@DocumentedFeature public class RevertOriginalBaseQualitiesAndAddMateCigar extends CommandLineProgram
| Modifier and Type | Class | Description |
|---|---|---|
static class |
RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile |
Used as a return for the canSkipSAMFile function.
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| Modifier and Type | Field | Description |
|---|---|---|
File |
INPUT |
|
int |
MAX_RECORDS_TO_EXAMINE |
|
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 | Description |
|---|---|
RevertOriginalBaseQualitiesAndAddMateCigar() |
| Modifier and Type | Method | Description |
|---|---|---|
static RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile |
canSkipSAMFile(File inputFile,
int maxRecordsToExamine,
boolean revertOriginalBaseQualities,
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(String[] args) |
Default main method impl.
|
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 File INPUT
@Argument(shortName="O",
doc="The output SAM/BAM file to create.")
public 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(String[] args)
public int doWork()
CommandLineProgramdoWork in class CommandLineProgrampublic static RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile canSkipSAMFile(File inputFile, int maxRecordsToExamine, boolean revertOriginalBaseQualities, 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