public abstract class AbstractOpticalDuplicateFinderCommandLineProgram extends CommandLineProgram
Modifier and Type | Field and Description |
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protected static htsjdk.samtools.util.Log |
LOG |
long |
MAX_OPTICAL_DUPLICATE_SET_SIZE |
int |
OPTICAL_DUPLICATE_PIXEL_DISTANCE |
protected OpticalDuplicateFinder |
opticalDuplicateFinder |
java.lang.String |
READ_NAME_REGEX |
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
Constructor and Description |
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AbstractOpticalDuplicateFinderCommandLineProgram() |
Modifier and Type | Method and Description |
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protected java.lang.String[] |
customCommandLineValidation()
Put any custom command-line validation in an override of this method.
|
void |
setupOpticalDuplicateFinder() |
doWork, getCommandLine, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
protected static htsjdk.samtools.util.Log LOG
@Argument(doc="Regular expression that can be used to parse read names in the incoming SAM file. Read names are parsed to extract three variables: tile/region, x coordinate and y coordinate. These values are used to estimate the rate of optical duplication in order to give a more accurate estimated library size. Set this option to null to disable optical duplicate detection, e.g. for RNA-seq or other data where duplicate sets are extremely large and estimating library complexity is not an aim. Note that without optical duplicate counts, library size estimation will be inaccurate. The regular expression should contain three capture groups for the three variables, in order. It must match the entire read name. Note that if the default regex is specified, a regex match is not actually done, but instead the read name is split on colon character. For 5 element names, the 3rd, 4th and 5th elements are assumed to be tile, x and y values. For 7 element names (CASAVA 1.8), the 5th, 6th, and 7th elements are assumed to be tile, x and y values.", optional=true) public java.lang.String READ_NAME_REGEX
@Argument(doc="The maximum offset between two duplicate clusters in order to consider them optical duplicates. The default is appropriate for unpatterned versions of the Illumina platform. For the patterned flowcell models, 2500 is moreappropriate. For other platforms and models, users should experiment to find what works best.") public int OPTICAL_DUPLICATE_PIXEL_DISTANCE
@Argument(doc="This number is the maximum size of a set of duplicate reads for which we will attempt to determine which are optical duplicates. Please be aware that if you raise this value too high and do encounter a very large set of duplicate reads, it will severely affect the runtime of this tool. To completely disable this check, set the value to -1.") public long MAX_OPTICAL_DUPLICATE_SET_SIZE
protected OpticalDuplicateFinder opticalDuplicateFinder
public AbstractOpticalDuplicateFinderCommandLineProgram()
public void setupOpticalDuplicateFinder()
protected java.lang.String[] customCommandLineValidation()
CommandLineProgram
customCommandLineValidation
in class CommandLineProgram