Commit 5c5e2f76 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 2.16.1+dfsg

parent 26feb9cc

.travis.yml

+14 −1
Original line number Diff line number Diff line
@@ -11,7 +11,20 @@ cache: 
jdk:

  - oraclejdk8

  - openjdk8

script: ./gradlew test jacocoTestReport;

matrix:

  fast_finish: true

  allow_failures: 

     - env: TEST_TYPE=FTP

  include:

     - jdk: oraclejdk8

       env: TEST_TYPE=FTP

script:

  - if [[ $TEST_TYPE == "FTP" ]]; then

        ./gradlew testFTP jacocoTestReport;

    else

        ./gradlew test jacocoTestReport;

    fi



after_success:

  - bash <(curl -s https://codecov.io/bash)

  - echo "TRAVIS_BRANCH='$TRAVIS_BRANCH'";

build.gradle

+21 −11
Original line number Diff line number Diff line
@@ -10,9 +10,9 @@ plugins { 
    id 'maven'

    id 'signing'

    id 'jacoco'

    id 'com.palantir.git-version' version '0.5.1'

    id 'com.github.johnrengelman.shadow' version '1.2.3'

    id 'com.github.maiflai.scalatest' version '0.15'

    id 'com.palantir.git-version' version '0.11.0'

    id 'com.github.johnrengelman.shadow' version '2.0.4'

    id 'com.github.maiflai.scalatest' version '0.22'

}



repositories {
@@ -36,12 +36,12 @@ dependencies { 
    compile "org.xerial.snappy:snappy-java:1.1.4"

    compile "org.apache.commons:commons-compress:1.4.1"

    compile "org.tukaani:xz:1.5"

    compile "gov.nih.nlm.ncbi:ngs-java:1.2.4"

    compile "gov.nih.nlm.ncbi:ngs-java:2.9.0"



    testCompile "org.scala-lang:scala-library:2.12.1"

    testCompile "org.scalatest:scalatest_2.12:3.0.1"

    testRuntime 'org.pegdown:pegdown:1.4.2' // Necessary for generating HTML reports with ScalaTest

    testCompile "org.testng:testng:6.9.9"

    testCompile "org.scala-lang:scala-library:2.12.6"

    testCompile "org.scalatest:scalatest_2.12:3.0.5"

    testRuntime 'org.pegdown:pegdown:1.6.0' // Necessary for generating HTML reports with ScalaTest

    testCompile "org.testng:testng:6.14.3"

    testCompile "com.google.jimfs:jimfs:1.1"

 }
@@ -100,11 +100,22 @@ test { 
    tags {

        exclude "slow"

        exclude "broken"

        exclude "ftp"

        if (System.env.CI == "false") exclude "sra"

        if (!OperatingSystem.current().isUnix()) exclude "unix"

    }

} dependsOn findScalaAndJavaTypes





task testFTP(type: Test) {

    description = "Runs the tests that require connection to a remote ftp server"

    tags {

        include "ftp"

        exclude "slow"

        exclude "broken"

    }

}



task testSRA(type: Test) {

    description = "Run the SRA tests"

    jvmArgs += '-Dsamjdk.sra_libraries_download=true'
@@ -115,9 +126,8 @@ task testSRA(type: Test) { 
    }

}



task wrapper(type: Wrapper) {

    description = "Regenerate the gradle wrapper"

    gradleVersion = '3.2.1'

wrapper {

    gradleVersion = '4.8.1'

