picard.sam

Class RevertOriginalBaseQualitiesAndAddMateCigar

java.lang.Object

picard.cmdline.CommandLineProgram

picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar

public class RevertOriginalBaseQualitiesAndAddMateCigar
extends CommandLineProgram

This tool reverts the original base qualities (if specified) and adds the mate cigar tag to mapped BAMs. If the file does not have OQs and already has mate cigar tags, nothing is done. New BAM/BAI/MD5 files are created.

Author:

Nils Homer

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile Used as a return for the canSkipSAMFile function.

Field Summary

Fields

Modifier and Type	Field and Description
java.io.File	INPUT
int	MAX_RECORDS_TO_EXAMINE
java.io.File	OUTPUT
boolean	RESTORE_ORIGINAL_QUALITIES
htsjdk.samtools.SAMFileHeader.SortOrder	SORT_ORDER

Fields inherited from class picard.cmdline.CommandLineProgram

COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY

Constructor Summary

Constructors

Constructor and Description
RevertOriginalBaseQualitiesAndAddMateCigar()

Method Summary

Modifier and Type	Method and Description
static RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile	canSkipSAMFile(java.io.File inputFile, int maxRecordsToExamine, boolean revertOriginalBaseQualities, java.io.File referenceFasta) Checks if we can skip the SAM/BAM file when reverting origin base qualities and adding mate cigars.
int	doWork() Do the work after command line has been parsed.
static void	main(java.lang.String[] args) Default main method impl.

Methods inherited from class picard.cmdline.CommandLineProgram

customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders

Methods inherited from class java.lang.Object

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

Field Detail

INPUT

@Option(shortName="I",
        doc="The input SAM/BAM file to revert the state of.")
public java.io.File INPUT

OUTPUT

@Option(shortName="O",
        doc="The output SAM/BAM file to create.")
public java.io.File OUTPUT

SORT_ORDER

@Option(shortName="SO",
        doc="The sort order to create the reverted output file with.By default, the sort order will be the same as the input.",
        optional=true)
public htsjdk.samtools.SAMFileHeader.SortOrder SORT_ORDER

RESTORE_ORIGINAL_QUALITIES

@Option(shortName="OQ",
        doc="True to restore original qualities from the OQ field to the QUAL field if available.")
public boolean RESTORE_ORIGINAL_QUALITIES

MAX_RECORDS_TO_EXAMINE

@Option(doc="The maximum number of records to examine to determine if we can exit early and not output, given that there are a no original base qualities (if we are to restore) and mate cigars exist. Set to 0 to never skip the file.")
public int MAX_RECORDS_TO_EXAMINE

Constructor Detail

RevertOriginalBaseQualitiesAndAddMateCigar

public RevertOriginalBaseQualitiesAndAddMateCigar()

Method Detail

main

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

Default main method impl.

doWork

public int doWork()

Description copied from class: CommandLineProgram

Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.

Specified by:

doWork in class CommandLineProgram

Returns:

program exit status.

canSkipSAMFile

public static RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile canSkipSAMFile(java.io.File inputFile,
                                                                                       int maxRecordsToExamine,
                                                                                       boolean revertOriginalBaseQualities,
                                                                                       java.io.File referenceFasta)

Checks if we can skip the SAM/BAM file when reverting origin base qualities and adding mate cigars.

Parameters:

inputFile - the SAM/BAM input file

maxRecordsToExamine - the maximum number of records to examine before quitting

revertOriginalBaseQualities - true if we are to revert original base qualities, false otherwise

Returns:

whether we can skip or not, and the explanation why.