You can download hadoop-bam-7.0.0.jar in this page.
MIT-License
hadoop-bam-7.0.0.jar file has the following types.
META-INF/MANIFEST.MF META-INF/maven/org.seqdoop/hadoop-bam/pom.properties META-INF/maven/org.seqdoop/hadoop-bam/pom.xml META-INF/services/org.seqdoop.hadoop_bam.cli.CLIPlugin hadoop.org.apache.hadoop.mapreduce.lib.output.MultipleOutputs.class hadoop.org.apache.hadoop.mapreduce.lib.partition.InputSampler.class hadoop.org.apache.hadoop.mapreduce.lib.partition.TotalOrderPartitioner.class hbparquet.hadoop.util.ContextUtil.class org.seqdoop.hadoop_bam.AnySAMInputFormat.class org.seqdoop.hadoop_bam.AnySAMOutputFormat.class org.seqdoop.hadoop_bam.BAMInputFormat.class org.seqdoop.hadoop_bam.BAMOutputFormat.class org.seqdoop.hadoop_bam.BAMRecordReader.class org.seqdoop.hadoop_bam.BAMRecordWriter.class org.seqdoop.hadoop_bam.BAMSplitGuesser.class org.seqdoop.hadoop_bam.BCFRecordReader.class org.seqdoop.hadoop_bam.BCFRecordWriter.class org.seqdoop.hadoop_bam.BCFSplitGuesser.class org.seqdoop.hadoop_bam.BCFStoppableOutputStream.class org.seqdoop.hadoop_bam.BGZFLimitingStream.class org.seqdoop.hadoop_bam.FastaInputFormat.class org.seqdoop.hadoop_bam.FastqInputFormat.class org.seqdoop.hadoop_bam.FastqOutputFormat.class org.seqdoop.hadoop_bam.FileVirtualSplit.class org.seqdoop.hadoop_bam.FormatConstants.class org.seqdoop.hadoop_bam.FormatException.class org.seqdoop.hadoop_bam.HeaderSettableVCFCodec.class org.seqdoop.hadoop_bam.KeyIgnoringAnySAMOutputFormat.class org.seqdoop.hadoop_bam.KeyIgnoringBAMOutputFormat.class org.seqdoop.hadoop_bam.KeyIgnoringBAMRecordWriter.class org.seqdoop.hadoop_bam.KeyIgnoringBCFRecordWriter.class org.seqdoop.hadoop_bam.KeyIgnoringSAMRecordWriter.class org.seqdoop.hadoop_bam.KeyIgnoringVCFOutputFormat.class org.seqdoop.hadoop_bam.KeyIgnoringVCFRecordWriter.class org.seqdoop.hadoop_bam.LazyBAMRecord.class org.seqdoop.hadoop_bam.LazyBAMRecordFactory.class org.seqdoop.hadoop_bam.LazyBCFGenotypesContext.class org.seqdoop.hadoop_bam.LazyParsingGenotypesContext.class org.seqdoop.hadoop_bam.LazyVCFGenotypesContext.class org.seqdoop.hadoop_bam.LineReader.class org.seqdoop.hadoop_bam.QseqInputFormat.class org.seqdoop.hadoop_bam.QseqOutputFormat.class org.seqdoop.hadoop_bam.ReferenceFragment.class org.seqdoop.hadoop_bam.SAMFormat.class org.seqdoop.hadoop_bam.SAMInputFormat.class org.seqdoop.hadoop_bam.SAMRecordReader.class org.seqdoop.hadoop_bam.SAMRecordWritable.class org.seqdoop.hadoop_bam.SAMRecordWriter.class org.seqdoop.hadoop_bam.SequencedFragment.class org.seqdoop.hadoop_bam.SplittingBAMIndex.class org.seqdoop.hadoop_bam.SplittingBAMIndexer.class org.seqdoop.hadoop_bam.StoppableOutputStream.class org.seqdoop.hadoop_bam.VCFFormat.class org.seqdoop.hadoop_bam.VCFInputFormat.class org.seqdoop.hadoop_bam.VCFOutputFormat.class org.seqdoop.hadoop_bam.VCFRecordReader.class org.seqdoop.hadoop_bam.VCFRecordWriter.class org.seqdoop.hadoop_bam.VariantContextCodec.class org.seqdoop.hadoop_bam.VariantContextWithHeader.class org.seqdoop.hadoop_bam.VariantContextWritable.class org.seqdoop.hadoop_bam.WorkaroundingStream.class org.seqdoop.hadoop_bam.cli.CLIMRBAMPlugin.class org.seqdoop.hadoop_bam.cli.CLIMRPlugin.class org.seqdoop.hadoop_bam.cli.CLIMergingAnySAMOutputFormat.class org.seqdoop.hadoop_bam.cli.CLIPlugin.class org.seqdoop.hadoop_bam.cli.Frontend.class org.seqdoop.hadoop_bam.cli.Utils.class org.seqdoop.hadoop_bam.cli.plugins.Cat.class