Package picard.analysis
Class CollectJumpingLibraryMetrics
- java.lang.Object
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- picard.cmdline.CommandLineProgram
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- picard.analysis.CollectJumpingLibraryMetrics
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@DocumentedFeature public class CollectJumpingLibraryMetrics extends CommandLineProgram
Command-line program to compute metrics about outward-facing pairs, inward-facing pairs, and chimeras in a jumping library.
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Field Summary
Fields Modifier and Type Field Description int
CHIMERA_KB_MIN
List<File>
INPUT
Integer
MINIMUM_MAPPING_QUALITY
File
OUTPUT
int
TAIL_LIMIT
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Fields inherited from class picard.cmdline.CommandLineProgram
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
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Constructor Summary
Constructors Constructor Description CollectJumpingLibraryMetrics()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected int
doWork()
Calculates the detailed statistics about the jumping library and then generates the results.-
Methods inherited from class picard.cmdline.CommandLineProgram
customCommandLineValidation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
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Field Detail
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INPUT
@Argument(shortName="I", doc="BAM file(s) of reads with duplicates marked") public List<File> INPUT
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OUTPUT
@Argument(shortName="O", doc="File to which metrics should be written") public File OUTPUT
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MINIMUM_MAPPING_QUALITY
@Argument(shortName="MQ", doc="Mapping quality minimum cutoff") public Integer MINIMUM_MAPPING_QUALITY
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TAIL_LIMIT
@Argument(shortName="T", doc="When calculating mean and stdev stop when the bins in the tail of the distribution contain fewer than mode/TAIL_LIMIT items") public int TAIL_LIMIT
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CHIMERA_KB_MIN
@Argument(doc="Jumps greater than or equal to the greater of this value or 2 times the mode of the outward-facing pairs are considered chimeras") public int CHIMERA_KB_MIN
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Method Detail
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doWork
protected int doWork()
Calculates the detailed statistics about the jumping library and then generates the results.- Specified by:
doWork
in classCommandLineProgram
- Returns:
- program exit status.
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