MarkDuplicates
, MarkDuplicatesWithMateCigar
public abstract class AbstractMarkDuplicatesCommandLineProgram extends AbstractOpticalDuplicateFinderCommandLineProgram
Modifier and Type | Class | Description |
---|---|---|
static class |
AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator |
Little class used to package up a header and an iterable/iterator.
|
Modifier and Type | Field | Description |
---|---|---|
htsjdk.samtools.SAMFileHeader.SortOrder |
ASSUME_SORT_ORDER |
|
boolean |
ASSUME_SORTED |
Deprecated.
|
List<String> |
COMMENT |
|
htsjdk.samtools.DuplicateScoringStrategy.ScoringStrategy |
DUPLICATE_SCORING_STRATEGY |
|
List<String> |
INPUT |
|
File |
METRICS_FILE |
|
File |
OUTPUT |
|
protected Set<String> |
pgIdsSeen |
The program groups that have been seen during the course of examining the input records.
|
String |
PROGRAM_GROUP_COMMAND_LINE |
|
String |
PROGRAM_GROUP_NAME |
|
String |
PROGRAM_GROUP_VERSION |
|
String |
PROGRAM_RECORD_ID |
|
boolean |
REMOVE_DUPLICATES |
LOG, OPTICAL_DUPLICATE_PIXEL_DISTANCE, opticalDuplicateFinder, READ_NAME_REGEX
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY
Constructor | Description |
---|---|
AbstractMarkDuplicatesCommandLineProgram() |
Modifier and Type | Method | Description |
---|---|---|
protected void |
finalizeAndWriteMetrics(LibraryIdGenerator libraryIdGenerator) |
Writes the metrics given by the libraryIdGenerator to the METRICS_FILE.
|
protected Map<String,String> |
getChainedPgIds(htsjdk.samtools.SAMFileHeader outputHeader) |
We have to re-chain the program groups based on this algorithm.
|
protected AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator |
openInputs() |
Since this may read its inputs more than once this method does all the opening
and checking of the inputs.
|
static void |
trackOpticalDuplicates(List<? extends ReadEnds> ends,
ReadEnds keeper,
OpticalDuplicateFinder opticalDuplicateFinder,
LibraryIdGenerator libraryIdGenerator) |
Looks through the set of reads and identifies how many of the duplicates are
in fact optical duplicates, and stores the data in the instance level histogram.
|
customCommandLineValidation, setupOpticalDuplicateFinder
doWork, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders
@Option(shortName="I", doc="One or more input SAM or BAM files to analyze. Must be coordinate sorted.") public List<String> INPUT
@Option(shortName="M", doc="File to write duplication metrics to") public File METRICS_FILE
@Option(doc="If true do not write duplicates to the output file instead of writing them with appropriate flags set.") public boolean REMOVE_DUPLICATES
@Deprecated @Option(shortName="AS", doc="If true, assume that the input file is coordinate sorted even if the header says otherwise. Deprecated, used ASSUME_SORT_ORDER=coordinate instead.", mutex="ASSUME_SORT_ORDER") public boolean ASSUME_SORTED
@Option(shortName="ASO", doc="If not null, assume that the input file has this order even if the header says otherwise.", optional=true, mutex="ASSUME_SORTED") public htsjdk.samtools.SAMFileHeader.SortOrder ASSUME_SORT_ORDER
@Option(shortName="DS", doc="The scoring strategy for choosing the non-duplicate among candidates.") public htsjdk.samtools.DuplicateScoringStrategy.ScoringStrategy DUPLICATE_SCORING_STRATEGY
@Option(shortName="PG", doc="The program record ID for the @PG record(s) created by this program. Set to null to disable PG record creation. This string may have a suffix appended to avoid collision with other program record IDs.", optional=true) public String PROGRAM_RECORD_ID
@Option(shortName="PG_VERSION", doc="Value of VN tag of PG record to be created. If not specified, the version will be detected automatically.", optional=true) public String PROGRAM_GROUP_VERSION
@Option(shortName="PG_COMMAND", doc="Value of CL tag of PG record to be created. If not supplied the command line will be detected automatically.", optional=true) public String PROGRAM_GROUP_COMMAND_LINE
@Option(shortName="PG_NAME", doc="Value of PN tag of PG record to be created.") public String PROGRAM_GROUP_NAME
@Option(shortName="CO", doc="Comment(s) to include in the output file\'s header.", optional=true) public List<String> COMMENT
public AbstractMarkDuplicatesCommandLineProgram()
protected Map<String,String> getChainedPgIds(htsjdk.samtools.SAMFileHeader outputHeader)
protected void finalizeAndWriteMetrics(LibraryIdGenerator libraryIdGenerator)
libraryIdGenerator
- protected AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator openInputs()
public static void trackOpticalDuplicates(List<? extends ReadEnds> ends, ReadEnds keeper, OpticalDuplicateFinder opticalDuplicateFinder, LibraryIdGenerator libraryIdGenerator)