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Hadoop-BAM

Hadoop-BAM: a library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework.

Build status

Build Status Coverage Status Maven Central License: MIT

The file formats currently supported are:

  • BAM (Binary Alignment/Map)
  • SAM (Sequence Alignment/Map)
  • CRAM
  • FASTQ
  • FASTA (input only)
  • QSEQ
  • VCF (Variant Call Format)
  • BCF (Binary VCF) (output is always BGZF-compressed)

For a longer high-level description of Hadoop-BAM, refer to the article "Hadoop-BAM: directly manipulating next generation sequencing data in the cloud" in Bioinformatics Volume 28 Issue 6 pp. 876-877, also available online at: http://dx.doi.org/10.1093/bioinformatics/bts054

If you are interested in using Apache Pig (http://pig.apache.org/) with Hadoop-BAM, refer to SeqPig at: http://seqpig.sourceforge.net/

Note that the library part of Hadoop-BAM is primarily intended for developers with experience in using Hadoop. SeqPig is a more versatile and higher-level interface to the file formats supported by Hadoop-BAM. In addition, ADAM and GATK version 4 both use Hadoop-BAM and offer high-level command-line bioinformatics tools that run on Spark clusters.

For examples of how to use Hadoop-BAM as a library to read data files in Hadoop see the examples/ directory.

Dependencies

Hadoop. Any recent version should work. Hadoop is a "provided" dependency in the Maven sense, which means that you must have Hadoop installed, or, if using Hadoop-BAM as a library, have the Hadoop Maven dependencies in your POM.

HTSJDK. Hadoop-BAM uses a particular version, but later ones can usually be substituted.

Note that starting from version 7.4.0 Hadoop-BAM requires Java 8.

Installation

A precompiled "hadoop-bam-X.Y.Z.jar" is available that you can use with most recent versions of Hadoop. Otherwise, you'll have to build Hadoop-BAM yourself by using Maven and following the instructions below.

Build

Build Hadoop-BAM with the following command:

mvn clean package -DskipTests

It will create two files:

target/hadoop-bam-X.Y.Z-SNAPSHOT.jar
target/hadoop-bam-X.Y.Z-SNAPSHOT-jar-with-dependencies.jar

The former contains only Hadoop-BAM whereas the latter one also contains all dependencies and can be run directly via

hadoop jar target/hadoop-bam-X.Y.Z-SNAPSHOT-jar-with-dependencies.jar

Javadoc documentation is generated automatically and can then be found in the target/apidocs subdirectory.

Finally, unit tests can be run via:

mvn test

Library usage

Hadoop-BAM provides the standard set of Hadoop file format classes for the file formats it supports: a FileInputFormat and one or more RecordReaders for input, and a FileOutputFormat and one or more RecordWriters for output. These are summarized in the table below.

File Format InputFormat OutputFormat
BAM BAMInputFormat KeyIgnoringBAMOutputFormat
SAM SAMInputFormat KeyIgnoringAnySAMOutputFormat
CRAM CRAMInputFormat KeyIgnoringCRAMOutputFormat
BAM, SAM, or CRAM AnySAMInputFormat KeyIgnoringAnySAMOutputFormat
FASTQ FastqInputFormat FastqOutputFormat
FASTA FastaInputFormat N/A
QSEQ QseqInputFormat QseqOutputFormat
VCF or BCF VCFInputFormat KeyIgnoringVCFOutputFormat

AnySAMInputFormat detects the format (BAM, SAM, or CRAM) by file extension, then by looking at the first few bytes of the file (if file extension detection is disabled or is inconclusive). VCFInputFormat works in a similar way for VCF and BCF files.

The output formats all discard the key and only use the value field when writing the output file. Some of the output formats indicate this explictly through the KeyIgnoring prefix in their name, but FastqOutputFormat and QseqOutputFormat actually ignore the key too.

The abstract base classes BAMOutputFormat, CRAMOutputFormat, AnySAMOutputFormat, and VCFOutputFormat cannot be used directly, but can be subclassed in order to add custom logic (to provide ValueIgnoring versions, for example).

When using KeyIgnoringAnySAMOutputFormat, the format of the files written (BAM, SAM, or CRAM) must be specified by setting the property hadoopbam.anysam.output-format. Similarly, set the property hadoopbam.vcf.output-format in order to specify which file format KeyIgnoringVCFOutputFormat will use (VCF or BCF).

