Package picard.analysis

Class CollectJumpingLibraryMetrics

java.lang.Object

picard.cmdline.CommandLineProgram

picard.analysis.CollectJumpingLibraryMetrics

@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.

Field Summary

Fields

Modifier and Type	Field	Description
int	CHIMERA_KB_MIN
List<File>	INPUT
Integer	MINIMUM_MAPPING_QUALITY
File	OUTPUT
int	TAIL_LIMIT

Fields inherited from class picard.cmdline.CommandLineProgram

COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, MAX_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, SYNTAX_TRANSITION_URL, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY

Constructor Summary

Constructors

Constructor	Description
CollectJumpingLibraryMetrics()

Method Summary

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

checkRInstallation, customCommandLineValidation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

INPUT

@Argument(shortName="I",
          doc="BAM file(s) of reads with duplicates marked")
public List<File> INPUT

OUTPUT

@Argument(shortName="O",
          doc="File to which metrics should be written")
public File OUTPUT

MINIMUM_MAPPING_QUALITY

@Argument(shortName="MQ",
          doc="Mapping quality minimum cutoff")
public Integer MINIMUM_MAPPING_QUALITY

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

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

Constructor Details

CollectJumpingLibraryMetrics

public CollectJumpingLibraryMetrics()

Method Details

doWork

protected int doWork()

Calculates the detailed statistics about the jumping library and then generates the results.

Specified by:

doWork in class CommandLineProgram

Returns:

program exit status.