@DocumentedFeature public class RevertOriginalBaseQualitiesAndAddMateCigar extends CommandLineProgram
Modifier and Type | Class and Description |
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static class |
RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
Used as a return for the canSkipSAMFile function.
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Modifier and Type | Field and Description |
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java.io.File |
INPUT |
int |
MAX_RECORDS_TO_EXAMINE |
java.io.File |
OUTPUT |
boolean |
RESTORE_ORIGINAL_QUALITIES |
htsjdk.samtools.SAMFileHeader.SortOrder |
SORT_ORDER |
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
Constructor and Description |
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RevertOriginalBaseQualitiesAndAddMateCigar() |
Modifier and Type | Method and Description |
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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.
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int |
doWork()
Do the work after command line has been parsed.
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static void |
main(java.lang.String[] args)
Default main method impl.
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customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
@Argument(shortName="I", doc="The input SAM/BAM file to revert the state of.") public java.io.File INPUT
@Argument(shortName="O", doc="The output SAM/BAM file to create.") public java.io.File OUTPUT
@Argument(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
@Argument(shortName="OQ", doc="True to restore original qualities from the OQ field to the QUAL field if available.") public boolean RESTORE_ORIGINAL_QUALITIES
@Argument(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
public RevertOriginalBaseQualitiesAndAddMateCigar()
public static void main(java.lang.String[] args)
public int doWork()
CommandLineProgram
doWork
in class CommandLineProgram
public static RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile canSkipSAMFile(java.io.File inputFile, int maxRecordsToExamine, boolean revertOriginalBaseQualities, java.io.File referenceFasta)
inputFile
- the SAM/BAM input filemaxRecordsToExamine
- the maximum number of records to examine before quittingrevertOriginalBaseQualities
- true if we are to revert original base qualities, false otherwise