You can download adam-core-0.16.0.jar in this page.
Open Source
adam-core-0.16.0.jar file has the following types.
META-INF/MANIFEST.MF META-INF/maven/org.bdgenomics.adam/adam-core/pom.properties META-INF/maven/org.bdgenomics.adam/adam-core/pom.xml git.properties log4j.properties org.bdgenomics.adam.algorithms.consensus.ConsensusGenerator.class org.bdgenomics.adam.algorithms.consensus.ConsensusGeneratorFromKnowns.class org.bdgenomics.adam.algorithms.consensus.ConsensusGeneratorFromReads.class org.bdgenomics.adam.algorithms.consensus.ConsensusGeneratorFromSmithWaterman.class org.bdgenomics.adam.algorithms.prefixtrie.DNAPrefixTrie.class org.bdgenomics.adam.algorithms.prefixtrie.FixedDepthDNAPrefixTrieValues.class org.bdgenomics.adam.algorithms.prefixtrie.NestedFixedDepthDNAPrefixTrie.class org.bdgenomics.adam.algorithms.smithwaterman.SmithWaterman.class org.bdgenomics.adam.algorithms.smithwaterman.SmithWatermanConstantGapScoring.class org.bdgenomics.adam.algorithms.smithwaterman.SmithWatermanGapScoringFromFn.class org.bdgenomics.adam.converters.AlignmentRecordConverter.class org.bdgenomics.adam.converters.AttrKey.class org.bdgenomics.adam.converters.FastaConverter.class org.bdgenomics.adam.converters.FastqRecordConverter.class org.bdgenomics.adam.converters.FragmentCollector.class org.bdgenomics.adam.converters.FragmentConverter.class org.bdgenomics.adam.converters.GenotypesToVariantsConverter.class org.bdgenomics.adam.converters.SAMRecordConverter.class org.bdgenomics.adam.converters.VariantAnnotationConverter.class org.bdgenomics.adam.converters.VariantContextConverter.class org.bdgenomics.adam.core.util.BuildInformation.class org.bdgenomics.adam.instrumentation.Timers.class org.bdgenomics.adam.io.InterleavedFastqInputFormat.class org.bdgenomics.adam.io.SingleFastqInputFormat.class org.bdgenomics.adam.metrics.BaseQualityScores.class org.bdgenomics.adam.metrics.BooleanComparisons.class org.bdgenomics.adam.metrics.BucketComparisons.class org.bdgenomics.adam.metrics.CombinedComparisons.class org.bdgenomics.adam.metrics.DefaultComparisons.class org.bdgenomics.adam.metrics.DupeMismatch.class org.bdgenomics.adam.metrics.LongComparisons.class org.bdgenomics.adam.metrics.MapQualityScores.class org.bdgenomics.adam.metrics.MappedPosition.class org.bdgenomics.adam.metrics.OverMatched.class org.bdgenomics.adam.metrics.PointComparisons.class org.bdgenomics.adam.metrics.filters.CombinedFilter.class org.bdgenomics.adam.metrics.filters.ComparisonsFilter.class org.bdgenomics.adam.metrics.filters.GeneratorFilter.class org.bdgenomics.adam.models.Attribute.class org.bdgenomics.adam.models.BEDFeature.class org.bdgenomics.adam.models.BaseFeature.class org.bdgenomics.adam.models.BlockExtractable.class org.bdgenomics.adam.models.CDS.class org.bdgenomics.adam.models.Consensus.class org.bdgenomics.adam.models.Exon.class org.bdgenomics.adam.models.Extractable.class org.bdgenomics.adam.models.GTFFeature.class org.bdgenomics.adam.models.Gene.class org.bdgenomics.adam.models.IndelTable.class org.bdgenomics.adam.models.Interval.class org.bdgenomics.adam.models.NarrowPeakFeature.class org.bdgenomics.adam.models.OrderedTrackedLayout.class org.bdgenomics.adam.models.ProgramRecord.class org.bdgenomics.adam.models.ReadBucket.class