org.seqdoop.hadoop_bam.cli.plugins.FixMate.class org.seqdoop.hadoop_bam.cli.plugins.FixMateMapper.class org.seqdoop.hadoop_bam.cli.plugins.FixMateReducer.class org.seqdoop.hadoop_bam.cli.plugins.Index.class org.seqdoop.hadoop_bam.cli.plugins.Sort.class org.seqdoop.hadoop_bam.cli.plugins.SortInputFormat.class org.seqdoop.hadoop_bam.cli.plugins.SortOutputFormat.class org.seqdoop.hadoop_bam.cli.plugins.SortRecordReader.class org.seqdoop.hadoop_bam.cli.plugins.SortReducer.class org.seqdoop.hadoop_bam.cli.plugins.VCFSort.class org.seqdoop.hadoop_bam.cli.plugins.VCFSortReducer.class org.seqdoop.hadoop_bam.cli.plugins.View.class org.seqdoop.hadoop_bam.cli.plugins.chipster.BlockCompressedLineRecordReader.class org.seqdoop.hadoop_bam.cli.plugins.chipster.Range.class org.seqdoop.hadoop_bam.cli.plugins.chipster.RangeCount.class org.seqdoop.hadoop_bam.cli.plugins.chipster.SortInputFormat.class org.seqdoop.hadoop_bam.cli.plugins.chipster.SortOutputFormat.class org.seqdoop.hadoop_bam.cli.plugins.chipster.SortRecordReader.class org.seqdoop.hadoop_bam.cli.plugins.chipster.SortReducer.class org.seqdoop.hadoop_bam.cli.plugins.chipster.Summarize.class org.seqdoop.hadoop_bam.cli.plugins.chipster.SummarizeInputFormat.class org.seqdoop.hadoop_bam.cli.plugins.chipster.SummarizeOutputFormat.class org.seqdoop.hadoop_bam.cli.plugins.chipster.SummarizeRecordReader.class org.seqdoop.hadoop_bam.cli.plugins.chipster.SummarizeReducer.class org.seqdoop.hadoop_bam.cli.plugins.chipster.SummaryGroup.class org.seqdoop.hadoop_bam.cli.plugins.chipster.SummarySort.class org.seqdoop.hadoop_bam.custom.jargs.gnu.CmdLineParser.class org.seqdoop.hadoop_bam.util.BGZFBlockIndex.class org.seqdoop.hadoop_bam.util.BGZFBlockIndexer.class org.seqdoop.hadoop_bam.util.BGZFSplitFileInputFormat.class org.seqdoop.hadoop_bam.util.BGZFSplitGuesser.class org.seqdoop.hadoop_bam.util.ConfHelper.class org.seqdoop.hadoop_bam.util.DataInputWrapper.class org.seqdoop.hadoop_bam.util.DataOutputWrapper.class org.seqdoop.hadoop_bam.util.GetSortedBAMHeader.class org.seqdoop.hadoop_bam.util.MurmurHash3.class org.seqdoop.hadoop_bam.util.Pair.class org.seqdoop.hadoop_bam.util.SAMHeaderReader.class org.seqdoop.hadoop_bam.util.SAMOutputPreparer.class org.seqdoop.hadoop_bam.util.SeekableArrayStream.class org.seqdoop.hadoop_bam.util.Timer.class org.seqdoop.hadoop_bam.util.VCFHeaderReader.class org.seqdoop.hadoop_bam.util.WrapSeekable.class
hadoop-bam-7.0.0.pom file content.
<?xml version="1.0" encoding="UTF-8"?>
<!--
~ Copyright (c) 2014 Aalto University
~
~ 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.
-->
<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">
<parent>
<groupId>org.sonatype.oss</groupId>
<artifactId>oss-parent</artifactId>
<version>7</version>
<relativePath />
</parent>
<modelVersion>4.0.0</modelVersion>
<groupId>org.seqdoop</groupId>
<artifactId>hadoop-bam</artifactId>
<version>7.0.0</version>
<packaging>jar</packaging>
<name>Hadoop-BAM</name>
<description>A Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework.</description>
<url>http://sourceforge.net/projects/hadoop-bam/</url>
<properties>
<java.version>1.6</java.version>
<htsjdk.version>1.118</htsjdk.version>
<!-- CHANGE THIS FOR A DIFFERENT VERSION OF HADOOP -->
<hadoop.version>1.2.1</hadoop.version>
<!--
Below you'll find some example hadoop.version tags. The value you set
must have a corresponding version in one of the repositories that are
checked during installation.
