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
protected htsjdk.samtools.util.CloseableIterator<htsjdk.samtools.DuplicateSet> getDuplicateSetIterator(AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator headerAndIterator, htsjdk.samtools.SAMRecordDuplicateComparator comparator)
getDuplicateSetIterator
in class SimpleMarkDuplicatesWithMateCigar