picard.analysis

Class CollectRrbsMetrics

java.lang.Object

picard.cmdline.CommandLineProgram

picard.analysis.CollectRrbsMetrics

@DocumentedFeature
public class CollectRrbsMetrics
extends CommandLineProgram

Calculates and reports QC metrics for RRBS data based on the methylation status at individual C/G bases as well as CpG sites across all reads in the input BAM/SAM file.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	CollectRrbsMetrics.CollectRrbsMetricsReferenceArgumentCollection

Field Summary

Fields

Modifier and Type	Field and Description
boolean	ASSUME_SORTED
int	C_QUALITY_THRESHOLD
static java.lang.String	DETAIL_FILE_EXTENSION
java.io.File	INPUT
double	MAX_MISMATCH_RATE
java.util.Set<MetricAccumulationLevel>	METRIC_ACCUMULATION_LEVEL
java.lang.String	METRICS_FILE_PREFIX
int	MINIMUM_READ_LENGTH
int	NEXT_BASE_QUALITY_THRESHOLD
static java.lang.String	PDF_FILE_EXTENSION
java.util.Set<java.lang.String>	SEQUENCE_NAMES
static java.lang.String	SUMMARY_FILE_EXTENSION

Fields inherited from class picard.cmdline.CommandLineProgram

COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY

Constructor Summary

Constructors

Constructor and Description
CollectRrbsMetrics()

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.
protected ReferenceArgumentCollection	makeReferenceArgumentCollection()

Methods inherited from class picard.cmdline.CommandLineProgram

getCommandLine, getCommandLineParser, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser

Methods inherited from class java.lang.Object

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

Field Detail

INPUT

@Argument(doc="The BAM or SAM file containing aligned reads. Must be coordinate sorted",
          shortName="I")
public java.io.File INPUT

METRICS_FILE_PREFIX

@Argument(doc="Base name for output files",
          shortName="M")
public java.lang.String METRICS_FILE_PREFIX

MINIMUM_READ_LENGTH

@Argument(doc="Minimum read length")
public int MINIMUM_READ_LENGTH

C_QUALITY_THRESHOLD

@Argument(doc="Threshold for base quality of a C base before it is considered")
public int C_QUALITY_THRESHOLD

NEXT_BASE_QUALITY_THRESHOLD

@Argument(doc="Threshold for quality of a base next to a C before the C base is considered")
public int NEXT_BASE_QUALITY_THRESHOLD

MAX_MISMATCH_RATE

@Argument(doc="Maximum percentage of mismatches in a read for it to be considered, with a range of 0-1")
public double MAX_MISMATCH_RATE

SEQUENCE_NAMES

@Argument(doc="Set of sequence names to consider, if not specified all sequences will be used",
          optional=true)
public java.util.Set<java.lang.String> SEQUENCE_NAMES

ASSUME_SORTED

@Argument(shortName="AS",
          doc="If true, assume that the input file is coordinate sorted even if the header says otherwise.")
public boolean ASSUME_SORTED

METRIC_ACCUMULATION_LEVEL

@Argument(shortName="LEVEL",
          doc="The level(s) at which to accumulate metrics.  ")
public java.util.Set<MetricAccumulationLevel> METRIC_ACCUMULATION_LEVEL

DETAIL_FILE_EXTENSION

public static final java.lang.String DETAIL_FILE_EXTENSION

See Also:

Constant Field Values

SUMMARY_FILE_EXTENSION

public static final java.lang.String SUMMARY_FILE_EXTENSION

See Also:

Constant Field Values

PDF_FILE_EXTENSION

public static final java.lang.String PDF_FILE_EXTENSION

See Also:

Constant Field Values

Constructor Detail

CollectRrbsMetrics

public CollectRrbsMetrics()

Method Detail

makeReferenceArgumentCollection

protected ReferenceArgumentCollection makeReferenceArgumentCollection()

Overrides:

makeReferenceArgumentCollection in class CommandLineProgram

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.

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.