@DocumentedFeature public class FixMateInformation extends CommandLineProgram
OUTPUT file is supplied then the output is written to a temporary file
and then copied over the INPUT file (with the original placed in a .old file.)
Reads marked with the secondary alignment flag are written to the output file unchanged.
However, supplementary reads are corrected so that they point to the primary,
non-supplemental mate record.
java -jar picard.jar FixMateInformation \
I=input.bam \
O=fixed_mate.bam \
ADD_MATE_CIGAR=true
| Modifier and Type | Field | Description |
|---|---|---|
Boolean |
ADD_MATE_CIGAR |
|
boolean |
ASSUME_SORTED |
|
Boolean |
IGNORE_MISSING_MATES |
|
List<File> |
INPUT |
|
protected htsjdk.samtools.SAMFileWriter |
out |
|
File |
OUTPUT |
|
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 |
|---|---|
FixMateInformation() |
| Modifier and Type | Method | Description |
|---|---|---|
protected void |
closeWriter() |
|
protected void |
createSamFileWriter(htsjdk.samtools.SAMFileHeader header) |
|
protected int |
doWork() |
Do the work after command line has been parsed.
|
static void |
main(String[] args) |
|
protected void |
writeAlignment(htsjdk.samtools.SAMRecord sam) |
customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser@Argument(shortName="I",
doc="The input files to check and fix. Multiple files will be merged and sorted.")
public List<File> INPUT
@Argument(shortName="O",
optional=true,
doc="The output file to write to. If no output file is supplied, the input file is overwritten (only available with single input file).")
public File OUTPUT
@Argument(shortName="SO",
optional=true,
doc="Optional sort order if the OUTPUT file should be sorted differently than the INPUT file.")
public htsjdk.samtools.SAMFileHeader.SortOrder SORT_ORDER
@Argument(doc="If true, assume that the input file is queryname sorted, even if the header says otherwise.",
shortName="AS")
public boolean ASSUME_SORTED
@Argument(shortName="MC",
optional=true,
doc="Adds the mate CIGAR tag (MC) if true, does not if false.")
public Boolean ADD_MATE_CIGAR
@Argument(doc="If true, ignore missing mates, otherwise will throw an exception when missing mates are found.",
optional=true)
public Boolean IGNORE_MISSING_MATES
protected htsjdk.samtools.SAMFileWriter out
public static void main(String[] args)
protected int doWork()
CommandLineProgramdoWork in class CommandLineProgramprotected void createSamFileWriter(htsjdk.samtools.SAMFileHeader header)
protected void writeAlignment(htsjdk.samtools.SAMRecord sam)
protected void closeWriter()