Package picard.analysis

Class CollectOxoGMetrics

java.lang.Object

picard.cmdline.CommandLineProgram

picard.analysis.CollectOxoGMetrics

@DocumentedFeature
public class CollectOxoGMetrics
extends CommandLineProgram

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

Nested Class Summary

Nested Classes

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

Field Summary

Fields

Modifier and Type	Field	Description
int	CONTEXT_SIZE
Set<String>	CONTEXTS
File	DB_SNP
boolean	INCLUDE_NON_PF_READS
File	INPUT
File	INTERVALS
int	MAXIMUM_INSERT_SIZE
int	MINIMUM_INSERT_SIZE
int	MINIMUM_MAPPING_QUALITY
int	MINIMUM_QUALITY_SCORE
File	OUTPUT
int	STOP_AFTER
boolean	USE_OQ

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
CollectOxoGMetrics()

Method Summary

Modifier and Type	Method	Description
protected 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.
protected boolean	requiresReference()

Methods inherited from class picard.cmdline.CommandLineProgram

checkRInstallation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, 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="Input SAM/BAM/CRAM file for analysis.")
public File INPUT

OUTPUT

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

INTERVALS

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

DB_SNP

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

MINIMUM_QUALITY_SCORE

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

MINIMUM_MAPPING_QUALITY

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

MINIMUM_INSERT_SIZE

@Argument(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

@Argument(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

INCLUDE_NON_PF_READS

@Argument(shortName="NON_PF",
          doc="Whether or not to include non-PF reads.")
public boolean INCLUDE_NON_PF_READS

USE_OQ

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

CONTEXT_SIZE

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

CONTEXTS

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

STOP_AFTER

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

Constructor Details

CollectOxoGMetrics

public CollectOxoGMetrics()

Method Details

requiresReference

protected boolean requiresReference()

Overrides:

requiresReference in class CommandLineProgram

customCommandLineValidation

protected 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.