length);
+    }
+
+    /**
+     * Reads a byte array from the input stream.
+     *
+     * @param buffer where to put bytes read
+     * @param offset offset to start putting bytes into buffer
+     * @param length number of bytes to read. Fewer bytes may be read if EOF is reached before
+     *        length bytes have been read.
+     * @return the total number of bytes read into the buffer, or -1 if there is no more data
+     *         because the end of the stream has been reached.
+     * @throws IOException
+     */
+    public int readBytesOrFewer(final byte[] buffer, final int offset, final int length) throws IOException {
+        if (isWriting) {
+            throw new IllegalStateException("Calling read method on BinaryCodec open for write.");
+        }
+
+        return inputStream.read(buffer, offset, length);
+    }
+
+    /**
+     * @return a single byte read from the input stream.
+     * @throws IOException
+     */
+    public byte readByte() throws IOException {
+        if (isWriting) {
+            throw new IllegalStateException("Calling read method on BinaryCodec open for write.");
+        }
+
+        final int ret = inputStream.read();
+        if (ret == -1) {
+            throw new EOFException(constructErrorMessage("Premature EOF"));
+        }
+        return (byte)ret;
+    }
+
+    /**
+     * @return true if it is possible to know for sure if at EOF, and it is known for sure. If the
+     *         input stream is a ByteArrayInputStream, this is faster than causing a
+     *         RuntimeEOFException to be thrown.
+     * @throws IOException
+     */
+    public boolean knownAtEof() throws IOException {
+        if (isWriting) {
+            throw new IllegalStateException(
+                "Calling knownAtEof method on BinaryCodec open for write.");
+        }
+
+        return inputStream instanceof ByteArrayInputStream && inputStream.available() == 0;
+    }
+
+    /**
+     * Read a string off the input stream, as ASCII bytes
+     *
+     * @param length length of string to read
+     * @return String read from stream
+     * @throws IOException
+     */
+    public String readString(final int length) throws IOException {
+        final byte[] buffer;
+        // Recycle single buffer if possible
+        if (length <= scratchBuffer.length) {
+            buffer = scratchBuffer;
+        } else {
+            buffer = new byte[length];
+
+        }
+        readBytes(buffer, 0, length);
+
+        final char[] charBuffer = new char[length];
+        for (int i = 0; i < length; ++i) {
+            charBuffer[i] = (char)buffer[i];
+        }
+        return new String(charBuffer);
+    }
+
+    /**
+     * Read ASCII bytes from the input stream until a null byte is read
+     *
+     * @return String constructed from the ASCII bytes read
+     * @throws IOException
+     */
+    public String readNullTerminatedString() throws IOException {
+        final StringBuilder ret = new StringBuilder();
+        for (byte b = this.readByte(); b != 0; b = this.readByte()) {
+            ret.append((char)(b & 0xff));
+        }
+        return ret.toString();
+    }
+
+    /**
+     * Read an int length, and then a String of that length
+     *
+     * @param devourNull if true, the length include a null terminator, which is read and discarded
+     * @throws IOException
+     */
+    public String readLengthAndString(final boolean devourNull) throws IOException {
+        int length = readInt();
+        if (devourNull) {
+            --length;
+        }
+        final String ret = readString(length);
+        if (devourNull) {
+            readByte();
+        }
+        return ret;
+    }
+
+    private void readByteBuffer(final int numBytes) throws IOException {
+        assert (numBytes <= byteBuffer.capacity());
+        readBytes(byteBuffer.array(), 0, numBytes);
+        byteBuffer.limit(byteBuffer.capacity());
+        byteBuffer.position(numBytes);
+    }
+
+    /**
+     * Read an int off the input stream
+     *
+     * @return int from input stream
+     * @throws IOException
+     */
+    public int readInt() throws IOException {
+        readByteBuffer(4);
+        byteBuffer.flip();
+        return byteBuffer.getInt();
+    }
+
+    /**
+     * Reads a double off the input stream
+     *
+     * @return double
+     * @throws IOException
+     */
+    public double readDouble() throws IOException {
+        readByteBuffer(8);
+        byteBuffer.flip();
+        return byteBuffer.getDouble();
+    }
+
+    /**
+     * Reads a long off the input stream
+     *
+     * @return long
+     * @throws IOException
+     */
+    public long readLong() throws IOException {
+        readByteBuffer(8);
+        byteBuffer.flip();
+        return byteBuffer.getLong();
+    }
+
+    public short readShort() throws IOException {
+        readByteBuffer(2);
+        byteBuffer.flip();
+        return byteBuffer.getShort();
+    }
+
+    /**
+     * Reads a float off the input stream
+     *
+     * @return float
+     * @throws IOException
+     */
+    public float readFloat() throws IOException {
+        readByteBuffer(4);
+        byteBuffer.flip();
+        return byteBuffer.getFloat();
+    }
+
+    /**
+     * Reads a boolean off the input stream, represented as a byte with value 1 or 0
+     *
+     * @return boolean
+     * @throws IOException
+     */
+    public boolean readBoolean() throws IOException {
+        return ((readByte()) == 1);
+    }
+
+    /**
+     * Reads an 8-bit unsigned byte from the input stream. This method assumes little-endianness.
+     *
+     * @throws IOException
+     */
+    public short readUByte() throws IOException {
+        readByteBuffer(1);
+        byteBuffer.put((byte)0);
+        byteBuffer.flip();
+        return byteBuffer.getShort();
+    }
+
+    /**
+     * Reads a 16-bit unsigned short from the input stream. This method assumes little-endianness.
+     *
+     * @throws IOException
+     */
+    public int readUShort() throws IOException {
+        readByteBuffer(2);
+        byteBuffer.putShort((short)0);
+        byteBuffer.flip();
+        return byteBuffer.getInt();
+    }
+
+    /**
+     * Reads a 32-bit unsigned int from the input stream. This method assumes little-endianness.
+     *
+     * @throws IOException
+     */
+    public long readUInt() throws IOException {
+        readByteBuffer(4);
+        byteBuffer.putInt(0);
+        byteBuffer.flip();
+        return byteBuffer.getLong();
+    }
+
+    /**
+     * Close the appropriate stream
+     *
+     * @throws IOException
+     */
+    public void close() throws IOException {
+        if (this.isWriting) {
+            // To the degree possible, make sure the bytes get forced to the file system,
+            // or else cause an exception to be thrown.
+            if (this.outputStream instanceof FileOutputStream) {
+                this.outputStream.flush();
+                FileOutputStream fos = (FileOutputStream)this.outputStream;
+                try {
+                    fos.getFD().sync();
+                } catch (SyncFailedException e) {
+                    // ignore
+                }
+            }
+            this.outputStream.close();
+        } else {
+            this.inputStream.close();
+        }
+    }
+
+    private String constructErrorMessage(final String msg) {
+        final StringBuilder sb = new StringBuilder(msg);
+        sb.append("; BinaryCodec in ");
+        sb.append(isWriting ? "write" : "read");
+        sb.append("mode; ");
+        final String filename = isWriting ? outputFileName : inputFileName;
+        if (filename != null) {
+            sb.append("file: ");
+            sb.append(filename);
+        } else {
+            sb.append("streamed file (filename not available)");
+        }
+        return sb.toString();
+    }
+
+    public String getInputFileName() {
+        return inputFileName;
+    }
+
+    public String getOutputFileName() {
+        return outputFileName;
+    }
+
+    public void setOutputFileName(final String outputFileName) {
+        this.outputFileName = outputFileName;
+    }
+
+    public void setInputFileName(final String inputFileName) {
+        this.inputFileName = inputFileName;
+    }
+
+    public boolean isWriting() {
+        return isWriting;
+    }
+
+    public OutputStream getOutputStream() {
+        return outputStream;
+    }
+
+    public InputStream getInputStream() {
+        return inputStream;
+    }
+
+    public void setInputStream(final InputStream is) {
+        isWriting = false;
+        this.inputStream = is;
+    }
+
+    public void setOutputStream(final OutputStream os) {
+        isWriting = true;
+        this.outputStream = os;
+    }
+}

io-compress-bgzf/src/main/java/org/xbib/io/compress/bgzf/BlockCompressedInputStream.java

