org.seqdoop.hadoop_bam.cli

Class Utils

java.lang.Object

org.seqdoop.hadoop_bam.cli.Utils

public final class Utils
extends Object

Field Summary

Fields

Modifier and Type	Field and Description
static String	HEADERMERGER_INPUTS_PROPERTY
static String	WORK_FILENAME_PROPERTY

Constructor Summary

Constructors

Constructor and Description
Utils()

Method Summary

Modifier and Type	Method and Description
static void	configureSampling(org.apache.hadoop.fs.Path workDir, String outName, org.apache.hadoop.conf.Configuration conf)
static void	correctSAMRecordForMerging(htsjdk.samtools.SAMRecord r, org.apache.hadoop.conf.Configuration conf) Changes the given SAMRecord as appropriate for being placed in a file whose header is getSAMHeaderMerger(conf).getMergedHeader().
static String	getArgv0()
static org.apache.hadoop.fs.Path	getMergeableWorkFile(org.apache.hadoop.fs.Path directory, String basePrefix, String basePostfix, org.apache.hadoop.mapreduce.TaskAttemptContext ctx, String extension) Returns a name that mergeInto() will recognize as a file to be merged.
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 String	getStringencyOptHelp()
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, 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.
static void	printWrapped(PrintStream out, String str)
static void	printWrapped(PrintStream out, String str, int indent)
static void	printWrapped(PrintStream out, String str, int indent, int wrapAt)
static void	setArgv0Class(Class<?> cl)
static void	setHeaderMergerSortOrder(org.apache.hadoop.conf.Configuration conf, htsjdk.samtools.SAMFileHeader.SortOrder order)
static htsjdk.samtools.ValidationStringency	toStringency(Object o, String cmdName) Sets the default validation stringency in addition to returning it.

Methods inherited from class java.lang.Object

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

Field Detail

WORK_FILENAME_PROPERTY

public static final String WORK_FILENAME_PROPERTY

See Also:

Constant Field Values

HEADERMERGER_INPUTS_PROPERTY

public static final String HEADERMERGER_INPUTS_PROPERTY

See Also:

Constant Field Values

Constructor Detail

Utils

public Utils()

Method Detail

printWrapped

public static void printWrapped(PrintStream out,
                                String str)

printWrapped

public static void printWrapped(PrintStream out,
                                String str,
                                int indent)

printWrapped

public static void printWrapped(PrintStream out,
                                String str,
                                int indent,
                                int wrapAt)

getArgv0

public static String getArgv0()

setArgv0Class

public static void setArgv0Class(Class<?> cl)

configureSampling

public static void configureSampling(org.apache.hadoop.fs.Path workDir,
                                     String outName,
                                     org.apache.hadoop.conf.Configuration conf)
                              throws IOException

Throws:

IOException

getMergeableWorkFile

public static org.apache.hadoop.fs.Path getMergeableWorkFile(org.apache.hadoop.fs.Path directory,
                                                             String basePrefix,
                                                             String basePostfix,
                                                             org.apache.hadoop.mapreduce.TaskAttemptContext ctx,
                                                             String extension)

Returns a name that mergeInto() will recognize as a file to be merged. The filename is the value of WORK_FILENAME_PROPERTY surrounded by basePrefix and basePostfix, followed by the part number and with the given extension.

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

setHeaderMergerSortOrder

public static void setHeaderMergerSortOrder(org.apache.hadoop.conf.Configuration conf,
                                            htsjdk.samtools.SAMFileHeader.SortOrder order)

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

correctSAMRecordForMerging

public static void correctSAMRecordForMerging(htsjdk.samtools.SAMRecord r,
                                              org.apache.hadoop.conf.Configuration conf)
                                       throws IOException

Changes the given SAMRecord as appropriate for being placed in a file whose header is getSAMHeaderMerger(conf).getMergedHeader().

Throws:

IOException

mergeSAMInto

public static void mergeSAMInto(org.apache.hadoop.fs.Path out,
                                org.apache.hadoop.fs.Path directory,
                                String basePrefix,
                                String basePostfix,
                                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

getStringencyOptHelp

public static String getStringencyOptHelp()

toStringency

public static htsjdk.samtools.ValidationStringency toStringency(Object o,
                                                                String cmdName)

Sets the default validation stringency in addition to returning it.