org.bdgenomics.adam.models.ReadBucketSerializer.class org.bdgenomics.adam.models.RecordGroup.class org.bdgenomics.adam.models.RecordGroupDictionary.class org.bdgenomics.adam.models.ReferenceMapping.class org.bdgenomics.adam.models.ReferencePosition.class org.bdgenomics.adam.models.ReferencePositionPair.class org.bdgenomics.adam.models.ReferencePositionPairSerializer.class org.bdgenomics.adam.models.ReferencePositionSerializer.class org.bdgenomics.adam.models.ReferencePositionWithOrientation.class org.bdgenomics.adam.models.ReferencePositionWithOrientationSerializer.class org.bdgenomics.adam.models.ReferenceRegion.class org.bdgenomics.adam.models.ReferenceRegionSerializer.class org.bdgenomics.adam.models.ReferenceRegionWithOrientation.class org.bdgenomics.adam.models.ReferenceUtils.class org.bdgenomics.adam.models.Rod.class org.bdgenomics.adam.models.SAMFileHeaderWritable.class org.bdgenomics.adam.models.SequenceDictionary.class org.bdgenomics.adam.models.SequenceRecord.class org.bdgenomics.adam.models.SingleReadBucket.class org.bdgenomics.adam.models.SingleReadBucketSerializer.class org.bdgenomics.adam.models.SnpTable.class org.bdgenomics.adam.models.TagType.class org.bdgenomics.adam.models.TrackedLayout.class org.bdgenomics.adam.models.Transcript.class org.bdgenomics.adam.models.UTR.class org.bdgenomics.adam.models.VCFHeaderWritable.class org.bdgenomics.adam.models.VariantContext.class org.bdgenomics.adam.plugins.ADAMPlugin.class org.bdgenomics.adam.plugins.AccessControl.class org.bdgenomics.adam.plugins.EmptyAccessControl.class org.bdgenomics.adam.predicates.ADAMPredicate.class org.bdgenomics.adam.predicates.AlignmentRecordConditions.class org.bdgenomics.adam.predicates.ColumnReaderInput.class org.bdgenomics.adam.predicates.FieldCondition.class org.bdgenomics.adam.predicates.GenotypeConditions.class org.bdgenomics.adam.predicates.GenotypeRecordPASSPredicate.class org.bdgenomics.adam.predicates.HighQualityReadPredicate.class org.bdgenomics.adam.predicates.LocusPredicate.class org.bdgenomics.adam.predicates.PredicateUtils.class org.bdgenomics.adam.predicates.RecordCondition.class org.bdgenomics.adam.predicates.UniqueMappedReadPredicate.class org.bdgenomics.adam.projections.AlignmentRecordField.class org.bdgenomics.adam.projections.DatabaseVariantAnnotationField.class org.bdgenomics.adam.projections.FeatureField.class org.bdgenomics.adam.projections.FieldEnumeration.class org.bdgenomics.adam.projections.FieldValue.class org.bdgenomics.adam.projections.Filter.class org.bdgenomics.adam.projections.GenotypeField.class org.bdgenomics.adam.projections.NucleotideContigFragmentField.class org.bdgenomics.adam.projections.Projection.class org.bdgenomics.adam.projections.VariantCallingAnnotationsField.class org.bdgenomics.adam.projections.VariantField.class org.bdgenomics.adam.rdd.ADAMContext.class org.bdgenomics.adam.rdd.ADAMParquetArgs.class org.bdgenomics.adam.rdd.ADAMRDDFunctions.class org.bdgenomics.adam.rdd.ADAMSaveAnyArgs.class org.bdgenomics.adam.rdd.ADAMSaveArgs.class org.bdgenomics.adam.rdd.ADAMSequenceDictionaryRDDAggregator.class org.bdgenomics.adam.rdd.ADAMSpecificRecordSequenceDictionaryRDDAggregator.class org.bdgenomics.adam.rdd.BroadcastRegionJoin.class org.bdgenomics.adam.rdd.Coverage.class org.bdgenomics.adam.rdd.GenomeBins.class