uk.ac.sanger.npg.picard
Class AlignmentFilter

java.lang.Object
  net.sf.picard.cmdline.CommandLineProgram
      uk.ac.sanger.npg.picard.PicardCommandLine
          uk.ac.sanger.npg.picard.AlignmentFilter

public class AlignmentFilter
extends PicardCommandLine

Field Summary

java.util.List<java.io.File>	INPUT_ALIGNMENT
java.io.File	METRICS_FILE
java.util.List<java.io.File>	OUTPUT_ALIGNMENT
java.io.File	OUTPUT_UNALIGNED
java.lang.String	USAGE

Fields inherited from class uk.ac.sanger.npg.picard.PicardCommandLine

version

Fields inherited from class net.sf.picard.cmdline.CommandLineProgram

COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, MAX_RECORDS_IN_RAM, QUIET, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY

Constructor Summary

AlignmentFilter()

Method Summary

int	checkOneRecord(java.util.List<net.sf.samtools.SAMRecord> recordList, java.util.List<net.sf.samtools.SAMRecord> pairedRecordList, boolean isPairedRead)
protected int	doWork()
static void	main(java.lang.String[] args)

Methods inherited from class uk.ac.sanger.npg.picard.PicardCommandLine

addProgramRecordToHead, getThisProgramRecord, makeUniqueProgramId

Methods inherited from class net.sf.picard.cmdline.CommandLineProgram

customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getProgramVersion, getStandardUsagePreamble, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders

Methods inherited from class java.lang.Object

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

Field Detail

USAGE

@Usage(programVersion="1.00")
public final java.lang.String USAGE

INPUT_ALIGNMENT

@Option(shortName="IN",
        doc="The input SAM or BAM file with alignment.",
        minElements=1,
        optional=false)
public final java.util.List<java.io.File> INPUT_ALIGNMENT

OUTPUT_ALIGNMENT

@Option(shortName="OUT",
        doc="The ouput SAM or BAM file. It should have the same number of files as the input.",
        minElements=1,
        optional=false)
public final java.util.List<java.io.File> OUTPUT_ALIGNMENT

OUTPUT_UNALIGNED

@Option(shortName="UNALIGNED",
        doc="The ouput SAM or BAM file for unaligned. If not given, the unaligned reads will put into the last output file.",
        optional=true)
public java.io.File OUTPUT_UNALIGNED

METRICS_FILE

@Option(shortName="METRICS",
        doc="Metrics file name",
        optional=true)
public java.io.File METRICS_FILE

Constructor Detail

AlignmentFilter

public AlignmentFilter()

Method Detail

doWork

protected int doWork()

Specified by:

doWork in class net.sf.picard.cmdline.CommandLineProgram

checkOneRecord

public int checkOneRecord(java.util.List<net.sf.samtools.SAMRecord> recordList,
                          java.util.List<net.sf.samtools.SAMRecord> pairedRecordList,
                          boolean isPairedRead)

Parameters:

recordList -

pairedRecordList -

isPairedRead -

Returns:

main

public static void main(java.lang.String[] args)

Parameters:

args -