}



// This is a hack to disable the java 8 default javadoc lint until we fix the html formatting

gradle/wrapper/gradle-wrapper.properties

+1 −2
Original line number Diff line number Diff line 
#Fri Jan 20 17:10:11 EST 2017

distributionBase=GRADLE_USER_HOME

distributionPath=wrapper/dists

distributionUrl=https\://services.gradle.org/distributions/gradle-4.8.1-bin.zip

zipStoreBase=GRADLE_USER_HOME

zipStorePath=wrapper/dists
 
distributionUrl=https\://services.gradle.org/distributions/gradle-3.2.1-all.zip

gradlew

+13 −10
Original line number Diff line number Diff line 
#!/usr/bin/env bash

#!/usr/bin/env sh



##############################################################################

##
@@ -154,16 +154,19 @@ if $cygwin ; then 
    esac

fi



# Split up the JVM_OPTS And GRADLE_OPTS values into an array, following the shell quoting and substitution rules

function splitJvmOpts() {

    JVM_OPTS=("$@")

# Escape application args

save () {

    for i do printf %s\\n "$i" | sed "s/'/'\\\\''/g;1s/^/'/;\$s/\$/' \\\\/" ; done

    echo " "

}

eval splitJvmOpts $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS

JVM_OPTS[${#JVM_OPTS[*]}]="-Dorg.gradle.appname=$APP_BASE_NAME"

APP_ARGS=$(save "$@")



# Collect all arguments for the java command, following the shell quoting and substitution rules

eval set -- $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS "\"-Dorg.gradle.appname=$APP_BASE_NAME\"" -classpath "\"$CLASSPATH\"" org.gradle.wrapper.GradleWrapperMain "$APP_ARGS"



# by default we should be in the correct project dir, but when run from Finder on Mac, the cwd is wrong

if [[ "$(uname)" == "Darwin" ]] && [[ "$HOME" == "$PWD" ]]; then

if [ "$(uname)" = "Darwin" ] && [ "$HOME" = "$PWD" ]; then

  cd "$(dirname "$0")"

fi



exec "$JAVACMD" "${JVM_OPTS[@]}" -classpath "$CLASSPATH" org.gradle.wrapper.GradleWrapperMain "$@"
 
exec "$JAVACMD" "$@"

src/main/java/htsjdk/samtools/BAMFileWriter.java

+9 −4
Original line number Diff line number Diff line
@@ -40,7 +40,7 @@ import java.nio.file.Path; 
/**

 * Concrete implementation of SAMFileWriter for writing gzipped BAM files.

 */

class BAMFileWriter extends SAMFileWriterImpl {

public class BAMFileWriter extends SAMFileWriterImpl {



    private final BinaryCodec outputBinaryCodec;

    private BAMRecordCodec bamRecordCodec = null;
@@ -78,7 +78,7 @@ class BAMFileWriter extends SAMFileWriterImpl { 
    }



    protected BAMFileWriter(final OutputStream os, final String absoluteFilename, final int compressionLevel, final DeflaterFactory deflaterFactory) {

      blockCompressedOutputStream = new BlockCompressedOutputStream(os, null, compressionLevel, deflaterFactory);

      blockCompressedOutputStream = new BlockCompressedOutputStream(os, (Path)null, compressionLevel, deflaterFactory);

      outputBinaryCodec = new BinaryCodec(blockCompressedOutputStream);

      outputBinaryCodec.setOutputFileName(absoluteFilename);

    }
@@ -200,8 +200,13 @@ class BAMFileWriter extends SAMFileWriterImpl { 
        writeHeader(outputBinaryCodec, samFileHeader, headerString);

    }



    protected static void writeHeader(final OutputStream outputStream, final SAMFileHeader samFileHeader) {

        final BlockCompressedOutputStream blockCompressedOutputStream = new BlockCompressedOutputStream(outputStream, null);

    /**

     * Write a BAM file header to an output stream in block compressed BAM format.

     * @param outputStream the stream to write the BAM header to

     * @param samFileHeader the header to write

     */

    public static void writeHeader(final OutputStream outputStream, final SAMFileHeader samFileHeader) {

        final BlockCompressedOutputStream blockCompressedOutputStream = new BlockCompressedOutputStream(outputStream, (Path)null);

        final BinaryCodec outputBinaryCodec = new BinaryCodec(blockCompressedOutputStream);

        writeHeader(outputBinaryCodec, samFileHeader);

        try {