public class CollectSequencingArtifactMetrics extends SinglePassSamProgram
Modifier and Type | Field | Description |
---|---|---|
int |
CONTEXT_SIZE |
|
Set<String> |
CONTEXTS_TO_PRINT |
|
File |
DB_SNP |
|
String |
FILE_EXTENSION |
|
boolean |
INCLUDE_DUPLICATES |
|
boolean |
INCLUDE_NON_PF_READS |
|
boolean |
INCLUDE_UNPAIRED |
|
File |
INTERVALS |
|
int |
MAXIMUM_INSERT_SIZE |
|
int |
MINIMUM_INSERT_SIZE |
|
int |
MINIMUM_MAPPING_QUALITY |
|
int |
MINIMUM_QUALITY_SCORE |
|
boolean |
TANDEM_READS |
|
boolean |
USE_OQ |
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY
ASSUME_SORTED, INPUT, OUTPUT, STOP_AFTER
Constructor | Description |
---|---|
CollectSequencingArtifactMetrics() |
Modifier and Type | Method | Description |
---|---|---|
protected void |
acceptRead(htsjdk.samtools.SAMRecord rec,
htsjdk.samtools.reference.ReferenceSequence ref) |
Should be implemented by subclasses to accept SAMRecords one at a time.
|
protected String[] |
customCommandLineValidation() |
Put any custom command-line validation in an override of this method.
|
protected void |
finish() |
Should be implemented by subclasses to do one-time finalization work.
|
protected void |
setup(htsjdk.samtools.SAMFileHeader header,
File samFile) |
Should be implemented by subclasses to do one-time initialization work.
|
protected boolean |
usesNoRefReads() |
Can be overriden and set to false if the section of unmapped reads at the end of the file isn't needed.
|
getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
doWork, makeItSo
@Option(doc="An optional list of intervals to restrict analysis to.", optional=true) public File INTERVALS
@Option(doc="VCF format dbSNP file, used to exclude regions around known polymorphisms from analysis.", optional=true) public File DB_SNP
@Option(shortName="Q", doc="The minimum base quality score for a base to be included in analysis.") public int MINIMUM_QUALITY_SCORE
@Option(shortName="MQ", doc="The minimum mapping quality score for a base to be included in analysis.") public int MINIMUM_MAPPING_QUALITY
@Option(shortName="MIN_INS", doc="The minimum insert size for a read to be included in analysis.") public int MINIMUM_INSERT_SIZE
@Option(shortName="MAX_INS", doc="The maximum insert size for a read to be included in analysis. Set to 0 to have no maximum.") public int MAXIMUM_INSERT_SIZE
@Option(shortName="UNPAIRED", doc="Include unpaired reads. If set to true then all paired reads will be included as well - MINIMUM_INSERT_SIZE and MAXIMUM_INSERT_SIZE will be ignored.") public boolean INCLUDE_UNPAIRED
@Option(shortName="DUPES", doc="Include duplicate reads. If set to true then all reads flagged as duplicates will be included as well.") public boolean INCLUDE_DUPLICATES
@Option(shortName="NON_PF", doc="Whether or not to include non-PF reads.") public boolean INCLUDE_NON_PF_READS
@Option(shortName="TANDEM", doc="Set to true if mate pairs are being sequenced from the same strand, i.e. they\'re expected to face the same direction.") public boolean TANDEM_READS
@Option(doc="When available, use original quality scores for filtering.") public boolean USE_OQ
@Option(doc="The number of context bases to include on each side of the assayed base.") public int CONTEXT_SIZE
@Option(doc="If specified, only print results for these contexts in the detail metrics output. However, the summary metrics output will still take all contexts into consideration.") public Set<String> CONTEXTS_TO_PRINT
protected String[] customCommandLineValidation()
CommandLineProgram
customCommandLineValidation
in class CommandLineProgram
protected void setup(htsjdk.samtools.SAMFileHeader header, File samFile)
SinglePassSamProgram
setup
in class SinglePassSamProgram
protected void acceptRead(htsjdk.samtools.SAMRecord rec, htsjdk.samtools.reference.ReferenceSequence ref)
SinglePassSamProgram
acceptRead
in class SinglePassSamProgram
protected void finish()
SinglePassSamProgram
finish
in class SinglePassSamProgram
protected boolean usesNoRefReads()
SinglePassSamProgram
usesNoRefReads
in class SinglePassSamProgram