The properties that can be set on input and output formats are summarized in the table below:

Format Property Default Description
AnySAMInputFormat hadoopbam.anysam.trust-exts true Whether to detect the file format (BAM, SAM, or CRAM) by file extension. If false, use the file contents to detect the format.
KeyIgnoringAnySAMOutputFormat hadoopbam.anysam.output-format (Required.) The file format to use when writing BAM, SAM, or CRAM files. Should be one of BAM, SAM, or CRAM.
hadoopbam.anysam.write-header true Whether to write the SAM header in each output file part. If true, call setSAMHeader() or readSAMHeaderFrom() to set the desired header.
BAMInputFormat hadoopbam.bam.bounded-traversal false If true, only include reads that match the intervals specified in hadoopbam.bam.intervals, and unplaced unmapped reads, if hadoopbam.bam.traverse-unplaced-unmapped is set to true.
hadoopbam.bam.intervals Only include reads that match the specified intervals. BAM files must be indexed in this case. Intervals are comma-separated and follow the same syntax as the -L option in SAMtools. E.g. chr1:1-20000,chr2:12000-20000. When using this option hadoopbam.bam.bounded-traversal should be set to true.
hadoopbam.bam.traverse-unplaced-unmapped false If true, include unplaced unmapped reads (that is, unmapped reads with no position) When using this option hadoopbam.bam.bounded-traversal should be set to true.
hadoopbam.bam.use-intel-inflater false If true, use the Intel inflater for decompressing DEFLATE compressed streams. When using this option the GKL library must be provided on the classpath.
KeyIgnoringBAMOutputFormat hadoopbam.bam.write-splitting-bai false If true, write .splitting-bai files for every BAM file.
hadoopbam.bam.use-intel-deflater false If true, use the Intel deflater for compressing DEFLATE compressed streams. When using this option the GKL library must be provided on the classpath.
CRAMInputFormat hadoopbam.cram.reference-source-path (Required.) The path to the reference. May be an hdfs:// path.
FastqInputFormat hbam.fastq-input.base-quality-encoding sanger The encoding used for base qualities. One of sanger or illumina.
hbam.fastq-input.filter-failed-qc false If true, filter out reads that didn't pass quality checks.
QseqInputFormat hbam.qseq-input.base-quality-encoding illumina The encoding used for base qualities. One of sanger or illumina.
hbam.qseq-input.filter-failed-qc false If true, filter out reads that didn't pass quality checks.
VCFInputFormat hadoopbam.vcf.trust-exts false Whether to detect the file format (VCF or BCF) by file extension. If false, use the file contents to detect the format.
KeyIgnoringVCFOutputFormat hadoopbam.vcf.output-format (Required.) The file format to use when writing VCF or BCF files. Should be one of VCF or BCF.
hadoopbam.vcf.write-header true Whether to write the VCF header in each output file part. If true, call setHeader() or readHeaderFrom() to set the desired header.

Note that Hadoop-BAM is based around the newer Hadoop API introduced in the 0.20 Hadoop releases instead of the older, deprecated API.

For examples of how to link to Hadoop-BAM in your own Maven project see the examples/ folder. There are examples for reading and writing BAM as well as VCF files.

When using Hadoop-BAM as a library in your program, remember to have hadoop-bam-X.Y.Z.jar as well as the HTSJDK .jars (including the Commons JEXL .jar) in your CLASSPATH and HADOOP_CLASSPATH; alternatively, use the *-jar-with-dependencies.jar which contains already all dependencies.

Linking against Hadoop-BAM

If your Maven project relies on Hadoop-BAM the easiest way to link against it is by relying on the OSS Sonatype repository:

<project>
...
    <dependencies>
        <dependency>
            <groupId>org.seqdoop</groupId>
            <artifactId>hadoop-bam</artifactId>
            <version>7.9.2</version>
        </dependency>
        ...
    </dependencies>
    ...
</project>

Running under Hadoop

To use Hadoop-BAM under Hadoop, the easiest method is to use the jar that comes packaged with all dependencies via

hadoop jar hadoop-bam-X.Y.Z-jar-with-dependencies.jar

Alternatively, you can use the "-libjars" command line argument when running Hadoop-BAM to provide different versions of dependencies as follows:

hadoop jar hadoop-bam-X.Y.Z.jar \
  -libjars htsjdk-2.3.0.jar,commons-jexl-2.1.1.jar

Finally, all jar files can also be added to HADOOP_CLASSPATH in the Hadoop configuration's hadoop-env.sh.

File paths under Hadoop

When running under Hadoop, keep in mind that file paths refer to the distributed file system, HDFS. To explicitly access a local file, instead of using the plain path such as "/foo/bar", you must use a file: URI, such as "file:/foo/bar". Note that paths in file: URIs must be absolute.