@@ -0,0 +1,709 @@
+package org.xbib.io.compress.bgzf;
+
+import java.io.BufferedInputStream;
+import java.io.ByteArrayOutputStream;
+import java.io.EOFException;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.nio.ByteBuffer;
+import java.nio.ByteOrder;
+import java.nio.channels.SeekableByteChannel;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.StandardOpenOption;
+import java.util.Arrays;
+
+/**
+ * Stream class for reading BGZF block compressed files.  The caller can treat this file like any other InputStream.
+ * It probably is not necessary to wrap this stream in a buffering stream, because there is internal buffering.
+ * The advantage of BGZF over conventional GZip format is that BGZF allows for seeking without having to read the
+ * entire file up to the location being sought.  Note that seeking is only possible if the input stream is seekable.
+ * 
+ * Note that this implementation is not synchronized. If multiple threads access an instance concurrently, it must be synchronized externally. 
+ *
+ * @see <a href="http://samtools.sourceforge.net/SAM1.pdf">http://samtools.sourceforge.net/SAM1.pdf</a> for details of BGZF file format.
+ */
+public class BlockCompressedInputStream extends InputStream {
+
+    public final static String INCORRECT_HEADER_SIZE_MSG = "Incorrect header size for file: ";
+    public final static String UNEXPECTED_BLOCK_LENGTH_MSG = "Unexpected compressed block length: ";
+    public final static String PREMATURE_END_MSG = "Premature end of file: ";
+    public final static String CANNOT_SEEK_STREAM_MSG = "Cannot seek a position for a non-file stream";
+    public final static String CANNOT_SEEK_CLOSED_STREAM_MSG = "Cannot seek a position for a closed stream";
+    public final static String INVALID_FILE_PTR_MSG = "Invalid file pointer: ";
+
+    private InputStream mStream;
+    private boolean mIsClosed = false;
+    private SeekableStream mFile;
+    private byte[] mFileBuffer = null;
+    private DecompressedBlock mCurrentBlock = null;
+    private int mCurrentOffset = 0;
+    private long mStreamOffset = 0;
+    private final BlockGunzipper blockGunzipper;
+
+    private volatile ByteArrayOutputStream buf = null;
+    private static final byte eol = '\n';
+    private static final byte eolCr = '\r';
+
+    /**
+     * Note that seek() is not supported if this ctor is used.
+     * @param stream source of bytes
+     */
+    public BlockCompressedInputStream(final InputStream stream) {
+        this(stream, true, BlockGunzipper.getDefaultInflaterFactory());
+    }
+
+    /**
+     * Note that seek() is not supported if this ctor is used.
+     * @param stream source of bytes
+     * @param inflaterFactory {@link InflaterFactory} used by {@link BlockGunzipper}
+     */
+    public BlockCompressedInputStream(final InputStream stream, final InflaterFactory inflaterFactory) {
+        this(stream, true, inflaterFactory);
+    }
+
+    /**
+     * Note that seek() is not supported if this ctor is used.
+     * @param stream source of bytes
+     * @param allowBuffering if true, allow buffering
+     */
+    public BlockCompressedInputStream(final InputStream stream, final boolean allowBuffering) {
+        this(stream, allowBuffering, BlockGunzipper.getDefaultInflaterFactory());
+    }
+
+    /**
+     * Note that seek() is not supported if this ctor is used.
+     * @param stream source of bytes
+     * @param allowBuffering if true, allow buffering
+     * @param inflaterFactory {@link InflaterFactory} used by {@link BlockGunzipper}
+     */
+    public BlockCompressedInputStream(final InputStream stream, final boolean allowBuffering, final InflaterFactory inflaterFactory) {
+        if (allowBuffering) {
+            mStream = new BufferedInputStream(stream);
+        }
+        else {
+            mStream = stream;
+        }
+
+        mFile = null;
+        blockGunzipper = new BlockGunzipper(inflaterFactory);
+    }
+
+    /**
+     * Use this ctor if you wish to call seek()
+     * @param file source of bytes
+     * @throws IOException
+     */
+    public BlockCompressedInputStream(final File file) throws IOException {
+        this(file, BlockGunzipper.getDefaultInflaterFactory());
+    }
+
+    /**
+     * Use this ctor if you wish to call seek()
+     * @param file source of bytes
+     * @param inflaterFactory {@link InflaterFactory} used by {@link BlockGunzipper}
+     * @throws IOException
+     */
+    public BlockCompressedInputStream(final File file, final InflaterFactory inflaterFactory) throws IOException {
+        mFile = new SeekableFileStream(file);
+        mStream = null;
+        blockGunzipper = new BlockGunzipper(inflaterFactory);
+    }
+
+    /**
+     * For providing some arbitrary data source.  No additional buffering is
+     * provided, so if the underlying source is not buffered, wrap it in a
+     * SeekableBufferedStream before passing to this ctor.
+     * @param strm source of bytes
+     */
+    public BlockCompressedInputStream(final SeekableStream strm) {
+        this(strm, BlockGunzipper.getDefaultInflaterFactory());
+    }
+
+    /**
+     * For providing some arbitrary data source.  No additional buffering is
+     * provided, so if the underlying source is not buffered, wrap it in a
+     * SeekableBufferedStream before passing to this ctor.
+     * @param strm source of bytes
+     * @param inflaterFactory {@link InflaterFactory} used by {@link BlockGunzipper}
+     */
+    public BlockCompressedInputStream(final SeekableStream strm, final InflaterFactory inflaterFactory) {
+        mFile = strm;
+        mStream = null;
+        blockGunzipper = new BlockGunzipper(inflaterFactory);
+    }
+
+    /**
+     * Determines whether or not the inflater will re-calculated the CRC on the decompressed data
+     * and check it against the value stored in the GZIP header.  CRC checking is an expensive
+     * operation and should be used accordingly.
+     */
+    public void setCheckCrcs(final boolean check) {
+        this.blockGunzipper.setCheckCrcs(check);
+    }
+
+    /**
+     * @return the number of bytes that can be read (or skipped over) from this input stream without blocking by the
+     * next caller of a method for this input stream. The next caller might be the same thread or another thread.
+     * Note that although the next caller can read this many bytes without blocking, the available() method call itself
+     * may block in order to fill an internal buffer if it has been exhausted.
+     */
+    @Override
+    public int available() throws IOException {
+        if (mCurrentBlock == null || mCurrentOffset == mCurrentBlock.mBlock.length) {
+            readBlock();
+        }
+        if (mCurrentBlock == null) {
+            return 0;
+        }
+        return mCurrentBlock.mBlock.length - mCurrentOffset;
+    }
+
+    /**
+     * @return <code>true</code> if the stream is at the end of a BGZF block,
+     * <code>false</code> otherwise.
+     */
+    public boolean endOfBlock() {
+        return (mCurrentBlock != null && mCurrentOffset == mCurrentBlock.mBlock.length);
+    }
+
+    /**
+     * Closes the underlying InputStream or RandomAccessFile
+     */
+    @Override
+    public void close() throws IOException {
+        if (mFile != null) {
+            mFile.close();
+            mFile = null;
+        } else if (mStream != null) {
+            mStream.close();
+            mStream = null;
+        }
+        // Encourage garbage collection
+        mFileBuffer = null;
+        mCurrentBlock = null;
+
+        // Mark as closed
+        mIsClosed = true;
+    }
+
+    /**
+     * Reads the next byte of data from the input stream. The value byte is returned as an int in the range 0 to 255.
+     * If no byte is available because the end of the stream has been reached, the value -1 is returned.
+     * This method blocks until input data is available, the end of the stream is detected, or an exception is thrown.
+
+     * @return the next byte of data, or -1 if the end of the stream is reached.
+     */
+    @Override
+    public int read() throws IOException {
+        return (available() > 0) ? (mCurrentBlock.mBlock[mCurrentOffset++] & 0xFF) : -1;
+    }
+
+    /**
+     * Reads some number of bytes from the input stream and stores them into the buffer array b. The number of bytes
+     * actually read is returned as an integer. This method blocks until input data is available, end of file is detected,
+     * or an exception is thrown.
+     *
+     * read(buf) has the same effect as read(buf, 0, buf.length).
+     *
+     * @param buffer the buffer into which the data is read.
+     * @return the total number of bytes read into the buffer, or -1 is there is no more data because the end of
+     * the stream has been reached.
+     */
+    @Override
+    public int read(final byte[] buffer) throws IOException {
+        return read(buffer, 0, buffer.length);
+    }
+
+    /**
+     * Reads a whole line. A line is considered to be terminated by either a line feed ('\n'), 
+     * carriage return ('\r') or carriage return followed by a line feed ("\r\n").
+     *
+     * @return  A String containing the contents of the line, excluding the line terminating
+     *          character, or null if the end of the stream has been reached
+     *
+     * @exception  IOException  If an I/O error occurs
+     */
+    public String readLine() throws IOException {
+        int available = available();
+        if (available == 0) {
+            return null;
+        }
+        if(null == buf){ // lazy initialisation 
+            buf = new ByteArrayOutputStream(8192);
+        }
+        buf.reset();
+        boolean done = false;
+        boolean foundCr = false; // \r found flag
+        while (!done) {
+            int linetmpPos = mCurrentOffset;
+            int bCnt = 0;
+            while((available-- > 0)){
+                final byte c = mCurrentBlock.mBlock[linetmpPos++];
+                if(c == eol){ // found \n
+                    done = true;
+                    break;
