You can download htsjdk-1.118.jar in this page.
MIT License
htsjdk-1.118.jar file has the following types.
META-INF/MANIFEST.MF htsjdk.samtools.AbstractBAMFileIndex.class htsjdk.samtools.AbstractSAMHeaderRecord.class htsjdk.samtools.AlignmentBlock.class htsjdk.samtools.AsyncSAMFileWriter.class htsjdk.samtools.BAMFileConstants.class htsjdk.samtools.BAMFileReader.class htsjdk.samtools.BAMFileSpan.class htsjdk.samtools.BAMFileWriter.class htsjdk.samtools.BAMIndex.class htsjdk.samtools.BAMIndexContent.class htsjdk.samtools.BAMIndexMetaData.class htsjdk.samtools.BAMIndexWriter.class htsjdk.samtools.BAMIndexer.class htsjdk.samtools.BAMRecord.class htsjdk.samtools.BAMRecordCodec.class htsjdk.samtools.BamFileIoUtils.class htsjdk.samtools.BamIndexValidator.class htsjdk.samtools.Bin.class htsjdk.samtools.BinList.class htsjdk.samtools.BinaryBAMIndexWriter.class htsjdk.samtools.BinaryCigarCodec.class htsjdk.samtools.BinaryTagCodec.class htsjdk.samtools.BinningIndexBuilder.class htsjdk.samtools.BinningIndexContent.class htsjdk.samtools.BrowseableBAMIndex.class htsjdk.samtools.CachingBAMFileIndex.class htsjdk.samtools.Chunk.class htsjdk.samtools.Cigar.class htsjdk.samtools.CigarElement.class htsjdk.samtools.CigarOperator.class htsjdk.samtools.ComparableSamRecordIterator.class htsjdk.samtools.CoordinateSortedPairInfoMap.class htsjdk.samtools.DefaultSAMRecordFactory.class htsjdk.samtools.Defaults.class htsjdk.samtools.DiskBasedBAMFileIndex.class htsjdk.samtools.FileInputResource.class htsjdk.samtools.FileTruncatedException.class htsjdk.samtools.FixBAMFile.class htsjdk.samtools.GenomicIndexUtil.class htsjdk.samtools.Indexer.class htsjdk.samtools.InputResource.class htsjdk.samtools.InputStreamInputResource.class htsjdk.samtools.LinearIndex.class htsjdk.samtools.MergingSamRecordIterator.class htsjdk.samtools.NotPrimarySkippingIterator.class htsjdk.samtools.QueryInterval.class htsjdk.samtools.ReservedTagConstants.class htsjdk.samtools.SAMBinaryTagAndUnsignedArrayValue.class htsjdk.samtools.SAMBinaryTagAndValue.class htsjdk.samtools.SAMException.class htsjdk.samtools.SAMFileHeader.class htsjdk.samtools.SAMFileReader.class htsjdk.samtools.SAMFileSource.class htsjdk.samtools.SAMFileSpan.class htsjdk.samtools.SAMFileTruncatedReader.class htsjdk.samtools.SAMFileWriter.class htsjdk.samtools.SAMFileWriterFactory.class htsjdk.samtools.SAMFileWriterImpl.class htsjdk.samtools.SAMFormatException.class htsjdk.samtools.SAMHeaderRecordComparator.class htsjdk.samtools.SAMLineParser.class htsjdk.samtools.SAMProgramRecord.class htsjdk.samtools.SAMReadGroupRecord.class htsjdk.samtools.SAMRecord.class htsjdk.samtools.SAMRecordComparator.class htsjdk.samtools.SAMRecordCoordinateComparator.class htsjdk.samtools.SAMRecordFactory.class htsjdk.samtools.SAMRecordIterator.class htsjdk.samtools.SAMRecordQueryNameComparator.class htsjdk.samtools.SAMRecordSetBuilder.class htsjdk.samtools.SAMRecordUtil.class htsjdk.samtools.SAMSequenceDictionary.class htsjdk.samtools.SAMSequenceRecord.class htsjdk.samtools.SAMSortOrderChecker.class htsjdk.samtools.SAMTag.class htsjdk.samtools.SAMTagUtil.class htsjdk.samtools.SAMTestUtil.class htsjdk.samtools.SAMTextHeaderCodec.class htsjdk.samtools.SAMTextReader.class htsjdk.samtools.SAMTextWriter.class htsjdk.samtools.SAMTools.class htsjdk.samtools.SAMUtils.class