Package fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop

Class HadoopBamUtils

java.lang.Object

fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.HadoopBamUtils

public class HadoopBamUtils
extends Object

Constructor Summary

Constructors

Constructor	Description
HadoopBamUtils()

Method Summary

Modifier and Type	Method	Description
static htsjdk.samtools.SamFileHeaderMerger	getSAMHeaderMerger(org.apache.hadoop.conf.Configuration conf)	Computes the merger of the SAM headers in the files listed in HEADERMERGER_INPUTS_PROPERTY.
static void	mergeInto(OutputStream out, org.apache.hadoop.fs.Path directory, String basePrefix, String basePostfix, org.apache.hadoop.conf.Configuration conf, String commandName)	Merges the files in the given directory that have names given by getMergeableWorkFile() into out.
static void	mergeSAMInto(org.apache.hadoop.fs.Path out, org.apache.hadoop.fs.Path directory, String basePrefix, String basePostfix, org.seqdoop.hadoop_bam.SAMFormat format, org.apache.hadoop.conf.Configuration conf, String commandName)	Merges the files in the given directory that have names given by getMergeableWorkFile() into out in the given SAMFormat, using getSAMHeaderMerger().getMergedHeader() as the header.

Methods inherited from class java.lang.Object

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

Constructor Detail

HadoopBamUtils

public HadoopBamUtils()

Method Detail

getSAMHeaderMerger

public static htsjdk.samtools.SamFileHeaderMerger getSAMHeaderMerger(org.apache.hadoop.conf.Configuration conf)
                                                              throws IOException

Computes the merger of the SAM headers in the files listed in HEADERMERGER_INPUTS_PROPERTY. The sort order of the result is set according to the last call to setHeaderMergerSortOrder, or otherwise to "unsorted". The result is cached locally to prevent it from being recomputed too often.

Throws:

IOException

mergeSAMInto

public static void mergeSAMInto(org.apache.hadoop.fs.Path out,
                                org.apache.hadoop.fs.Path directory,
                                String basePrefix,
                                String basePostfix,
                                org.seqdoop.hadoop_bam.SAMFormat format,
                                org.apache.hadoop.conf.Configuration conf,
                                String commandName)
                         throws IOException

Merges the files in the given directory that have names given by getMergeableWorkFile() into out in the given SAMFormat, using getSAMHeaderMerger().getMergedHeader() as the header. Outputs progress reports if commandName is non-null.

Throws:

IOException

mergeInto

public static void mergeInto(OutputStream out,
                             org.apache.hadoop.fs.Path directory,
                             String basePrefix,
                             String basePostfix,
                             org.apache.hadoop.conf.Configuration conf,
                             String commandName)
                      throws IOException

Merges the files in the given directory that have names given by getMergeableWorkFile() into out. Outputs progress reports if commandName is non-null.

Throws:

IOException