+                } else if(foundCr){  // previous char was \r
+                    --linetmpPos; // current char is not \n so put it back
+                    done = true;
+                    break;
+                } else if(c == eolCr){ // found \r
+                    foundCr = true;
+                    continue; // no ++bCnt
+                }
+                ++bCnt;
+            }
+            if(mCurrentOffset < linetmpPos) {
+                buf.write(mCurrentBlock.mBlock, mCurrentOffset, bCnt);
+                mCurrentOffset = linetmpPos;
+            }
+            available = available();
+            if(available == 0) {
+                // EOF
+                done = true;
+            }
+        }
+        return buf.toString();
+    }
+
+    /**
+     * Reads up to len bytes of data from the input stream into an array of bytes. An attempt is made to read
+     * as many as len bytes, but a smaller number may be read. The number of bytes actually read is returned as an integer.
+     *
+     * This method blocks until input data is available, end of file is detected, or an exception is thrown.
+     *
+     * @param buffer buffer into which data is read.
+     * @param offset the start offset in array b  at which the data is written.
+     * @param length the maximum number of bytes to read.
+     * @return the total number of bytes read into the buffer, or -1 if there is no more data because the end of
+     * the stream has been reached.
+     */
+    @Override
+    public int read(final byte[] buffer, int offset, int length) throws IOException {
+        final int originalLength = length;
+        while (length > 0) {
+            final int available = available();
+            if (available == 0) {
+                // Signal EOF to caller
+                if (originalLength == length) {
+                    return -1;
+                }
+                break;
+            }
+            final int copyLength = Math.min(length, available);
+            System.arraycopy(mCurrentBlock.mBlock, mCurrentOffset, buffer, offset, copyLength);
+            mCurrentOffset += copyLength;
+            offset += copyLength;
+            length -= copyLength;
+        }
+        return originalLength - length;
+    }
+
+    /**
+     * Seek to the given position in the file.  Note that pos is a special virtual file pointer,
+     * not an actual byte offset.
+     *
+     * @param pos virtual file pointer position
+     * @throws IOException if stream is closed or not a file based stream
+     */
+    public void seek(final long pos) throws IOException {
+        // Must be before the mFile == null check because mFile == null for closed files and streams
+        if (mIsClosed) {
+            throw new IOException(CANNOT_SEEK_CLOSED_STREAM_MSG);
+        }
+
+        // Cannot seek on streams that are not file based
+        if (mFile == null) {
+            throw new IOException(CANNOT_SEEK_STREAM_MSG);
+        }
+
+        // Decode virtual file pointer
+        // Upper 48 bits is the byte offset into the compressed stream of a
+        // block.
+        // Lower 16 bits is the byte offset into the uncompressed stream inside
+        // the block.
+        final long compressedOffset = BGZFFilePointerUtil.getBlockAddress(pos);
+        final int uncompressedOffset = BGZFFilePointerUtil.getBlockOffset(pos);
+        final int available;
+        if (mCurrentBlock != null && mCurrentBlock.mBlockAddress == compressedOffset) {
+            available = mCurrentBlock.mBlock.length;
+        } else {
+            prepareForSeek();
+            mFile.seek(compressedOffset);
+            mStreamOffset = compressedOffset;
+            mCurrentBlock = nextBlock(getBufferForReuse(mCurrentBlock));
+            mCurrentOffset = 0;
+            available = available();
+        }
+        if (uncompressedOffset > available || (uncompressedOffset == available && !eof())) {
+            throw new IOException(INVALID_FILE_PTR_MSG + pos + " for " + getSource());
+        }
+        mCurrentOffset = uncompressedOffset;
+    }
+    
+    /**
+     * Performs cleanup required before seek is called on the underlying stream 
+     */
+    protected void prepareForSeek() {
+    }
+
+    private boolean eof() throws IOException {
+        if (mFile.eof()) {
+            return true;
+        }
+        // If the last remaining block is the size of the EMPTY_GZIP_BLOCK, this is the same as being at EOF.
+        return (mFile.length() - (mCurrentBlock.mBlockAddress
+                + mCurrentBlock.mBlockCompressedSize) == BGZFStreamConstants.EMPTY_GZIP_BLOCK.length);
+    }
+
+    /**
+     * @return virtual file pointer that can be passed to seek() to return to the current position.  This is
+     * not an actual byte offset, so arithmetic on file pointers cannot be done to determine the distance between
+     * the two.
+     */
+    public long getFilePointer() {
+        if (mCurrentBlock == null) {
+            // Haven't read anything yet = at start of stream
+            return BGZFFilePointerUtil.makeFilePointer(0, 0);
+        }
+        if (mCurrentOffset > 0 && mCurrentOffset == mCurrentBlock.mBlock.length) {
+            // If current offset is at the end of the current block, file
+            // pointer should point
+            // to the beginning of the next block.
+            return BGZFFilePointerUtil.makeFilePointer(mCurrentBlock.mBlockAddress + mCurrentBlock.mBlockCompressedSize, 0);
+        }
+        return BGZFFilePointerUtil.makeFilePointer(mCurrentBlock.mBlockAddress, mCurrentOffset);
+    }
+
+    public long getPosition() {
+        return getFilePointer();
+    }
+
+    public static long getFileBlock(final long bgzfOffset) {
+        return BGZFFilePointerUtil.getBlockAddress(bgzfOffset);
+    }
+    
+    /**
+     * @param stream Must be at start of file.  Throws RuntimeException if !stream.markSupported().
+     * @return true if the given file looks like a valid BGZF file.
+     */
+    public static boolean isValidFile(final InputStream stream) throws IOException {
+        if (!stream.markSupported()) {
+            throw new RuntimeException("Cannot test non-buffered stream");
+        }
+        stream.mark(BGZFStreamConstants.BLOCK_HEADER_LENGTH);
+        final byte[] buffer = new byte[BGZFStreamConstants.BLOCK_HEADER_LENGTH];
+        final int count = readBytes(stream, buffer, 0, BGZFStreamConstants.BLOCK_HEADER_LENGTH);
+        stream.reset();
+        return count == BGZFStreamConstants.BLOCK_HEADER_LENGTH && isValidBlockHeader(buffer);
+    }
+
+    private static boolean isValidBlockHeader(final byte[] buffer) {
+        return (buffer[0] == BGZFStreamConstants.GZIP_ID1 &&
+                (buffer[1] & 0xFF) == BGZFStreamConstants.GZIP_ID2 &&
+                (buffer[3] & BGZFStreamConstants.GZIP_FLG) != 0 &&
+                buffer[10] == BGZFStreamConstants.GZIP_XLEN &&
+                buffer[12] == BGZFStreamConstants.BGZF_ID1 &&
+                buffer[13] == BGZFStreamConstants.BGZF_ID2);
+    }
+
+    private void readBlock() throws IOException {
+        mCurrentBlock = nextBlock(getBufferForReuse(mCurrentBlock));
+        mCurrentOffset = 0;
+        checkAndRethrowDecompressionException();
+    }
+    /**
+     * Reads and decompresses the next block
+     * @param bufferAvailableForReuse decompression buffer available for reuse
+     * @return next block in the decompressed stream
+     */
+    protected DecompressedBlock nextBlock(byte[] bufferAvailableForReuse) {
+        return processNextBlock(bufferAvailableForReuse);
+    }
+    /**
+     * Rethrows an exception encountered during decompression
+     * @throws IOException
+     */
+    private void checkAndRethrowDecompressionException() throws IOException {
+        if (mCurrentBlock.mException != null) {
+            if (mCurrentBlock.mException instanceof IOException) {
+                throw (IOException) mCurrentBlock.mException;
+            } else if (mCurrentBlock.mException instanceof RuntimeException) {
+                throw (RuntimeException) mCurrentBlock.mException;
+            } else {
+                throw new RuntimeException(mCurrentBlock.mException);
+            }
+        }
+    }
+    
+    /**
+     * Attempt to reuse the buffer of the given block 
+     * @param block owning block
+     * @return null decompressing buffer to reuse, null if no buffer is available
+     */
+    private byte[] getBufferForReuse(DecompressedBlock block) {
+        if (block == null) return null;
+        return block.mBlock;
+    }
+    
+    /**
+     * Decompress the next block from the input stream. When using asynchronous 
+     * IO, this will be called by the background thread.
+     * @param bufferAvailableForReuse buffer in which to place decompressed block. A null or
+     *  incorrectly sized buffer will result in the buffer being ignored and
+     *  a new buffer allocated for decompression.
+     * @return next block in input stream
+     */
+    protected DecompressedBlock processNextBlock(byte[] bufferAvailableForReuse) {
+        if (mFileBuffer == null) {
+            mFileBuffer = new byte[BGZFStreamConstants.MAX_COMPRESSED_BLOCK_SIZE];
+        }
+        long blockAddress = mStreamOffset;
+        try {
+            final int headerByteCount = readBytes(mFileBuffer, 0, BGZFStreamConstants.BLOCK_HEADER_LENGTH);
+            mStreamOffset += headerByteCount;
+            if (headerByteCount == 0) {
+                // Handle case where there is no empty gzip block at end.
+                return new DecompressedBlock(blockAddress, new byte[0], 0);
+            }
+            if (headerByteCount != BGZFStreamConstants.BLOCK_HEADER_LENGTH) {
+                return new DecompressedBlock(blockAddress, headerByteCount, new IOException(INCORRECT_HEADER_SIZE_MSG + getSource()));
+            }
+            final int blockLength = unpackInt16(mFileBuffer, BGZFStreamConstants.BLOCK_LENGTH_OFFSET) + 1;
+            if (blockLength < BGZFStreamConstants.BLOCK_HEADER_LENGTH || blockLength > mFileBuffer.length) {