htsjdk.samtools.SAMValidationError.class htsjdk.samtools.SQTagUtil.class htsjdk.samtools.SamFileHeaderMerger.class htsjdk.samtools.SamFileValidator.class htsjdk.samtools.SamFiles.class htsjdk.samtools.SamInputResource.class htsjdk.samtools.SamPairUtil.class htsjdk.samtools.SamReader.class htsjdk.samtools.SamReaderFactory.class htsjdk.samtools.SamStreams.class htsjdk.samtools.SecondaryOrSupplementarySkippingIterator.class htsjdk.samtools.SeekableStreamInputResource.class htsjdk.samtools.StreamInflatingIndexingOutputStream.class htsjdk.samtools.TagValueAndUnsignedArrayFlag.class htsjdk.samtools.TextCigarCodec.class htsjdk.samtools.TextTagCodec.class htsjdk.samtools.TextualBAMIndexWriter.class htsjdk.samtools.UrlInputResource.class htsjdk.samtools.ValidationStringency.class htsjdk.samtools.apps.TimeChannel.class htsjdk.samtools.apps.TimeRandomAccessFile.class htsjdk.samtools.example.ExampleSamUsage.class htsjdk.samtools.fastq.AsyncFastqWriter.class htsjdk.samtools.fastq.BasicFastqWriter.class htsjdk.samtools.fastq.FastqConstants.class htsjdk.samtools.fastq.FastqReader.class htsjdk.samtools.fastq.FastqRecord.class htsjdk.samtools.fastq.FastqWriter.class htsjdk.samtools.fastq.FastqWriterFactory.class htsjdk.samtools.filter.AggregateFilter.class htsjdk.samtools.filter.AlignedFilter.class htsjdk.samtools.filter.DuplicateReadFilter.class htsjdk.samtools.filter.FailsVendorReadQualityFilter.class htsjdk.samtools.filter.FilteringIterator.class htsjdk.samtools.filter.IntervalFilter.class htsjdk.samtools.filter.NotPrimaryAlignmentFilter.class htsjdk.samtools.filter.ReadNameFilter.class htsjdk.samtools.filter.SamRecordFilter.class htsjdk.samtools.filter.SecondaryAlignmentFilter.class htsjdk.samtools.filter.SecondaryOrSupplementaryFilter.class htsjdk.samtools.filter.SolexaNoiseFilter.class htsjdk.samtools.filter.TagFilter.class htsjdk.samtools.filter.WholeReadClippedFilter.class htsjdk.samtools.liftover.Chain.class htsjdk.samtools.liftover.LiftOver.class htsjdk.samtools.metrics.Header.class htsjdk.samtools.metrics.MetricBase.class htsjdk.samtools.metrics.MetricsFile.class htsjdk.samtools.metrics.StringHeader.class htsjdk.samtools.metrics.VersionHeader.class htsjdk.samtools.reference.AbstractFastaSequenceFile.class htsjdk.samtools.reference.FastaSequenceFile.class htsjdk.samtools.reference.FastaSequenceIndex.class htsjdk.samtools.reference.FastaSequenceIndexEntry.class htsjdk.samtools.reference.IndexedFastaSequenceFile.class htsjdk.samtools.reference.ReferenceSequence.class htsjdk.samtools.reference.ReferenceSequenceFile.class htsjdk.samtools.reference.ReferenceSequenceFileFactory.class htsjdk.samtools.reference.ReferenceSequenceFileWalker.class htsjdk.samtools.seekablestream.ISeekableStreamFactory.class htsjdk.samtools.seekablestream.SeekableBufferedStream.class htsjdk.samtools.seekablestream.SeekableFTPStream.class htsjdk.samtools.seekablestream.SeekableFTPStreamHelper.class htsjdk.samtools.seekablestream.SeekableFileStream.class htsjdk.samtools.seekablestream.SeekableHTTPStream.class htsjdk.samtools.seekablestream.SeekableStream.class htsjdk.samtools.seekablestream.SeekableStreamFactory.class htsjdk.samtools.seekablestream.UserPasswordInput.class htsjdk.samtools.util.AbstractAsyncWriter.class htsjdk.samtools.util.AbstractIterator.class