Package picard.sam
Class SetNmMdAndUqTags
- java.lang.Object
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- picard.cmdline.CommandLineProgram
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- picard.sam.SetNmMdAndUqTags
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- Direct Known Subclasses:
SetNmAndUqTags
@DocumentedFeature public class SetNmMdAndUqTags extends CommandLineProgram
Fixes the NM, MD, and UQ tags in a SAM or BAM file.This tool takes in a coordinate-sorted SAM or BAM file and calculates the NM, MD, and UQ tags by comparing with the reference.
This may be needed when MergeBamAlignment was run with SORT_ORDER other than 'coordinate' and thus could not fix these tags then. The input must be coordinate sorted in order to run. If specified, the MD and NM tags can be ignored and only the UQ tag be set.
Inputs
- The BAM or SAM file to fix
- A reference sequence
Output
A BAM or SAM output file with recalculated NM, MD, and UQ tags
Usage example:
Fix the tags in a BAM file:
java -jar picard.jar SetNmMdAndUqTags \ R=reference_sequence.fasta \ I=sorted.bam \ O=fixed.bam
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Field Summary
Fields Modifier and Type Field Description File
INPUT
boolean
IS_BISULFITE_SEQUENCE
File
OUTPUT
boolean
SET_ONLY_UQ
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Fields inherited from class picard.cmdline.CommandLineProgram
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
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Constructor Summary
Constructors Constructor Description SetNmMdAndUqTags()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected int
doWork()
Do the work after command line has been parsed.protected boolean
requiresReference()
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Methods inherited from class picard.cmdline.CommandLineProgram
customCommandLineValidation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, setDefaultHeaders, useLegacyParser
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Field Detail
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INPUT
@Argument(doc="The BAM or SAM file to fix. ", shortName="I") public File INPUT
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OUTPUT
@Argument(doc="The fixed BAM or SAM output file. ", shortName="O") public File OUTPUT
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IS_BISULFITE_SEQUENCE
@Argument(doc="Whether the file contains bisulfite sequence (used when calculating the NM tag).") public boolean IS_BISULFITE_SEQUENCE
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SET_ONLY_UQ
@Argument(doc="Only set the UQ tag, ignore MD and NM.") public boolean SET_ONLY_UQ
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Method Detail
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requiresReference
protected boolean requiresReference()
- Overrides:
requiresReference
in classCommandLineProgram
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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 classCommandLineProgram
- Returns:
- program exit status.
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