+                return new DecompressedBlock(blockAddress, blockLength,
+                        new IOException(UNEXPECTED_BLOCK_LENGTH_MSG + blockLength + " for " + getSource()));
+            }
+            final int remaining = blockLength - BGZFStreamConstants.BLOCK_HEADER_LENGTH;
+            final int dataByteCount = readBytes(mFileBuffer, BGZFStreamConstants.BLOCK_HEADER_LENGTH,
+                    remaining);
+            mStreamOffset += dataByteCount;
+            if (dataByteCount != remaining) {
+                return new DecompressedBlock(blockAddress, blockLength,
+                        new BGZFException(PREMATURE_END_MSG + getSource()));
+            }
+            final byte[] decompressed = inflateBlock(mFileBuffer, blockLength, bufferAvailableForReuse);
+            return new DecompressedBlock(blockAddress, decompressed, blockLength);
+        } catch (IOException e) {
+            return new DecompressedBlock(blockAddress, 0, e);
+        }
+    }
+
+    private byte[] inflateBlock(final byte[] compressedBlock, final int compressedLength,
+            final byte[] bufferAvailableForReuse) throws IOException {
+        final int uncompressedLength = unpackInt32(compressedBlock, compressedLength - 4);
+        if (uncompressedLength < 0) {
+            throw new BGZFException(getSource() + " has invalid uncompressedLength: " + uncompressedLength);
+        }
+        byte[] buffer = bufferAvailableForReuse;
+        if (buffer == null || uncompressedLength != buffer.length) {
+        	// can't reuse the buffer since the size is incorrect
+            buffer = new byte[uncompressedLength];
+        }
+        blockGunzipper.unzipBlock(buffer, compressedBlock, compressedLength);
+        return buffer;
+    }
+
+    private String getSource() {
+        return mFile == null ? "data stream" : mFile.getSource();
+    }
+
+    private int readBytes(final byte[] buffer, final int offset, final int length) throws IOException {
+        if (mFile != null) {
+            return readBytes(mFile, buffer, offset, length);
+        } else if (mStream != null) {
+            return readBytes(mStream, buffer, offset, length);
+        } else {
+            return 0;
+        }
+    }
+
+    private static int readBytes(final SeekableStream file, final byte[] buffer, final int offset, final int length) throws IOException {
+        int bytesRead = 0;
+        while (bytesRead < length) {
+            final int count = file.read(buffer, offset + bytesRead, length - bytesRead);
+            if (count <= 0) {
+                break;
+            }
+            bytesRead += count;
+        }
+        return bytesRead;
+    }
+
+    private static int readBytes(final InputStream stream, final byte[] buffer, final int offset, final int length) throws IOException {
+        int bytesRead = 0;
+        while (bytesRead < length) {
+            final int count = stream.read(buffer, offset + bytesRead, length - bytesRead);
+            if (count <= 0) {
+                break;
+            }
+            bytesRead += count;
+        }
+        return bytesRead;
+    }
+
+    private int unpackInt16(final byte[] buffer, final int offset) {
+        return ((buffer[offset] & 0xFF) |
+                ((buffer[offset+1] & 0xFF) << 8));
+    }
+
+    private int unpackInt32(final byte[] buffer, final int offset) {
+        return ((buffer[offset] & 0xFF) |
+                ((buffer[offset+1] & 0xFF) << 8) |
+                ((buffer[offset+2] & 0xFF) << 16) |
+                ((buffer[offset+3] & 0xFF) << 24));
+    }
+
+    public enum FileTermination {HAS_TERMINATOR_BLOCK, HAS_HEALTHY_LAST_BLOCK, DEFECTIVE}
+
+    /**
+     *
+     * @param file the file to check
+     * @return status of the last compressed block
+     * @throws IOException
+     */
+    public static FileTermination checkTermination(final File file) throws IOException {
+        return checkTermination(file.toPath());
+    }
+
+    /**
+     *
+     * @param path to the file to check
+     * @return status of the last compressed block
+     * @throws IOException
+     */
+    public static FileTermination checkTermination(final Path path) throws IOException {
+        try( final SeekableByteChannel channel = Files.newByteChannel(path, StandardOpenOption.READ) ){
+            return checkTermination(channel);
+        }
+    }
+
+    /**
+     * check the status of the final bzgipped block for the given bgzipped resource
+     *
+     * @param channel an open channel to read from,
+     * the channel will remain open and the initial position will be restored when the operation completes
+     * this makes no guarantee about the state of the channel if an exception is thrown during reading
+     *
+     * @return the status of the last compressed black
+     * @throws IOException
+     */
+    public static FileTermination checkTermination(SeekableByteChannel channel) throws IOException {
+        final long fileSize = channel.size();
+        if (fileSize < BGZFStreamConstants.EMPTY_GZIP_BLOCK.length) {
+            return FileTermination.DEFECTIVE;
+        }
+        final long initialPosition = channel.position();
+        boolean exceptionThrown = false;
+        try {
+            channel.position(fileSize - BGZFStreamConstants.EMPTY_GZIP_BLOCK.length);
+
+            //Check if the end of the file is an empty gzip block which is used as the terminator for a bgzipped file
+            final ByteBuffer lastBlockBuffer = ByteBuffer.allocate(BGZFStreamConstants.EMPTY_GZIP_BLOCK.length);
+            readFully(channel, lastBlockBuffer);
+            if (Arrays.equals(lastBlockBuffer.array(), BGZFStreamConstants.EMPTY_GZIP_BLOCK)) {
+                return FileTermination.HAS_TERMINATOR_BLOCK;
+            }
+
+            //if the last block isn't an empty gzip block, check to see if it is a healthy compressed block or if it's corrupted
+            final int bufsize = (int) Math.min(fileSize, BGZFStreamConstants.MAX_COMPRESSED_BLOCK_SIZE);
+            final byte[] bufferArray = new byte[bufsize];
+            channel.position(fileSize - bufsize);
+            readFully(channel, ByteBuffer.wrap(bufferArray));
+            for (int i = bufferArray.length - BGZFStreamConstants.EMPTY_GZIP_BLOCK.length;
+                 i >= 0; --i) {
+                if (!preambleEqual(BGZFStreamConstants.GZIP_BLOCK_PREAMBLE,
+                                   bufferArray, i, BGZFStreamConstants.GZIP_BLOCK_PREAMBLE.length)) {
+                    continue;
+                }
+                final ByteBuffer byteBuffer = ByteBuffer.wrap(bufferArray,
+                                                              i + BGZFStreamConstants.GZIP_BLOCK_PREAMBLE.length,
+                                                              4);
+                byteBuffer.order(ByteOrder.LITTLE_ENDIAN);
+                final int totalBlockSizeMinusOne = byteBuffer.getShort() & 0xFFFF;
+                if (bufferArray.length - i == totalBlockSizeMinusOne + 1) {
+                    return FileTermination.HAS_HEALTHY_LAST_BLOCK;
+                } else {
+                    return FileTermination.DEFECTIVE;
+                }
+            }
+            return FileTermination.DEFECTIVE;
+        } catch (final Throwable e) {
+            exceptionThrown = true;
+            throw e;
+        } finally {
+            //if an exception was thrown we don't want to reset the position because that would be likely to throw again
+            //and suppress the initial exception
+            if(!exceptionThrown) {
+                channel.position(initialPosition);
+            }
+        }
+    }
+
+    /**
+     * read as many bytes as dst's capacity into dst or throw if that's not possible
+     *
+     * @throws EOFException if channel has fewer bytes available than dst's capacity
+     */
+    static void readFully(SeekableByteChannel channel, ByteBuffer dst) throws IOException {
+        int totalBytesRead = 0;
+        final int capacity = dst.capacity();
+        while (totalBytesRead < capacity) {
+            final int bytesRead = channel.read(dst);
+            if (bytesRead == -1) {
+                throw new EOFException();
+            }
+            totalBytesRead += bytesRead;
+        }
+    }
+
+    public static void assertNonDefectiveFile(final File file) throws IOException {
+        if (checkTermination(file) == FileTermination.DEFECTIVE) {
+            throw new BGZFException(file.getAbsolutePath() + " does not have a valid GZIP block at the end of the file.");
+        }
+    }
+
+    private static boolean preambleEqual(final byte[] preamble, final byte[] buf, final int startOffset, final int length) {
+        for (int i = 0; i < length; ++i) {
+            if (preamble[i] != buf[i + startOffset]) {
+                return false;
+            }
+        }
+        return true;
+    }
+
+    protected static class DecompressedBlock {
+        /**
+         * Decompressed block
+         */
+        private final byte[] mBlock;
+        /**
+         * Compressed size of block (the uncompressed size can be found using
+         * mBlock.length)
+         */
+        private final int mBlockCompressedSize;
+        /**
+         * Stream offset of start of block
+         */
+        private final long mBlockAddress;
+        /**
+         * Exception thrown (if any) when attempting to decompress block
+         */
+        private final Exception mException;
+
+        public DecompressedBlock(long blockAddress, byte[] block, int compressedSize) {
+            mBlock = block;
+            mBlockAddress = blockAddress;
+            mBlockCompressedSize = compressedSize;
+            mException = null;
+        }
+
+        public DecompressedBlock(long blockAddress, int compressedSize, Exception exception) {
+            mBlock = new byte[0];
+            mBlockAddress = blockAddress;
+            mBlockCompressedSize = compressedSize;
+            mException = exception;
+        }
+    }
+}