htsjdk.samtools.util.AsciiWriter.class htsjdk.samtools.util.BinaryCodec.class htsjdk.samtools.util.BlockCompressedFilePointerUtil.class htsjdk.samtools.util.BlockCompressedInputStream.class htsjdk.samtools.util.BlockCompressedOutputStream.class htsjdk.samtools.util.BlockCompressedStreamConstants.class htsjdk.samtools.util.BlockGunzipper.class htsjdk.samtools.util.BufferedLineReader.class htsjdk.samtools.util.CigarUtil.class htsjdk.samtools.util.CloseableIterator.class htsjdk.samtools.util.CloserUtil.class htsjdk.samtools.util.CollectionUtil.class htsjdk.samtools.util.CoordMath.class htsjdk.samtools.util.CustomGzipOutputStream.class htsjdk.samtools.util.DateParser.class htsjdk.samtools.util.DelegatingIterator.class htsjdk.samtools.util.FastLineReader.class htsjdk.samtools.util.FastqQualityFormat.class htsjdk.samtools.util.FileAppendStreamLRUCache.class htsjdk.samtools.util.FormatUtil.class htsjdk.samtools.util.Histogram.class htsjdk.samtools.util.HttpUtils.class htsjdk.samtools.util.IOUtil.class htsjdk.samtools.util.Interval.class htsjdk.samtools.util.IntervalCoordinateComparator.class htsjdk.samtools.util.IntervalList.class htsjdk.samtools.util.IntervalListReferenceSequenceMask.class htsjdk.samtools.util.IntervalTree.class htsjdk.samtools.util.IntervalTreeMap.class htsjdk.samtools.util.IntervalUtil.class htsjdk.samtools.util.Iso8601Date.class htsjdk.samtools.util.IterableAdapter.class htsjdk.samtools.util.IterableOnceIterator.class htsjdk.samtools.util.Iterables.class htsjdk.samtools.util.Lazy.class htsjdk.samtools.util.LineReader.class htsjdk.samtools.util.ListMap.class htsjdk.samtools.util.LocationAware.class htsjdk.samtools.util.Locus.class htsjdk.samtools.util.LocusComparator.class htsjdk.samtools.util.LocusImpl.class htsjdk.samtools.util.Log.class htsjdk.samtools.util.Md5CalculatingInputStream.class htsjdk.samtools.util.Md5CalculatingOutputStream.class htsjdk.samtools.util.MergingIterator.class htsjdk.samtools.util.OverlapDetector.class htsjdk.samtools.util.PeekIterator.class htsjdk.samtools.util.PeekableIterator.class htsjdk.samtools.util.ProcessExecutor.class htsjdk.samtools.util.ProgressLogger.class htsjdk.samtools.util.ProgressLoggerInterface.class htsjdk.samtools.util.QualityEncodingDetector.class htsjdk.samtools.util.QualityUtil.class htsjdk.samtools.util.ReferenceSequenceMask.class htsjdk.samtools.util.RelativeIso8601Date.class htsjdk.samtools.util.ResourceLimitedMap.class htsjdk.samtools.util.ResourceLimitedMapFunctor.class htsjdk.samtools.util.RuntimeEOFException.class htsjdk.samtools.util.RuntimeIOException.class htsjdk.samtools.util.SamLocusIterator.class htsjdk.samtools.util.SamRecordIntervalIteratorFactory.class htsjdk.samtools.util.SequenceUtil.class htsjdk.samtools.util.SnappyLoader.class htsjdk.samtools.util.SolexaQualityConverter.class htsjdk.samtools.util.SortingCollection.class htsjdk.samtools.util.SortingLongCollection.class htsjdk.samtools.util.StopWatch.class htsjdk.samtools.util.StringLineReader.class htsjdk.samtools.util.StringUtil.class htsjdk.samtools.util.TempStreamFactory.class htsjdk.samtools.util.TestUtil.class htsjdk.samtools.util.Tuple.class htsjdk.samtools.util.WholeGenomeReferenceSequenceMask.class htsjdk.samtools.util.ftp.FTPClient.class htsjdk.samtools.util.ftp.FTPReply.class