<hadoop.version>2.0.0-cdh4.6.0</hadoop.version>
<hadoop.version>2.0.0-alpha</hadoop.version>
<hadoop.version>1.2.1</hadoop.version>
<hadoop.version>1.1.2</hadoop.version>
-->
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
</properties>
<licenses>
<license>
<name>MIT-License</name>
<url>https://raw.githubusercontent.com/HadoopGenomics/Hadoop-BAM/master/LICENSE.txt</url>
<distribution>repo</distribution>
</license>
</licenses>
<scm>
<connection>scm:git:git@github.com:HadoopGenomics/Hadoop-BAM.git</connection>
<developerConnection>scm:git:git@github.com:HadoopGenomics/Hadoop-BAM.git</developerConnection>
<url>scm:git:git@github.com:HadoopGenomics/Hadoop-BAM.git</url>
<tag>7.0.0</tag>
</scm>
<developers>
<developer>
<id>andre</id>
<name>Andre Schumacher</name>
<email>andre.schumacher@iki.fi</email>
<url>https://github.com/AndreSchumacher</url>
</developer>
<developer>
<id>ridvan</id>
<name>Ridvan Dongelci</name>
<email>ridvandongelci@gmail.com</email>
<organization>Aalto University</organization>
</developer>
</developers>
<issueManagement>
<system>github</system>
<url>https://github.com/HadoopGenomics/Hadoop-BAM/issues</url>
</issueManagement>
<build>
<outputDirectory>target/classes</outputDirectory>
<testOutputDirectory>target/test-classes</testOutputDirectory>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-release-plugin</artifactId>
<version>2.5</version>
<configuration>
<mavenExecutorId>forked-path</mavenExecutorId>
<useReleaseProfile>false</useReleaseProfile>
<arguments>-Psonatype-oss-release</arguments>
</configuration>
</plugin>
<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-clean-plugin</artifactId>
<version>2.5</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
<version>2.4</version>
<executions>
<execution>
<goals>
<goal>test-jar</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.1</version>
<configuration>
<source>${java.version}</source>
<target>${java.version}</target>
<!-- disable cofoja for Variant -->
<compilerArgument>-proc:none</compilerArgument>
</configuration>
</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-enforcer-plugin</artifactId>
<version>1.3.1</version>
<executions>
<execution>
<id>enforce-versions</id>
<goals>
<goal>enforce</goal>
</goals>
<configuration>
<rules>
<requireMavenVersion>
<version>[3.0.4,)</version>
<message>Hadoop-BAM requires Maven 3.0.4 or greater</message>
</requireMavenVersion>
<requireJavaVersion>
<version>[1.6,)</version>
<message>Hadoop-BAM requires Java 1.6 or greater</message>
</requireJavaVersion>
</rules>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-install-plugin</artifactId>
<version>2.5.1</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-resources-plugin</artifactId>
<version>2.6</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>2.1</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
<version>2.16</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-assembly-plugin</artifactId>
<configuration>
<descriptorRefs>
<descriptorRef>jar-with-dependencies</descriptorRef>
</descriptorRefs>
<archive>
<index>true</index>
<manifest>
<addClasspath>true</addClasspath>
<mainClass>org.seqdoop.hadoop_bam.cli.Frontend</mainClass>
</manifest>
</archive>
<attach>false</attach>
</configuration>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</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>
</plugins>
<resources>
<resource>
<directory>src/main/resources/services</directory>
<targetPath>META-INF/services</targetPath>
</resource>
</resources>
</build>
<repositories>
<repository>
<id>cloudera</id>
<url>https://repository.cloudera.com/artifactory/cloudera-repos/</url>
</repository>
</repositories>
<dependencies>
<dependency>
<groupId>org.apache.hadoop</groupId>
<artifactId>hadoop-client</artifactId>
<version>${hadoop.version}</version>
</dependency>
<dependency>
<groupId>commons-cli</groupId>
<artifactId>commons-cli</artifactId>
<version>1.2</version>
</dependency>
<dependency>
<groupId>commons-httpclient</groupId>
<artifactId>commons-httpclient</artifactId>
<version>3.1</version>
</dependency>
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>2.4</version>
</dependency>
<dependency>
<groupId>org.seqdoop</groupId>
<artifactId>htsjdk</artifactId>
<version>${htsjdk.version}</version>
<exclusions>
<!-- testng breaks our tests so exclude it -->
<exclusion>
<groupId>org.testng</groupId>
<artifactId>testng</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.8.1</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-all</artifactId>
<version>1.9.5</version>
<scope>test</scope>
</dependency>
</dependencies>
<!-- The following shamelessly copied from ADAM -->
<profiles>
<!-- Only sign artifacts when we are performing a release, not snapshots -->
<profile>
<id>sonatype-oss-release</id>
<build>
<plugins>
<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-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-gpg-plugin</artifactId>
<version>1.5</version>
<executions>
<execution>
<id>sign-artifacts</id>
<phase>verify</phase>
<goals>
<goal>sign</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
</profiles>
</project>
<dependency> <groupId>org.seqdoop</groupId> <artifactId>hadoop-bam</artifactId> <version>7.0.0</version> </dependency>
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Download hadoop-bam-7.0.0.jar file