io-compress-bgzf/src/main/java/org/xbib/io/compress/bgzf/BlockCompressedOutputStream.java

@@ -0,0 +1,358 @@
+package org.xbib.io.compress.bgzf;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.zip.CRC32;
+import java.util.zip.Deflater;
+
+/**
+ * Stream class for a file that is a series of gzip blocks (BGZF format). The caller just treats it as an
+ * OutputStream, and under the covers a gzip block is written when the amount of uncompressed as-yet-unwritten
+ * bytes reaches a threshold.
+ *
+ * The advantage of BGZF over conventional gzip is that BGZF allows for seeking without having to scan through
+ * the entire file up to the position being sought.
+ *
+ * Note that the flush() method should not be called by client
+ * unless you know what you're doing, because it forces a gzip block to be written even if the
+ * number of buffered bytes has not reached threshold.  close(), on the other hand, must be called
+ * when done writing in order to force the last gzip block to be written.
+ *
+ * @see <a href="http://samtools.sourceforge.net/SAM1.pdf">http://samtools.sourceforge.net/SAM1.pdf</a> for details of BGZF file format.
+ */
+public class BlockCompressedOutputStream extends OutputStream {
+
+    private static int defaultCompressionLevel = BGZFStreamConstants.DEFAULT_COMPRESSION_LEVEL;
+    private static DeflaterFactory defaultDeflaterFactory = new DeflaterFactory();
+
+    public static void setDefaultCompressionLevel(final int compressionLevel) {
+        if (compressionLevel < Deflater.NO_COMPRESSION || compressionLevel > Deflater.BEST_COMPRESSION) {
+            throw new IllegalArgumentException("Invalid compression level: " + compressionLevel);
+        }
+        defaultCompressionLevel = compressionLevel;
+    }
+
+    public static int getDefaultCompressionLevel() {
+        return defaultCompressionLevel;
+    }
+
+    /**
+     * Sets the default {@link DeflaterFactory} that will be used for all instances unless specified otherwise in the constructor.
+     * If this method is not called the default is a factory that will create the JDK {@link Deflater}.
+     * @param deflaterFactory non-null default factory.
+     */
+    public static void setDefaultDeflaterFactory(final DeflaterFactory deflaterFactory) {
+        if (deflaterFactory == null) {
+            throw new IllegalArgumentException("null deflaterFactory");
+        }
+        defaultDeflaterFactory = deflaterFactory;
+    }
+
+    public static DeflaterFactory getDefaultDeflaterFactory() {
+        return defaultDeflaterFactory;
+    }
+
+    private final BinaryCodec codec;
+    private final byte[] uncompressedBuffer = new byte[BGZFStreamConstants.DEFAULT_UNCOMPRESSED_BLOCK_SIZE];
+    private int numUncompressedBytes = 0;
+    private final byte[] compressedBuffer =
+            new byte[BGZFStreamConstants.MAX_COMPRESSED_BLOCK_SIZE -
+                    BGZFStreamConstants.BLOCK_HEADER_LENGTH];
+    private final Deflater deflater;
+
+    // A second deflater is created for the very unlikely case where the regular deflation actually makes
+    // things bigger, and the compressed block is too big.  It should be possible to downshift the
+    // primary deflater to NO_COMPRESSION level, recompress, and then restore it to its original setting,
+    // but in practice that doesn't work.
+    // The motivation for deflating at NO_COMPRESSION level is that it will predictably produce compressed
+    // output that is 10 bytes larger than the input, and the threshold at which a block is generated is such that
+    // the size of tbe final gzip block will always be <= 64K.  This is preferred over the previous method,
+    // which would attempt to compress up to 64K bytes, and if the resulting compressed block was too large,
+    // try compressing fewer input bytes (aka "downshifting').  The problem with downshifting is that
+    // getFilePointer might return an inaccurate value.
+    // I assume (AW 29-Oct-2013) that there is no value in using hardware-assisted deflater for no-compression mode,
+    // so just use JDK standard.
+    private final Deflater noCompressionDeflater = new Deflater(Deflater.NO_COMPRESSION, true);
+    private final CRC32 crc32 = new CRC32();
+    private Path file = null;
+    private long mBlockAddress = 0;
+
+    /**
+     * Uses default compression level, which is 5 unless changed by setCompressionLevel
+     * Note: this constructor uses the default {@link DeflaterFactory}, see {@link #getDefaultDeflaterFactory()}.
+     * Use {@link #BlockCompressedOutputStream(File, int, DeflaterFactory)} to specify a custom factory.
+     */
+    public BlockCompressedOutputStream(final String filename) throws FileNotFoundException {
+        this(filename, defaultCompressionLevel);
+    }
+
+    /**
+     * Uses default compression level, which is 5 unless changed by setCompressionLevel
+     * Note: this constructor uses the default {@link DeflaterFactory}, see {@link #getDefaultDeflaterFactory()}.
+     * Use {@link #BlockCompressedOutputStream(File, int, DeflaterFactory)} to specify a custom factory.
+     */
+    public BlockCompressedOutputStream(final File file) throws FileNotFoundException {
+        this(file, defaultCompressionLevel);
+    }
+
+    public BlockCompressedOutputStream(final String filename, final int compressionLevel) throws FileNotFoundException {
+        this(new File(filename), compressionLevel);
+    }
+
+    public BlockCompressedOutputStream(final File file, final int compressionLevel) throws FileNotFoundException {
+        this(file, compressionLevel, defaultDeflaterFactory);
+    }
+
+    public BlockCompressedOutputStream(final File file, final int compressionLevel, final DeflaterFactory deflaterFactory) throws FileNotFoundException {
+        this.file = file.toPath();
+        codec = new BinaryCodec(file, true);
+        deflater = deflaterFactory.makeDeflater(compressionLevel, true);
+    }
+
+    /**
+     * Uses default compression level, which is 5 unless changed by setCompressionLevel
+     * Note: this constructor uses the default {@link DeflaterFactory}, see {@link #getDefaultDeflaterFactory()}.
+     * Use {@link #BlockCompressedOutputStream(OutputStream, File, int, DeflaterFactory)} to specify a custom factory.
+     */
+    public BlockCompressedOutputStream(final OutputStream os) {
+        this(os, (File)null, defaultCompressionLevel);
+    }
+
+    /**
+     * Uses default compression level, which is 5 unless changed by setCompressionLevel
+     * Note: this constructor uses the default {@link DeflaterFactory}, see {@link #getDefaultDeflaterFactory()}.
+     * Use {@link #BlockCompressedOutputStream(OutputStream, File, int, DeflaterFactory)} to specify a custom factory.
+     *
+     * @param file may be null
+     */
+    public BlockCompressedOutputStream(final OutputStream os, final Path file) {
+        this(os, file, defaultCompressionLevel);
+    }
+
+    /**
+     * Note: this constructor uses the default {@link DeflaterFactory}, see {@link #getDefaultDeflaterFactory()}.
+     * Use {@link #BlockCompressedOutputStream(OutputStream, File, int, DeflaterFactory)} to specify a custom factory.
+     */
+    public BlockCompressedOutputStream(final OutputStream os, final File file, final int compressionLevel) {
+        this(os, file, compressionLevel, defaultDeflaterFactory);
+    }
+
+    /**
+     * Note: this constructor uses the default {@link DeflaterFactory}, see {@link #getDefaultDeflaterFactory()}.
+     * Use {@link #BlockCompressedOutputStream(OutputStream, File, int, DeflaterFactory)} to specify a custom factory.
+     */
+    public BlockCompressedOutputStream(final OutputStream os, final Path file, final int compressionLevel) {
+        this(os, file, compressionLevel, defaultDeflaterFactory);
+    }
+
+    /**
+     * Creates the output stream.
+     * @param os output stream to create a BlockCompressedOutputStream from
+     * @param file file to which to write the output or null if not available
+     * @param compressionLevel the compression level (0-9)
+     * @param deflaterFactory custom factory to create deflaters (overrides the default)
+     */
+    public BlockCompressedOutputStream(final OutputStream os, final File file, final int compressionLevel, final DeflaterFactory deflaterFactory) {
+        this(os, file != null ? file.toPath() : null, compressionLevel, deflaterFactory);
+    }
+
+    /**
+     * Creates the output stream.
+     * @param os output stream to create a BlockCompressedOutputStream from
+     * @param file file to which to write the output or null if not available