htsjdk.samtools.util.ftp.FTPStream.class htsjdk.samtools.util.ftp.FTPUtils.class htsjdk.samtools.util.zip.DeflaterFactory.class htsjdk.samtools.util.zip.IntelDeflater.class htsjdk.samtools.util.zip.ZStreamRef.class htsjdk.tribble.AbstractFeatureCodec.class htsjdk.tribble.AbstractFeatureReader.class htsjdk.tribble.AsciiFeatureCodec.class htsjdk.tribble.BasicFeature.class htsjdk.tribble.BinaryFeatureCodec.class htsjdk.tribble.CloseableTribbleIterator.class htsjdk.tribble.Feature.class htsjdk.tribble.FeatureCodec.class htsjdk.tribble.FeatureCodecHeader.class htsjdk.tribble.FeatureReader.class htsjdk.tribble.NameAwareCodec.class htsjdk.tribble.TabixFeatureReader.class htsjdk.tribble.Tribble.class htsjdk.tribble.TribbleException.class htsjdk.tribble.TribbleIndexedFeatureReader.class htsjdk.tribble.annotation.Strand.class htsjdk.tribble.bed.BEDCodec.class htsjdk.tribble.bed.BEDFeature.class htsjdk.tribble.bed.FullBEDFeature.class htsjdk.tribble.bed.SimpleBEDFeature.class htsjdk.tribble.dbsnp.OldDbSNPCodec.class htsjdk.tribble.dbsnp.OldDbSNPFeature.class htsjdk.tribble.example.CountRecords.class htsjdk.tribble.example.ExampleBinaryCodec.class htsjdk.tribble.example.IndexToTable.class htsjdk.tribble.example.IndicesAreEqual.class htsjdk.tribble.example.ProfileIndexReading.class htsjdk.tribble.exception.CodecLineParsingException.class htsjdk.tribble.exception.UnsortedFileException.class htsjdk.tribble.gelitext.DiploidGenotype.class htsjdk.tribble.gelitext.DiploidGenotypeException.class htsjdk.tribble.gelitext.GeliTextCodec.class htsjdk.tribble.gelitext.GeliTextFeature.class htsjdk.tribble.index.AbstractIndex.class htsjdk.tribble.index.Block.class htsjdk.tribble.index.ChrIndex.class htsjdk.tribble.index.DynamicIndexCreator.class htsjdk.tribble.index.Index.class htsjdk.tribble.index.IndexCreator.class htsjdk.tribble.index.IndexFactory.class htsjdk.tribble.index.MutableIndex.class htsjdk.tribble.index.TribbleIndexCreator.class htsjdk.tribble.index.interval.Interval.class htsjdk.tribble.index.interval.IntervalIndexCreator.class htsjdk.tribble.index.interval.IntervalTree.class htsjdk.tribble.index.interval.IntervalTreeIndex.class htsjdk.tribble.index.interval.MutableInterval.class htsjdk.tribble.index.linear.LinearIndex.class htsjdk.tribble.index.linear.LinearIndexCreator.class htsjdk.tribble.index.tabix.TabixFormat.class htsjdk.tribble.index.tabix.TabixIndex.class htsjdk.tribble.index.tabix.TabixIndexCreator.class htsjdk.tribble.readers.AsciiLineReader.class htsjdk.tribble.readers.AsciiLineReaderIterator.class htsjdk.tribble.readers.AsynchronousLineReader.class htsjdk.tribble.readers.LineIterator.class htsjdk.tribble.readers.LineIteratorImpl.class htsjdk.tribble.readers.LineReader.class htsjdk.tribble.readers.LineReaderUtil.class htsjdk.tribble.readers.LongLineBufferedReader.class htsjdk.tribble.readers.Positional.class htsjdk.tribble.readers.PositionalBufferedStream.class htsjdk.tribble.readers.TabixIteratorLineReader.class htsjdk.tribble.readers.TabixReader.class htsjdk.tribble.util.FTPHelper.class htsjdk.tribble.util.HTTPHelper.class htsjdk.tribble.util.LittleEndianInputStream.class htsjdk.tribble.util.LittleEndianOutputStream.class htsjdk.tribble.util.MathUtils.class htsjdk.tribble.util.ParsingUtils.class htsjdk.tribble.util.RemoteURLHelper.class