picard.illumina.quality

Class CollectHiSeqXPfFailMetrics

java.lang.Object

picard.cmdline.CommandLineProgram

picard.illumina.quality.CollectHiSeqXPfFailMetrics

public class CollectHiSeqXPfFailMetrics
extends CommandLineProgram

Collect metrics regarding the reason for reads (sequenced by HiSeqX) not passing the Illumina PF Filter. (BETA)

Author:

Yossi Farjoun

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	CollectHiSeqXPfFailMetrics.PFFailDetailedMetric a metric class for describing FP failing reads from an Illumina HiSeqX lane *
static class	CollectHiSeqXPfFailMetrics.PFFailSummaryMetric Metrics produced by the GetHiSeqXPFFailMetrics program.
protected static class	CollectHiSeqXPfFailMetrics.ReadClassifier

Field Summary

Fields

Modifier and Type	Field and Description
java.io.File	BASECALLS_DIR
static java.lang.String	detailedMetricsExtension
java.lang.Integer	LANE
int	N_CYCLES
int	NUM_PROCESSORS
java.io.File	OUTPUT
double	PROB_EXPLICIT_READS
static java.lang.String	summaryMetricsExtension

Fields inherited from class picard.cmdline.CommandLineProgram

COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY

Constructor Summary

Constructors

Constructor and Description
CollectHiSeqXPfFailMetrics()

Method Summary

Modifier and Type	Method and Description
protected java.lang.String[]	customCommandLineValidation() Put any custom command-line validation in an override of this method.
protected int	doWork() Do the work after command line has been parsed.
static void	main(java.lang.String[] args) Stock main method.

Methods inherited from class picard.cmdline.CommandLineProgram

getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders

Methods inherited from class java.lang.Object

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

Field Detail

BASECALLS_DIR

@Option(doc="The Illumina basecalls directory. ",
        shortName="B")
public java.io.File BASECALLS_DIR

OUTPUT

@Option(shortName="O",
        doc="Basename for metrics file. Resulting file will be <OUTPUT>.pffail_summary_metrics",
        optional=false)
public java.io.File OUTPUT

PROB_EXPLICIT_READS

@Option(shortName="P",
        doc="The fraction of (non-PF) reads for which to output explicit classification. Output file will be <OUTPUT>.pffail_detailed_metrics (if PROB_EXPLICIT_READS != 0)",
        optional=true)
public double PROB_EXPLICIT_READS

LANE

@Option(doc="Lane number.",
        shortName="L")
public java.lang.Integer LANE

NUM_PROCESSORS

@Option(shortName="NP",
        doc="Run this many PerTileBarcodeExtractors in parallel.  If NUM_PROCESSORS = 0, number of cores is automatically set to the number of cores available on the machine. If NUM_PROCESSORS < 0 then the number of cores used will be the number available on the machine less NUM_PROCESSORS.",
        optional=true)
public int NUM_PROCESSORS

N_CYCLES

@Option(doc="Number of cycles to look at. At time of writing PF status gets determined at cycle 24 so numbers greater than this will yield strange results. In addition, PF status is currently determined at cycle 24, so running this with any other value is neither tested nor recommended.",
        optional=true)
public int N_CYCLES

detailedMetricsExtension

public static final java.lang.String detailedMetricsExtension

See Also:

Constant Field Values

summaryMetricsExtension

public static final java.lang.String summaryMetricsExtension

See Also:

Constant Field Values

Constructor Detail

CollectHiSeqXPfFailMetrics

public CollectHiSeqXPfFailMetrics()

Method Detail

customCommandLineValidation

protected java.lang.String[] customCommandLineValidation()

Description copied from class: CommandLineProgram

Put any custom command-line validation in an override of this method. clp is initialized at this point and can be used to print usage and access argv. Any options set by command-line parser can be validated.

Overrides:

customCommandLineValidation in class CommandLineProgram

Returns:

null if command line is valid. If command line is invalid, returns an array of error message to be written to the appropriate place.

main

public static void main(java.lang.String[] args)

Stock main method.

doWork

protected int doWork()

Description copied from class: CommandLineProgram

Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.

Specified by:

doWork in class CommandLineProgram

Returns:

program exit status.