+     * @param compressionLevel the compression level (0-9)
+     * @param deflaterFactory custom factory to create deflaters (overrides the default)
+     */
+    public BlockCompressedOutputStream(final OutputStream os, final Path file, final int compressionLevel, final DeflaterFactory deflaterFactory) {
+        this.file = file;
+        codec = new BinaryCodec(os);
+        if (file != null) {
+            codec.setOutputFileName(file.toAbsolutePath().toUri().toString());
+        }
+        deflater = deflaterFactory.makeDeflater(compressionLevel, true);
+    }
+
+    /**
+     * @param output May or not already be a BlockCompressedOutputStream.
+     * @return A BlockCompressedOutputStream, either by wrapping the given OutputStream, or by casting if it already
+     *         is a BCOS.
+     */
+    public static BlockCompressedOutputStream maybeBgzfWrapOutputStream(OutputStream output) {
+        if (!(output instanceof BlockCompressedOutputStream)) {
+           return new BlockCompressedOutputStream(output);
+        } else {
+           return (BlockCompressedOutputStream)output;
+        }
+    }
+
+    /**
+     * Writes b.length bytes from the specified byte array to this output stream. The general contract for write(b)
+     * is that it should have exactly the same effect as the call write(b, 0, b.length).
+     * @param bytes the data
+     */
+    @Override
+    public void write(final byte[] bytes) throws IOException {
+        write(bytes, 0, bytes.length);
+    }
+
+    /**
+     * Writes len bytes from the specified byte array starting at offset off to this output stream. The general
+     * contract for write(b, off, len) is that some of the bytes in the array b are written to the output stream in order;
+     * element b[off] is the first byte written and b[off+len-1] is the last byte written by this operation.
+     *
+     * @param bytes the data
+     * @param startIndex the start offset in the data
+     * @param numBytes the number of bytes to write
+     */
+    @Override
+    public void write(final byte[] bytes, int startIndex, int numBytes) throws IOException {
+        while (numBytes > 0) {
+            final int bytesToWrite = Math.min(uncompressedBuffer.length - numUncompressedBytes, numBytes);
+            System.arraycopy(bytes, startIndex, uncompressedBuffer, numUncompressedBytes, bytesToWrite);
+            numUncompressedBytes += bytesToWrite;
+            startIndex += bytesToWrite;
+            numBytes -= bytesToWrite;
+            if (numUncompressedBytes == uncompressedBuffer.length) {
+                deflateBlock();
+            }
+        }
+    }
+
+    @Override
+    public void write(final int b) throws IOException {
+        uncompressedBuffer[numUncompressedBytes++] = (byte) b;
+        if (numUncompressedBytes == uncompressedBuffer.length) deflateBlock();
+    }
+
+    /**
+     * WARNING: flush() affects the output format, because it causes the current contents of uncompressedBuffer
+     * to be compressed and written, even if it isn't full.  Unless you know what you're doing, don't call flush().
+     * Instead, call close(), which will flush any unwritten data before closing the underlying stream.
+     *
+     */
+    @Override
+    public void flush() throws IOException {
+        while (numUncompressedBytes > 0) {
+            deflateBlock();
+        }
+        codec.getOutputStream().flush();
+    }
+
+    /**
+     * close() must be called in order to flush any remaining buffered bytes.  An unclosed file will likely be
+     * defective.
+     *
+     */
+    @Override
+    public void close() throws IOException {
+        close(true);
+    }
+
+    public void close(final boolean writeTerminatorBlock) throws IOException {
+        flush();
+        // For debugging...
+        // if (numberOfThrottleBacks > 0) {
+        //     System.err.println("In BlockCompressedOutputStream, had to throttle back " + numberOfThrottleBacks +
+        //                        " times for file " + codec.getOutputFileName());
+        // }
+        if (writeTerminatorBlock) {
+            codec.writeBytes(BGZFStreamConstants.EMPTY_GZIP_BLOCK);
+        }
+        codec.close();
+
+        // If a terminator block was written, ensure that it's there and valid
+        if (writeTerminatorBlock) {
+            // Can't re-open something that is not a regular file, e.g. a named pipe or an output stream
+            if (this.file == null || !Files.isRegularFile(this.file)) return;
+            if (BlockCompressedInputStream.checkTermination(this.file) !=
+                    BlockCompressedInputStream.FileTermination.HAS_TERMINATOR_BLOCK) {
+                throw new IOException("Terminator block not found after closing BGZF file " + this.file);
+            }
+        }
+    }
+
+    /** Encode virtual file pointer
+     * Upper 48 bits is the byte offset into the compressed stream of a block.
+     * Lower 16 bits is the byte offset into the uncompressed stream inside the block.
+     */
+    public long getFilePointer(){
+        return BGZFFilePointerUtil.makeFilePointer(mBlockAddress, numUncompressedBytes);
+    }
+
+    public long getPosition() {
+        return getFilePointer();
+    }
+
+    /**
+     * Attempt to write the data in uncompressedBuffer to the underlying file in a gzip block.
+     * If the entire uncompressedBuffer does not fit in the maximum allowed size, reduce the amount
+     * of data to be compressed, and slide the excess down in uncompressedBuffer so it can be picked
+     * up in the next deflate event.
+     * @return size of gzip block that was written.
+     */
+    private int deflateBlock() throws IOException {
+        if (numUncompressedBytes == 0) {
+            return 0;
+        }
+        final int bytesToCompress = numUncompressedBytes;
+        // Compress the input
+        deflater.reset();
+        deflater.setInput(uncompressedBuffer, 0, bytesToCompress);
+        deflater.finish();
+        int compressedSize = deflater.deflate(compressedBuffer, 0, compressedBuffer.length);
+
+        // If it didn't all fit in compressedBuffer.length, set compression level to NO_COMPRESSION
+        // and try again.  This should always fit.
+        if (!deflater.finished()) {
+            noCompressionDeflater.reset();
+            noCompressionDeflater.setInput(uncompressedBuffer, 0, bytesToCompress);
+            noCompressionDeflater.finish();
+            compressedSize = noCompressionDeflater.deflate(compressedBuffer, 0, compressedBuffer.length);
+            if (!noCompressionDeflater.finished()) {
+                throw new IllegalStateException("unpossible");
+            }
+        }
+        // Data compressed small enough, so write it out.
+        crc32.reset();
+        crc32.update(uncompressedBuffer, 0, bytesToCompress);
+
+        final int totalBlockSize = writeGzipBlock(compressedSize, bytesToCompress, crc32.getValue());
+
+        // Clear out from uncompressedBuffer the data that was written
+        numUncompressedBytes = 0;
+        mBlockAddress += totalBlockSize;
+        return totalBlockSize;
+    }
+
+    /**
+     * Writes the entire gzip block, assuming the compressed data is stored in compressedBuffer
+     * @return  size of gzip block that was written.
+     */
+    private int writeGzipBlock(final int compressedSize, final int uncompressedSize, final long crc) throws IOException {
+        // Init gzip header
+        codec.writeByte(BGZFStreamConstants.GZIP_ID1);
+        codec.writeByte(BGZFStreamConstants.GZIP_ID2);
+        codec.writeByte(BGZFStreamConstants.GZIP_CM_DEFLATE);
+        codec.writeByte(BGZFStreamConstants.GZIP_FLG);
+        codec.writeInt(0); // Modification time
+        codec.writeByte(BGZFStreamConstants.GZIP_XFL);
+        codec.writeByte(BGZFStreamConstants.GZIP_OS_UNKNOWN);
+        codec.writeShort(BGZFStreamConstants.GZIP_XLEN);
+        codec.writeByte(BGZFStreamConstants.BGZF_ID1);
+        codec.writeByte(BGZFStreamConstants.BGZF_ID2);
+        codec.writeShort(BGZFStreamConstants.BGZF_LEN);
+        final int totalBlockSize = compressedSize + BGZFStreamConstants.BLOCK_HEADER_LENGTH +
+                BGZFStreamConstants.BLOCK_FOOTER_LENGTH;
+
+        // I don't know why we store block size - 1, but that is what the spec says
+        codec.writeShort((short)(totalBlockSize - 1));
+        codec.writeBytes(compressedBuffer, 0, compressedSize);
+        codec.writeInt((int)crc);
+        codec.writeInt(uncompressedSize);
+        return totalBlockSize;
+    }
+}