htsjdk.tribble.util.TabixUtils.class htsjdk.tribble.util.URLHelper.class htsjdk.tribble.util.popgen.HardyWeinbergCalculation.class htsjdk.variant.bcf2.BCF2Codec.class htsjdk.variant.bcf2.BCF2Decoder.class htsjdk.variant.bcf2.BCF2GenotypeFieldDecoders.class htsjdk.variant.bcf2.BCF2LazyGenotypesDecoder.class htsjdk.variant.bcf2.BCF2Type.class htsjdk.variant.bcf2.BCF2Utils.class htsjdk.variant.bcf2.BCFVersion.class htsjdk.variant.utils.GeneralUtils.class htsjdk.variant.variantcontext.Allele.class htsjdk.variant.variantcontext.CommonInfo.class htsjdk.variant.variantcontext.FastGenotype.class htsjdk.variant.variantcontext.Genotype.class htsjdk.variant.variantcontext.GenotypeBuilder.class htsjdk.variant.variantcontext.GenotypeLikelihoods.class htsjdk.variant.variantcontext.GenotypeType.class htsjdk.variant.variantcontext.GenotypesContext.class htsjdk.variant.variantcontext.JEXLMap.class htsjdk.variant.variantcontext.LazyGenotypesContext.class htsjdk.variant.variantcontext.VariantContext.class htsjdk.variant.variantcontext.VariantContextBuilder.class htsjdk.variant.variantcontext.VariantContextComparator.class htsjdk.variant.variantcontext.VariantContextUtils.class htsjdk.variant.variantcontext.VariantJEXLContext.class htsjdk.variant.variantcontext.writer.AsyncVariantContextWriter.class htsjdk.variant.variantcontext.writer.BCF2Encoder.class htsjdk.variant.variantcontext.writer.BCF2FieldEncoder.class htsjdk.variant.variantcontext.writer.BCF2FieldWriter.class htsjdk.variant.variantcontext.writer.BCF2FieldWriterManager.class htsjdk.variant.variantcontext.writer.BCF2Writer.class htsjdk.variant.variantcontext.writer.IndexingVariantContextWriter.class htsjdk.variant.variantcontext.writer.IntGenotypeFieldAccessors.class htsjdk.variant.variantcontext.writer.Options.class htsjdk.variant.variantcontext.writer.PositionalOutputStream.class htsjdk.variant.variantcontext.writer.SortingVariantContextWriter.class htsjdk.variant.variantcontext.writer.SortingVariantContextWriterBase.class htsjdk.variant.variantcontext.writer.VCFWriter.class htsjdk.variant.variantcontext.writer.VariantContextWriter.class htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder.class htsjdk.variant.variantcontext.writer.VariantContextWriterFactory.class htsjdk.variant.vcf.AbstractVCFCodec.class htsjdk.variant.vcf.VCF3Codec.class htsjdk.variant.vcf.VCF3Parser.class htsjdk.variant.vcf.VCF4Parser.class htsjdk.variant.vcf.VCFCodec.class htsjdk.variant.vcf.VCFCompoundHeaderLine.class htsjdk.variant.vcf.VCFConstants.class htsjdk.variant.vcf.VCFContigHeaderLine.class htsjdk.variant.vcf.VCFEncoder.class htsjdk.variant.vcf.VCFFileReader.class htsjdk.variant.vcf.VCFFilterHeaderLine.class htsjdk.variant.vcf.VCFFormatHeaderLine.class htsjdk.variant.vcf.VCFHeader.class htsjdk.variant.vcf.VCFHeaderLine.class htsjdk.variant.vcf.VCFHeaderLineCount.class htsjdk.variant.vcf.VCFHeaderLineTranslator.class htsjdk.variant.vcf.VCFHeaderLineType.class htsjdk.variant.vcf.VCFHeaderVersion.class htsjdk.variant.vcf.VCFIDHeaderLine.class htsjdk.variant.vcf.VCFInfoHeaderLine.class htsjdk.variant.vcf.VCFLineParser.class htsjdk.variant.vcf.VCFRecordCodec.class htsjdk.variant.vcf.VCFSimpleHeaderLine.class htsjdk.variant.vcf.VCFStandardHeaderLines.class htsjdk.variant.vcf.VCFUtils.class
htsjdk-1.118.pom file content.