org.bdgenomics.adam.rdd.GenomicPositionPartitioner.class org.bdgenomics.adam.rdd.GenomicRegionPartitioner.class org.bdgenomics.adam.rdd.InstrumentedADAMAvroParquetOutputFormat.class org.bdgenomics.adam.rdd.ManualRegionPartitioner.class org.bdgenomics.adam.rdd.MultiContigNonoverlappingRegions.class org.bdgenomics.adam.rdd.NonoverlappingRegions.class org.bdgenomics.adam.rdd.PairingRDD.class org.bdgenomics.adam.rdd.ShuffleRegionJoin.class org.bdgenomics.adam.rdd.SortedIntervalPartitionJoin.class org.bdgenomics.adam.rdd.contig.NucleotideContigFragmentRDDFunctions.class org.bdgenomics.adam.rdd.features.BEDParser.class org.bdgenomics.adam.rdd.features.FeatureFile.class org.bdgenomics.adam.rdd.features.FeatureParser.class org.bdgenomics.adam.rdd.features.GTFParser.class org.bdgenomics.adam.rdd.features.GeneFeatureRDDFunctions.class org.bdgenomics.adam.rdd.features.NarrowPeakParser.class org.bdgenomics.adam.rdd.normalization.LengthNormalization.class org.bdgenomics.adam.rdd.normalization.ZScoreNormalization.class org.bdgenomics.adam.rdd.pileup.PileupRDDFunctions.class org.bdgenomics.adam.rdd.pileup.RodRDDFunctions.class org.bdgenomics.adam.rdd.read.ADAMBAMOutputFormat.class org.bdgenomics.adam.rdd.read.ADAMSAMOutputFormat.class org.bdgenomics.adam.rdd.read.AlignmentRecordRDDFunctions.class org.bdgenomics.adam.rdd.read.DuplicateMetrics.class org.bdgenomics.adam.rdd.read.FlagStat.class org.bdgenomics.adam.rdd.read.FlagStatMetrics.class org.bdgenomics.adam.rdd.read.InstrumentedADAMBAMOutputFormat.class org.bdgenomics.adam.rdd.read.InstrumentedADAMSAMOutputFormat.class org.bdgenomics.adam.rdd.read.MarkDuplicates.class org.bdgenomics.adam.rdd.read.Reads2PileupProcessor.class org.bdgenomics.adam.rdd.read.comparisons.ComparisonTraversalEngine.class org.bdgenomics.adam.rdd.read.correction.ErrorCorrection.class org.bdgenomics.adam.rdd.read.correction.TrimReads.class org.bdgenomics.adam.rdd.read.realignment.IndelRealignmentTarget.class org.bdgenomics.adam.rdd.read.realignment.RealignIndels.class org.bdgenomics.adam.rdd.read.realignment.RealignmentTargetFinder.class org.bdgenomics.adam.rdd.read.realignment.TargetOrdering.class org.bdgenomics.adam.rdd.read.realignment.TargetSet.class org.bdgenomics.adam.rdd.read.realignment.TargetSetSerializer.class org.bdgenomics.adam.rdd.read.realignment.ZippedTargetOrdering.class org.bdgenomics.adam.rdd.read.realignment.ZippedTargetSet.class org.bdgenomics.adam.rdd.read.realignment.ZippedTargetSetSerializer.class org.bdgenomics.adam.rdd.read.recalibration.AbstractCovariate.class org.bdgenomics.adam.rdd.read.recalibration.Aggregate.class org.bdgenomics.adam.rdd.read.recalibration.BaseQualityRecalibration.class org.bdgenomics.adam.rdd.read.recalibration.Covariate.class org.bdgenomics.adam.rdd.read.recalibration.CovariateKey.class org.bdgenomics.adam.rdd.read.recalibration.CovariateSpace.class org.bdgenomics.adam.rdd.read.recalibration.CycleCovariate.class org.bdgenomics.adam.rdd.read.recalibration.DinucCovariate.class org.bdgenomics.adam.rdd.read.recalibration.Observation.class org.bdgenomics.adam.rdd.read.recalibration.ObservationAccumulator.class org.bdgenomics.adam.rdd.read.recalibration.ObservationTable.class org.bdgenomics.adam.rdd.read.recalibration.RecalibrationTable.class org.bdgenomics.adam.rdd.read.recalibration.Recalibrator.class