picard.analysis

Class CollectOxoGMetrics

java.lang.Object

picard.cmdline.CommandLineProgram

picard.analysis.CollectOxoGMetrics

public class CollectOxoGMetrics
extends CommandLineProgram

Class for trying to quantify the CpCG->CpCA error rate.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	CollectOxoGMetrics.CpcgMetrics Metrics class for outputs.

Field Summary

Fields

Modifier and Type	Field and Description
int	CONTEXT_SIZE
java.util.Set<java.lang.String>	CONTEXTS
java.io.File	DB_SNP
java.io.File	INPUT
java.io.File	INTERVALS
int	MAXIMUM_INSERT_SIZE
int	MINIMUM_INSERT_SIZE
int	MINIMUM_MAPPING_QUALITY
int	MINIMUM_QUALITY_SCORE
java.io.File	OUTPUT
java.io.File	REFERENCE_SEQUENCE
int	STOP_AFTER
boolean	USE_OQ

Fields inherited from class picard.cmdline.CommandLineProgram

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

Constructor Summary

Constructors

Constructor and Description
CollectOxoGMetrics()

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)

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

INPUT

@Option(shortName="I",
        doc="Input BAM file for analysis.")
public java.io.File INPUT

OUTPUT

@Option(shortName="O",
        doc="Location of output metrics file to write.")
public java.io.File OUTPUT

REFERENCE_SEQUENCE

@Option(shortName="R",
        doc="Reference sequence to which BAM is aligned.")
public java.io.File REFERENCE_SEQUENCE

INTERVALS

@Option(doc="An optional list of intervals to restrict analysis to.",
        optional=true)
public java.io.File INTERVALS

DB_SNP

@Option(doc="VCF format dbSNP file, used to exclude regions around known polymorphisms from analysis.",
        optional=true)
public java.io.File DB_SNP

MINIMUM_QUALITY_SCORE

@Option(shortName="Q",
        doc="The minimum base quality score for a base to be included in analysis.")
public int MINIMUM_QUALITY_SCORE

MINIMUM_MAPPING_QUALITY

@Option(shortName="MQ",
        doc="The minimum mapping quality score for a base to be included in analysis.")
public int MINIMUM_MAPPING_QUALITY

MINIMUM_INSERT_SIZE

@Option(shortName="MIN_INS",
        doc="The minimum insert size for a read to be included in analysis. Set of 0 to allow unpaired reads.")
public int MINIMUM_INSERT_SIZE

MAXIMUM_INSERT_SIZE

@Option(shortName="MAX_INS",
        doc="The maximum insert size for a read to be included in analysis. Set of 0 to allow unpaired reads.")
public int MAXIMUM_INSERT_SIZE

USE_OQ

@Option(doc="When available, use original quality scores for filtering.")
public boolean USE_OQ

CONTEXT_SIZE

@Option(doc="The number of context bases to include on each side of the assayed G/C base.")
public int CONTEXT_SIZE

CONTEXTS

@Option(doc="The optional set of sequence contexts to restrict analysis to. If not supplied all contexts are analyzed.")
public java.util.Set<java.lang.String> CONTEXTS

STOP_AFTER

@Option(doc="For debugging purposes: stop after visiting this many sites with at least 1X coverage.")
public int STOP_AFTER

Constructor Detail

CollectOxoGMetrics

public CollectOxoGMetrics()

Method Detail

main

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

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.

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.