io-compress-bgzf/src/main/java/org/xbib/io/compress/bgzf/BlockGunzipper.java

@@ -0,0 +1,114 @@
+package org.xbib.io.compress.bgzf;
+
+import java.nio.ByteBuffer;
+import java.nio.ByteOrder;
+import java.util.zip.CRC32;
+import java.util.zip.DataFormatException;
+import java.util.zip.Inflater;
+
+/**
+ * For decompressing GZIP blocks that are already loaded into a byte[].
+ * The main advantage is that this object can be used over and over again to decompress many blocks,
+ * whereas a new GZIPInputStream and ByteArrayInputStream would otherwise need to be created for each
+ * block to be decompressed.
+ *
+ * This code requires that the GZIP header conform to the GZIP blocks written to BAM files, with
+ * a specific subfield and no other optional stuff.
+ */
+public class BlockGunzipper {
+    private static InflaterFactory defaultInflaterFactory = new InflaterFactory();
+    private final Inflater inflater;
+    private final CRC32 crc32 = new CRC32();
+    private boolean checkCrcs = false;
+    BlockGunzipper() {
+        inflater = defaultInflaterFactory.makeInflater(true); // GZIP mode
+    }
+
+    /**
+     * Create a BlockGunzipper using the provided inflaterFactory
+     * @param inflaterFactory
+     */
+    BlockGunzipper(InflaterFactory inflaterFactory) {
+        inflater = inflaterFactory.makeInflater(true); // GZIP mode
+    }
+
+    /**
+     * Sets the default {@link InflaterFactory} that will be used for all instances unless specified otherwise in the constructor.
+     * If this method is not called the default is a factory that will create the JDK {@link Inflater}.
+     * @param inflaterFactory non-null default factory.
+     */
+    public static void setDefaultInflaterFactory(final InflaterFactory inflaterFactory) {
+        if (inflaterFactory == null) {
+            throw new IllegalArgumentException("null inflaterFactory");
+        }
+        defaultInflaterFactory = inflaterFactory;
+    }
+
+    public static InflaterFactory getDefaultInflaterFactory() {
+        return defaultInflaterFactory;
+    }
+    /** Allows the caller to decide whether or not to check CRCs on when uncompressing blocks. */
+    public void setCheckCrcs(final boolean check) {
+        this.checkCrcs = check;
+    }
+
+    /**
+     * Decompress GZIP-compressed data
+     * @param uncompressedBlock must be big enough to hold decompressed output.
+     * @param compressedBlock compressed data starting at offset 0
+     * @param compressedLength size of compressed data, possibly less than the size of the buffer.
+     */
+    void unzipBlock(byte[] uncompressedBlock, byte[] compressedBlock, int compressedLength) {
+        try {
+            ByteBuffer byteBuffer = ByteBuffer.wrap(compressedBlock, 0, compressedLength);
+            byteBuffer.order(ByteOrder.LITTLE_ENDIAN);
+
+            // Validate GZIP header
+            if (byteBuffer.get() != BGZFStreamConstants.GZIP_ID1 ||
+                    byteBuffer.get() != (byte)BGZFStreamConstants.GZIP_ID2 ||
+                    byteBuffer.get() != BGZFStreamConstants.GZIP_CM_DEFLATE ||
+                    byteBuffer.get() != BGZFStreamConstants.GZIP_FLG
+                    ) {
+                throw new BGZFFormatException("Invalid GZIP header");
+            }
+            // Skip MTIME, XFL, OS fields
+            byteBuffer.position(byteBuffer.position() + 6);
+            if (byteBuffer.getShort() != BGZFStreamConstants.GZIP_XLEN) {
+                throw new BGZFFormatException("Invalid GZIP header");
+            }
+            // Skip blocksize subfield intro
+            byteBuffer.position(byteBuffer.position() + 4);
+            // Read ushort
+            final int totalBlockSize = (byteBuffer.getShort() & 0xffff) + 1;
+            if (totalBlockSize != compressedLength) {
+                throw new BGZFFormatException("GZIP blocksize disagreement");
+            }
+
+            // Read expected size and CRD from end of GZIP block
+            final int deflatedSize = compressedLength - BGZFStreamConstants.BLOCK_HEADER_LENGTH - BGZFStreamConstants.BLOCK_FOOTER_LENGTH;
+            byteBuffer.position(byteBuffer.position() + deflatedSize);
+            int expectedCrc = byteBuffer.getInt();
+            int uncompressedSize = byteBuffer.getInt();
+            inflater.reset();
+
+            // Decompress
+            inflater.setInput(compressedBlock, BGZFStreamConstants.BLOCK_HEADER_LENGTH, deflatedSize);
+            final int inflatedBytes = inflater.inflate(uncompressedBlock, 0, uncompressedSize);
+            if (inflatedBytes != uncompressedSize) {
+                throw new BGZFFormatException("Did not inflate expected amount");
+            }
+
+            // Validate CRC if so desired
+            if (this.checkCrcs) {
+                crc32.reset();
+                crc32.update(uncompressedBlock, 0, uncompressedSize);
+                final long crc = crc32.getValue();
+                if ((int)crc != expectedCrc) {
+                    throw new BGZFFormatException("CRC mismatch");
+                }
+            }
+        } catch (DataFormatException e) {
+            throw new BGZFException(e);
+        }
+    }
+}

io-compress-bgzf/src/main/java/org/xbib/io/compress/bgzf/DeflaterFactory.java

@@ -0,0 +1,24 @@
+package org.xbib.io.compress.bgzf;
+
+import java.util.zip.Deflater;
+
+/**
+ * Factory for {@link Deflater} objects used by {@link BlockCompressedOutputStream}.
+ * This class may be extended to provide alternative deflaters (e.g., for improved performance).
+ */
+public class DeflaterFactory {
+
+    public DeflaterFactory() {
+        //Note: made explicit constructor to make searching for references easier
+    }
+
+    /**
+     * Returns a deflater object that will be used when writing BAM files.
+     * Subclasses may override to provide their own deflater implementation.
+     * @param compressionLevel the compression level (0-9)
+     * @param gzipCompatible if true then use GZIP compatible compression
+     */
+    public Deflater makeDeflater(final int compressionLevel, final boolean gzipCompatible) {
+        return new Deflater(compressionLevel, gzipCompatible);
+    }
+}

io-compress-bgzf/src/main/java/org/xbib/io/compress/bgzf/InflaterFactory.java

@@ -0,0 +1,20 @@
+package org.xbib.io.compress.bgzf;
+
+import java.util.zip.Inflater;
+
+/**
+ * Factory for {@link Inflater} objects used by {@link BlockGunzipper}.
+ * This class may be extended to provide alternative inflaters (e.g., for improved performance).
+ * The default implementation returns a JDK {@link Inflater}
+ */
+public class InflaterFactory {
+    /**
+     * Returns an inflater object that will be used when reading DEFLATE compressed files.
+     * Subclasses may override to provide their own inflater implementation.
+     * The default implementation returns a JDK {@link Inflater}
+     * @param gzipCompatible if true then use GZIP compatible compression
+     */
+    public Inflater makeInflater(final boolean gzipCompatible) {
+        return new Inflater(gzipCompatible);
+    }
+}

io-compress-bgzf/src/main/java/org/xbib/io/compress/bgzf/SeekableBufferedStream.java

@@ -0,0 +1,105 @@
+package org.xbib.io.compress.bgzf;
+
+import java.io.BufferedInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+
+/**
+ * A wrapper class to provide buffered read access to a SeekableStream.  Just wrapping such a stream with
+ * a BufferedInputStream will not work as it does not support seeking.  In this implementation a
+ * seek call is delegated to the wrapped stream, and the buffer reset.
+ */
+public class SeekableBufferedStream extends SeekableStream {
+
+    /** Little extension to buffered input stream to give access to the available bytes in the buffer. */
+    private static class ExtBufferedInputStream extends BufferedInputStream {
+        private ExtBufferedInputStream(final InputStream inputStream, final int i) {
+            super(inputStream, i);
+        }
+
+        /** Returns the number of bytes that can be read from the buffer without reading more into the buffer. */
+        int getBytesInBufferAvailable() {
+            if (this.count == this.pos) return 0; // documented test for "is buffer empty"
+            else return this.buf.length - this.pos;
+        }
+    }
+
+    public static final int DEFAULT_BUFFER_SIZE = 512000;
+
+    final private int bufferSize;
+    final SeekableStream wrappedStream;
+    ExtBufferedInputStream bufferedStream;
+    long position;
+
+    public SeekableBufferedStream(final SeekableStream stream, final int bufferSize) {
+        this.bufferSize = bufferSize;
+        this.wrappedStream = stream;
+        this.position = 0;
+        bufferedStream = new ExtBufferedInputStream(wrappedStream, bufferSize);
+    }
+
+    public SeekableBufferedStream(final SeekableStream stream) {
+        this(stream, DEFAULT_BUFFER_SIZE);
+    }
+
+    @Override
+    public long length() {
+        return wrappedStream.length();
+    }
+
+    @Override
+    public long skip(final long skipLength) throws IOException {
+        if (skipLength < this.bufferedStream.getBytesInBufferAvailable()) {
+            final long retval = this.bufferedStream.skip(skipLength);
+            this.position += retval;
+            return retval;
+        } else {
+            final long position = this.position + skipLength;
+            seek(position);
+            return skipLength;
+        }
+    }
+
+    @Override
+    public void seek(final long position) throws IOException {
+        this.position = position;
+        wrappedStream.seek(position);
+        bufferedStream = new ExtBufferedInputStream(wrappedStream, bufferSize);
+    }
+
+    @Override
+    public int read() throws IOException {
+        int b = bufferedStream.read();
+        position++;
+        return b;
+    }
+
+    @Override
+    public int read(final byte[] buffer, final int offset, final int length) throws IOException {
+        final int nBytesRead = bufferedStream.read(buffer, offset, length);
+        if (nBytesRead > 0) {
+            position += nBytesRead;
+        }
+        return nBytesRead;
+    }
+
+    @Override
+    public void close() throws IOException {
+        wrappedStream.close();
+    }
+
+    @Override
+    public boolean eof() throws IOException {
+        return position >= wrappedStream.length();
+    }
+
+    @Override
+    public String getSource() {
+        return wrappedStream.getSource();
+    }
+
+    @Override
+    public long position() throws IOException {
+        return position;
+    }
+}