org.bdgenomics.adam.rdd.variation.ADAMVCFOutputFormat.class org.bdgenomics.adam.rdd.variation.ConcordanceTable.class org.bdgenomics.adam.rdd.variation.GenotypeRDDFunctions.class org.bdgenomics.adam.rdd.variation.GenotypesSummary.class org.bdgenomics.adam.rdd.variation.GenotypesSummaryCounts.class org.bdgenomics.adam.rdd.variation.GenotypesSummaryFormatting.class org.bdgenomics.adam.rdd.variation.VariantContextRDDFunctions.class org.bdgenomics.adam.rich.DecadentRead.class org.bdgenomics.adam.rich.IlluminaOptics.class org.bdgenomics.adam.rich.ReferenceMappingContext.class org.bdgenomics.adam.rich.ReferenceSequenceContext.class org.bdgenomics.adam.rich.RichAlignmentRecord.class org.bdgenomics.adam.rich.RichCigar.class org.bdgenomics.adam.rich.RichGenotype.class org.bdgenomics.adam.rich.RichVariant.class org.bdgenomics.adam.serialization.ADAMKryoRegistrator.class org.bdgenomics.adam.serialization.AvroSerializer.class org.bdgenomics.adam.serialization.InputStreamWithDecoder.class org.bdgenomics.adam.util.AttributeUtils.class org.bdgenomics.adam.util.Base.class org.bdgenomics.adam.util.DeletionEvent.class org.bdgenomics.adam.util.HadoopUtil.class org.bdgenomics.adam.util.ImplicitJavaConversions.class org.bdgenomics.adam.util.InsertionEvent.class org.bdgenomics.adam.util.IntervalListReader.class org.bdgenomics.adam.util.MapTools.class org.bdgenomics.adam.util.MatchEvent.class org.bdgenomics.adam.util.MdTag.class org.bdgenomics.adam.util.MdTagEvent.class org.bdgenomics.adam.util.MismatchEvent.class org.bdgenomics.adam.util.NormalizationUtils.class org.bdgenomics.adam.util.ParquetFileTraversable.class org.bdgenomics.adam.util.ParquetLogger.class org.bdgenomics.adam.util.PhredUtils.class org.bdgenomics.adam.util.Pileup.class org.bdgenomics.adam.util.PileupEvent.class org.bdgenomics.adam.util.PileupTraversable.class org.bdgenomics.adam.util.QualityScore.class org.bdgenomics.adam.util.RegExp.class org.bdgenomics.adam.util.SequenceUtils.class org.bdgenomics.adam.util.TwoBitFile.class org.bdgenomics.adam.util.TwoBitRecord.class org.bdgenomics.adam.util.Util.class org.bdgenomics.adam.util.VcfHeaderBuilder.class org.bdgenomics.adam.util.VcfHeaderUtils.class org.bdgenomics.adam.util.VcfStringUtils.class
adam-core-0.16.0.pom file content.
<?xml version="1.0" encoding="UTF-8"?>
<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>
<parent>
<groupId>org.bdgenomics.adam</groupId>
<artifactId>adam-parent</artifactId>
<version>0.16.0</version>
<relativePath>../pom.xml</relativePath>
</parent>
<artifactId>adam-core</artifactId>
<packaging>jar</packaging>
<name>ADAM: Core</name>
<build>
<plugins>
<!-- disable surefire -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<configuration>
<skipTests>true</skipTests>
</configuration>
</plugin>
<!-- enable scalatest -->
<plugin>
<groupId>org.scalatest</groupId>
<artifactId>scalatest-maven-plugin</artifactId>
<configuration>
<reportsDirectory>${project.build.directory}/surefire-reports</reportsDirectory>
<junitxml>.</junitxml>
<filereports>ADAMTestSuite.txt</filereports>
<!--
As explained here: http://stackoverflow.com/questions/1660441/java-flag-to-enable-extended-serialization-debugging-info
The second option allows us better debugging for serialization-based errors.
