org.seqdoop.hadoop_bam.util

Class SAMFileMerger

java.lang.Object

org.seqdoop.hadoop_bam.util.SAMFileMerger

public class SAMFileMerger
extends Object

Merges headerless BAM or CRAM files produced by KeyIgnoringAnySAMOutputFormat into a single file.

Method Summary

Modifier and Type	Method and Description
static void	mergeParts(String partDirectory, String outputFile, SAMFormat samOutputFormat, htsjdk.samtools.SAMFileHeader header) Merge part file shards produced by KeyIgnoringAnySAMOutputFormat into a single file with the given header.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

mergeParts

public static void mergeParts(String partDirectory,
                              String outputFile,
                              SAMFormat samOutputFormat,
                              htsjdk.samtools.SAMFileHeader header)
                       throws IOException

Merge part file shards produced by KeyIgnoringAnySAMOutputFormat into a single file with the given header.

Parameters:

partDirectory - the directory containing part files

outputFile - the file to write the merged file to

samOutputFormat - the format (must be BAM or CRAM; SAM is not supported)

header - the header for the merged file

Throws:

IOException