public class UmiAwareMarkDuplicatesWithMateCigar extends SimpleMarkDuplicatesWithMateCigar
MarkDuplicates.DuplicateTaggingPolicy, MarkDuplicates.DuplicateType
AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator
Modifier and Type | Field and Description |
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boolean |
ALLOW_MISSING_UMIS |
String |
ASSIGNED_UMI_TAG |
int |
MAX_EDIT_DISTANCE_TO_JOIN |
String |
UMI_TAG_NAME |
BARCODE_TAG, DUPLICATE_TYPE_LIBRARY, DUPLICATE_TYPE_SEQUENCING, DUPLICATE_TYPE_TAG, libraryIdGenerator, MAX_FILE_HANDLES_FOR_READ_ENDS_MAP, MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP, READ_ONE_BARCODE_TAG, READ_TWO_BARCODE_TAG, REMOVE_SEQUENCING_DUPLICATES, SORTING_COLLECTION_SIZE_RATIO, TAGGING_POLICY
ASSUME_SORT_ORDER, ASSUME_SORTED, COMMENT, DUPLICATE_SCORING_STRATEGY, INPUT, METRICS_FILE, OUTPUT, pgIdsSeen, PROGRAM_GROUP_COMMAND_LINE, PROGRAM_GROUP_NAME, PROGRAM_GROUP_VERSION, PROGRAM_RECORD_ID, 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 and Description |
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UmiAwareMarkDuplicatesWithMateCigar() |
Modifier and Type | Method and Description |
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protected htsjdk.samtools.util.CloseableIterator<htsjdk.samtools.DuplicateSet> |
getDuplicateSetIterator(AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator headerAndIterator,
htsjdk.samtools.SAMRecordDuplicateComparator comparator) |
doWork, main
finalizeAndWriteMetrics, getChainedPgIds, openInputs, trackOpticalDuplicates
customCommandLineValidation, setupOpticalDuplicateFinder
getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders
@Option(shortName="MAX_EDIT_DISTANCE_TO_JOIN", doc="Largest edit distance that UMIs must have in order to be considered as coming from distinct source molecules.", optional=true) public int MAX_EDIT_DISTANCE_TO_JOIN
@Option(shortName="UMI_TAG_NAME", doc="Tag name to use for UMI", optional=true) public String UMI_TAG_NAME
@Option(shortName="ASSIGNED_UMI_TAG", doc="Tag name to use for assigned UMI", optional=true) public String ASSIGNED_UMI_TAG
@Option(doc="FOR TESTING ONLY: allow for missing UMIs if data doesn\'t have UMIs. This option is intended to be used ONLY for testing the code. Use MarkDuplicatesWithMateCigar if data has no UMIs. Mixed data (where some reads have UMIs and others do not) is not supported.", optional=true) public boolean ALLOW_MISSING_UMIS
protected htsjdk.samtools.util.CloseableIterator<htsjdk.samtools.DuplicateSet> getDuplicateSetIterator(AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator headerAndIterator, htsjdk.samtools.SAMRecordDuplicateComparator comparator)
getDuplicateSetIterator
in class SimpleMarkDuplicatesWithMateCigar