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_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 Static 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.static void
main(String[] args)
Stock main method.-
Methods inherited from class picard.cmdline.CommandLineProgram
customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, 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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main
public static void main(String[] args)
Stock main method.
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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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