picard.sam

Class RevertSam

java.lang.Object

picard.cmdline.CommandLineProgram

picard.sam.RevertSam

public class RevertSam
extends CommandLineProgram

Reverts a SAM file by optionally restoring original quality scores and by removing all alignment information.

Field Summary

Fields

Modifier and Type	Field and Description
java.util.List<java.lang.String>	ATTRIBUTE_TO_CLEAR
java.io.File	INPUT
java.lang.String	LIBRARY_NAME
double	MAX_DISCARD_FRACTION
java.io.File	OUTPUT
boolean	OUTPUT_BY_READGROUP
java.io.File	OUTPUT_MAP
boolean	REMOVE_ALIGNMENT_INFORMATION
boolean	REMOVE_DUPLICATE_INFORMATION
boolean	RESTORE_ORIGINAL_QUALITIES
java.lang.String	SAMPLE_ALIAS
boolean	SANITIZE
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
RevertSam()

Method Summary

Modifier and Type	Method and Description
protected java.lang.String[]	customCommandLineValidation() Enforce that output ordering is queryname when sanitization is turned on since it requires a queryname sort.
protected int	doWork() Do the work after command line has been parsed.
static void	main(java.lang.String[] args) Default main method impl.
void	revertSamRecord(htsjdk.samtools.SAMRecord rec) Takes an individual SAMRecord and applies the set of changes/reversions to it that have been requested by program level options.

Methods inherited from class picard.cmdline.CommandLineProgram

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(mutex="OUTPUT_MAP",
        shortName="O",
        doc="The output SAM/BAM file to create, or an output directory if OUTPUT_BY_READGROUP is true.")
public java.io.File OUTPUT

OUTPUT_MAP

@Option(mutex="OUTPUT",
        shortName="OM",
        doc="Tab separated file with two columns, READ_GROUP_ID and OUTPUT, providing file mapping only used if OUTPUT_BY_READGROUP is true.")
public java.io.File OUTPUT_MAP

OUTPUT_BY_READGROUP

@Option(shortName="OBR",
        doc="When true, outputs each read group in a separate file.")
public boolean OUTPUT_BY_READGROUP

SORT_ORDER

@Option(shortName="SO",
        doc="The sort order to create the reverted output file with.")
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

REMOVE_DUPLICATE_INFORMATION

@Option(doc="Remove duplicate read flags from all reads.  Note that if this is true and REMOVE_ALIGNMENT_INFORMATION==false,  the output may have the unusual but sometimes desirable trait of having unmapped reads that are marked as duplicates.")
public boolean REMOVE_DUPLICATE_INFORMATION

REMOVE_ALIGNMENT_INFORMATION

@Option(doc="Remove all alignment information from the file.")
public boolean REMOVE_ALIGNMENT_INFORMATION

ATTRIBUTE_TO_CLEAR

@Option(doc="When removing alignment information, the set of optional tags to remove.")
public java.util.List<java.lang.String> ATTRIBUTE_TO_CLEAR

SANITIZE

@Option(doc="WARNING: This option is potentially destructive. If enabled will discard reads in order to produce a consistent output BAM. Reads discarded include (but are not limited to) paired reads with missing mates, duplicated records, records with mismatches in length of bases and qualities. This option can only be enabled if the output sort order is queryname and will always cause sorting to occur.")
public boolean SANITIZE

MAX_DISCARD_FRACTION

@Option(doc="If SANITIZE=true and higher than MAX_DISCARD_FRACTION reads are discarded due to sanitization thenthe program will exit with an Exception instead of exiting cleanly. Output BAM will still be valid.")
public double MAX_DISCARD_FRACTION

SAMPLE_ALIAS

@Option(doc="The sample alias to use in the reverted output file.  This will override the existing sample alias in the file and is used only if all the read groups in the input file have the same sample alias ",
        shortName="ALIAS",
        optional=true)
public java.lang.String SAMPLE_ALIAS

LIBRARY_NAME

@Option(doc="The library name to use in the reverted output file.  This will override the existing sample alias in the file and is used only if all the read groups in the input file have the same library name ",
        shortName="LIB",
        optional=true)
public java.lang.String LIBRARY_NAME

Constructor Detail

RevertSam

public RevertSam()

Method Detail

main

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

Default main method impl.

customCommandLineValidation

protected java.lang.String[] customCommandLineValidation()

Enforce that output ordering is queryname when sanitization is turned on since it requires a queryname sort.

Overrides:

customCommandLineValidation in class CommandLineProgram

Returns:

null if command line is valid. If command line is invalid, returns an array of error message to be written to the appropriate place.

doWork

protected 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.

revertSamRecord

public void revertSamRecord(htsjdk.samtools.SAMRecord rec)

Takes an individual SAMRecord and applies the set of changes/reversions to it that have been requested by program level options.