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<!--
**** NOTE: HTSJDK (formerly part of Picard/Samtools) is a
**** third-party dependency of Hadoop-BAM. This artifact was
**** released since currently there is no first-party artifact
**** for HTSJDK available.
****
**** For further information on HTSJDK see:
**** https://github.com/samtools/htsjdk/
****
**** This POM file is based on:
**** https://github.com/azymer/htsjdk/blob/271692b2406b1ae980b43fa95981672798b4f295/pom.xml
-->
<!-- add this to your shell:
export MAVEN_OPTS="-Xms256m -Xmx1g -XX:MaxPermSize=256m" -->
<!-- when running tests from an intellij project that was setup
via importing a project from maven, be sure to set the
working directory to the top level htsjdk directory -->
<parent>
<groupId>org.sonatype.oss</groupId>
<artifactId>oss-parent</artifactId>
<version>7</version>
<relativePath />
</parent>
<groupId>org.seqdoop</groupId>
<artifactId>htsjdk</artifactId>
<version>1.118</version>
<packaging>jar</packaging>
<name>HTS JDK</name>
<description>A Java API for high-throughput sequencing data (HTS) formats.</description>
<url>https://github.com/samtools/htsjdk/</url>
<dependencies>
<dependency>
<groupId>org.apache.ant</groupId>
<artifactId>ant</artifactId>
<version>1.8.2</version>
</dependency>
<dependency>
<groupId>org.apache.bcel</groupId>
<artifactId>bcel</artifactId>
<version>5.2</version>
</dependency>
<dependency>
<groupId>org.seqdoop</groupId>
<artifactId>cofoja</artifactId>
<version>1.1-r150</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-jexl</artifactId>
<version>2.1.1</version>
</dependency>
<dependency>
<groupId>commons-logging</groupId>
<artifactId>commons-logging</artifactId>
<version>1.1.1</version>
</dependency>
<dependency>
<groupId>org.xerial.snappy</groupId>
<artifactId>snappy-java</artifactId>
<version>1.0.3-rc3</version>
</dependency>
<dependency>
<groupId>org.testng</groupId>
<artifactId>testng</artifactId>
<!-- was 5.5; this was failing to compile with maven-->
<version>6.8.8</version>
<scope>compile</scope>
</dependency>
</dependencies>
<build>
<sourceDirectory>src/java</sourceDirectory>
<testSourceDirectory>src/tests/java</testSourceDirectory>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-gpg-plugin</artifactId>
<version>1.5</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-deploy-plugin</artifactId>
<version>2.7</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>2.9.1</version>
<executions>
<execution>
<id>attach-javadocs</id>
<goals>
<goal>jar</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-source-plugin</artifactId>
<version>2.2.1</version>
<executions>
<execution>
<id>attach-sources</id>
<goals>
<goal>jar-no-fork</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>2.5</version>
<configuration>
<archive>
<addMavenDescriptor>false</addMavenDescriptor>
<manifestEntries>
<Implementation-Vendor>${project.groupId}</Implementation-Vendor>
<Implementation-Version>${project.version}</Implementation-Version>
</manifestEntries>
</archive>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.1</version>
<configuration>
<source>1.6</source>
<target>1.6</target>
<!-- not sure if this plays nice with cofoja but the build fails without it,
complaining about cofoja "error in contract"-->
<compilerArgument>-proc:none</compilerArgument>
<debug>true</debug>
<optimize>false</optimize>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.17</version>
<configuration>
<!-- without bumping up memory, maven tests fail -->
<argLine>-Xms256m -Xmx1g -XX:MaxPermSize=256m</argLine>
</configuration>
</plugin>
</plugins>
</build>
</project>
<dependency> <groupId>org.seqdoop</groupId> <artifactId>htsjdk</artifactId> <version>1.118</version> </dependency>
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Download htsjdk-1.118.jar file