-->
<argLine>-Xmx1024m -Dsun.io.serialization.extendedDebugInfo=true</argLine>
</configuration>
<executions>
<execution>
<id>test</id>
<goals>
<goal>test</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<executions>
<execution>
<goals>
<goal>test-jar</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>pl.project13.maven</groupId>
<artifactId>git-commit-id-plugin</artifactId>
<executions>
<execution>
<goals>
<goal>revision</goal>
</goals>
</execution>
</executions>
<configuration>
<verbose>true</verbose>
<generateGitPropertiesFile>true</generateGitPropertiesFile>
<!-- <generateGitPropertiesFilename>adam-cli/src/main/resources/git.properties</generateGitPropertiesFilename> -->
<generateGitPropertiesFilename>src/main/resources/git.properties</generateGitPropertiesFilename>
<failOnNoGitDirectory>false</failOnNoGitDirectory>
<excludeProperties>
<!-- Avoid email addresses and names: -->
<excludeProperty>git.commit.user.*</excludeProperty>
<excludeProperty>git.build.user.*</excludeProperty>
</excludeProperties>
</configuration>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>build-helper-maven-plugin</artifactId>
<executions>
<execution>
<id>add-source</id>
<phase>generate-sources</phase>
<goals>
<goal>add-source</goal>
</goals>
<configuration>
<sources>
<source>src/main/scala</source>
</sources>
</configuration>
</execution>
<execution>
<id>add-test-source</id>
<phase>generate-test-sources</phase>
<goals>
<goal>add-test-source</goal>
</goals>
<configuration>
<sources>
<source>src/test/scala</source>
</sources>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
<dependencies>
<dependency>
<groupId>org.bdgenomics.bdg-utils</groupId>
<artifactId>bdg-utils-misc</artifactId>
<type>test-jar</type>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.bdgenomics.bdg-utils</groupId>
<artifactId>bdg-utils-metrics</artifactId>
</dependency>
<dependency>
<groupId>org.bdgenomics.bdg-utils</groupId>
<artifactId>bdg-utils-parquet</artifactId>
</dependency>
<dependency>
<groupId>com.esotericsoftware.kryo</groupId>
<artifactId>kryo</artifactId>
</dependency>
<dependency>
<groupId>org.scoverage</groupId>
<artifactId>scalac-scoverage-plugin_${scala.artifact.suffix}</artifactId>
</dependency>
<dependency>
<groupId>org.bdgenomics.bdg-formats</groupId>
<artifactId>bdg-formats</artifactId>
</dependency>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
</dependency>
<dependency>
<groupId>org.scala-lang</groupId>
<artifactId>scala-library</artifactId>
</dependency>
<dependency>
<groupId>org.apache.hadoop</groupId>
<artifactId>hadoop-client</artifactId>
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-core_${scala.artifact.suffix}</artifactId>
</dependency>
<dependency>
<groupId>it.unimi.dsi</groupId>
<artifactId>fastutil</artifactId>
</dependency>
<dependency>
<groupId>org.apache.avro</groupId>
<artifactId>avro</artifactId>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-log4j12</artifactId>
</dependency>
<dependency>
<groupId>com.twitter</groupId>
<artifactId>parquet-avro</artifactId>
</dependency>
<dependency>
<groupId>org.seqdoop</groupId>
<artifactId>hadoop-bam</artifactId>
</dependency>
<dependency>
<groupId>org.seqdoop</groupId>
<artifactId>cofoja</artifactId>
</dependency>
<dependency>
<groupId>org.seqdoop</groupId>
<artifactId>htsjdk</artifactId>
</dependency>
<dependency>
<groupId>org.scalatest</groupId>
<artifactId>scalatest_${scala.artifact.suffix}</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>com.amazonaws</groupId>
<artifactId>aws-java-sdk</artifactId>
</dependency>
<dependency>
<groupId>org.apache.httpcomponents</groupId>
<artifactId>httpclient</artifactId>
</dependency>
<dependency>
<groupId>com.netflix.servo</groupId>
<artifactId>servo-core</artifactId>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-core</artifactId>
</dependency>
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
</dependency>
</dependencies>
<profiles>
<profile>
<id>coverage</id>
<build>
<plugins>
<plugin>
<groupId>org.scoverage</groupId>
<artifactId>maven-scoverage-plugin</artifactId>
<version>${scoverage.version}</version>
<executions>
<execution>
<id>test</id>
<goals>
<goal>report</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
<profile>
<id>default</id>
<activation>
<activeByDefault>true</activeByDefault>
</activation>
<build>
<plugins>
<plugin>
<groupId>org.scalatest</groupId>
<artifactId>scalatest-maven-plugin</artifactId>
<configuration>
<tagsToExclude>org.bdgenomics.adam.util.NetworkConnected,org.bdgenomics.adam.util.S3Test</tagsToExclude>
</configuration>
</plugin>
</plugins>
</build>
</profile>
<profile>
<id>network-connected</id>
<activation>
<property>
<name>networkconnected</name>
</property>
</activation>
<build>
<plugins>
<plugin>
<groupId>org.scalatest</groupId>
<artifactId>scalatest-maven-plugin</artifactId>
<configuration>
<tagsToExclude>org.bdgenomics.adam.util.S3Test</tagsToExclude>
<tagsToInclude>org.bdgenomics.adam.util.NetworkConnected</tagsToInclude>
</configuration>
</plugin>
</plugins>
</build>
</profile>
</profiles>
</project>
<dependency> <groupId>org.bdgenomics.adam</groupId> <artifactId>adam-core</artifactId> <version>0.16.0</version> </dependency>
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Download adam-core-0.16.0.jar file