io-compress-bgzf/src/main/java/org/xbib/io/compress/bgzf/SeekableFileStream.java

@@ -0,0 +1,110 @@
+package org.xbib.io.compress.bgzf;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.RandomAccessFile;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashSet;
+
+public class SeekableFileStream extends SeekableStream {
+
+    /**
+     * Collection of all open instances.  SeekableFileStream objects are usually open and kept open for the
+     * duration of a session.  This collection supports a method to close them all.
+     */
+    private static final Collection<SeekableFileStream> allInstances = Collections.synchronizedCollection(new HashSet<>());
+
+    File file;
+    RandomAccessFile fis;
+
+    public SeekableFileStream(final File file) throws FileNotFoundException {
+        this.file = file;
+        fis = new RandomAccessFile(file, "r");
+        allInstances.add(this);
+    }
+
+    @Override
+    public long length() {
+        return file.length();
+    }
+
+    @Override
+    public boolean eof() throws IOException {
+        return fis.length() == fis.getFilePointer();
+    }
+
+    @Override
+    public void seek(final long position) throws IOException {
+        fis.seek(position);
+    }
+
+    @Override
+    public long position() throws IOException {
+        return fis.getChannel().position();
+    }
+
+    @Override
+    public long skip(long n) throws IOException {
+        long initPos = position();
+        fis.getChannel().position(initPos + n);
+        return position() - initPos;
+    }
+
+    @Override
+    public int read(final byte[] buffer, final int offset, final int length) throws IOException {
+        if (length < 0) {
+            throw new IndexOutOfBoundsException();
+        }
+        int n = 0;
+        while (n < length) {
+            final int count = fis.read(buffer, offset + n, length - n);
+            if (count < 0) {
+              if (n > 0) {
+                return n;
+              } else {
+                return count;
+              }
+            }
+            n += count;
+        }
+        return n;
+
+    }
+
+    @Override
+    public int read() throws IOException {
+        return fis.read();
+    }
+
+    @Override
+    public int read(byte[] b) throws IOException {
+        return fis.read(b);
+    }
+
+    @Override
+    public String getSource() {
+        return file.getAbsolutePath();
+    }
+
+
+    @Override
+    public void close() throws IOException {
+        allInstances.remove(this);
+        fis.close();
+
+    }
+
+    public static synchronized void closeAllInstances() {
+        Collection<SeekableFileStream> clonedInstances = new HashSet<>(allInstances);
+        for (SeekableFileStream sfs : clonedInstances) {
+            try {
+                sfs.close();
+            } catch (IOException e) {
+                //
+            }
+        }
+        allInstances.clear();
+    }
+}

io-compress-bgzf/src/main/java/org/xbib/io/compress/bgzf/SeekableStream.java

@@ -0,0 +1,44 @@
+package org.xbib.io.compress.bgzf;
+
+import java.io.EOFException;
+import java.io.IOException;
+import java.io.InputStream;
+
+public abstract class SeekableStream extends InputStream {
+
+    public abstract long length();
+
+    public abstract long position() throws IOException;
+
+    public abstract void seek(long position) throws IOException;
+
+    @Override
+    public abstract int read(byte[] buffer, int offset, int length) throws IOException;
+
+    @Override
+    public abstract void close() throws IOException;
+
+    public abstract boolean eof() throws IOException;
+
+    /**
+     * @return String representation of source (e.g. URL, file path, etc.), or null if not available.
+     */
+    public abstract String getSource();
+
+    /**
+     * Read enough bytes to fill the input buffer.
+     * @param b byte array
+     * @throws EOFException If EOF is reached before buffer is filled
+     */
+    public void readFully(byte[] b) throws IOException {
+        int len = b.length;
+        int n = 0;
+        while (n < len) {
+            int count = read(b, n, len - n);
+            if (count < 0){
+                throw new EOFException();
+            }
+            n += count;
+        }
+    }
+}

io-compress-bgzf/src/main/java/org/xbib/io/compress/bgzf/SeekableStreamFactory.java

@@ -0,0 +1,11 @@
+package org.xbib.io.compress.bgzf;
+
+import java.io.File;
+import java.io.IOException;
+
+public class SeekableStreamFactory {
+
+    public static SeekableStream getStreamFor(String path) throws IOException {
+        return new SeekableFileStream(new File(path));
+    }
+}

io-compress-lzf/src/main/java/org/xbib/io/compress/lzf/ChunkDecoderFactory.java

@@ -30,7 +30,7 @@ public class ChunkDecoderFactory {
      */
     public static ChunkDecoder optimalInstance() {
         try {
-            return INSTANCE.implClass.newInstance();
+            return INSTANCE.implClass.getDeclaredConstructor().newInstance();
         } catch (Exception e) {
             throw new IllegalStateException("Failed to load a ChunkDecoder instance (" + e.getClass().getName() + "): "
                     + e.getMessage(), e);

io-compress-xz/src/main/java/org/xbib/io/compress/xz/IndexIndicatorException.java

@@ -1,5 +1,5 @@
-
 package org.xbib.io.compress.xz;
 
+@SuppressWarnings("serial")
 class IndexIndicatorException extends Exception {
 }

io-compress-xz/src/main/java/org/xbib/io/compress/xz/index/IndexEncoder.java

@@ -1,4 +1,3 @@
-
 package org.xbib.io.compress.xz.index;
 
 import org.xbib.io.compress.xz.XZIOException;
@@ -7,11 +6,12 @@ import org.xbib.io.compress.xz.common.EncoderUtil;
 import java.io.IOException;
 import java.io.OutputStream;
 import java.util.ArrayList;
-import java.util.Iterator;
+import java.util.List;
 import java.util.zip.CheckedOutputStream;
 
 public class IndexEncoder extends IndexBase {
-    private final ArrayList records = new ArrayList();
+
+    private final List<IndexRecord> records = new ArrayList<>();
 
     public IndexEncoder() {
         super(new XZIOException("XZ Stream or its Index has grown too big"));
@@ -34,8 +34,7 @@ public class IndexEncoder extends IndexBase {
         EncoderUtil.encodeVLI(outChecked, recordCount);
 
         // List of Records
-        for (Iterator i = records.iterator(); i.hasNext(); ) {
+        for (IndexRecord record : records) {
-            IndexRecord record = (IndexRecord) i.next();
             EncoderUtil.encodeVLI(outChecked, record.unpadded);
             EncoderUtil.encodeVLI(outChecked, record.uncompressed);
         }

settings.gradle

@@ -1,3 +1,21 @@
+dependencyResolutionManagement {
+    versionCatalogs {
+        libs {
+            version('gradle', '8.5')
+        }
+        testLibs {
+            version('junit', '5.10.1')
+            library('junit-jupiter-api', 'org.junit.jupiter', 'junit-jupiter-api').versionRef('junit')
+            library('junit-jupiter-params', 'org.junit.jupiter', 'junit-jupiter-params').versionRef('junit')
+            library('junit-jupiter-engine', 'org.junit.jupiter', 'junit-jupiter-engine').versionRef('junit')
+            library('junit-jupiter-platform-launcher', 'org.junit.platform', 'junit-platform-launcher').version('1.10.1')
+            library('junit4', 'junit', 'junit').version('4.13.2')
+            library('hamcrest', 'org.hamcrest', 'hamcrest-library').version('2.2')
+        }
+    }
+}
+
+include 'io-compress-bgzf'
 include 'io-compress-bzip2'
 include 'io-compress-lzf'
 include 'io-compress-xz'