public class MarkDuplicates extends AbstractMarkDuplicatesCommandLineProgram
AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator
Modifier and Type | Field and Description |
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protected LibraryIdGenerator |
libraryIdGenerator |
int |
MAX_FILE_HANDLES_FOR_READ_ENDS_MAP |
int |
MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP
If more than this many sequences in SAM file, don't spill to disk because there will not
be enough file handles.
|
double |
SORTING_COLLECTION_SIZE_RATIO |
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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MarkDuplicates() |
Modifier and Type | Method and Description |
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protected int |
doWork()
Main work method.
|
static void |
main(String[] args)
Stock main method.
|
finalizeAndWriteMetrics, getChainedPgIds, openInputs, trackOpticalDuplicates
customCommandLineValidation, setupOpticalDuplicateFinder
getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders
@Option(shortName="MAX_SEQS", doc="This option is obsolete. ReadEnds will always be spilled to disk.") public int MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP
@Option(shortName="MAX_FILE_HANDLES", doc="Maximum number of file handles to keep open when spilling read ends to disk. Set this number a little lower than the per-process maximum number of file that may be open. This number can be found by executing the \'ulimit -n\' command on a Unix system.") public int MAX_FILE_HANDLES_FOR_READ_ENDS_MAP
@Option(doc="This number, plus the maximum RAM available to the JVM, determine the memory footprint used by some of the sorting collections. If you are running out of memory, try reducing this number.") public double SORTING_COLLECTION_SIZE_RATIO
protected LibraryIdGenerator libraryIdGenerator
public static void main(String[] args)
protected int doWork()
doWork
in class CommandLineProgram