picard.illumina

Class MarkIlluminaAdapters

java.lang.Object

picard.cmdline.CommandLineProgram

picard.illumina.MarkIlluminaAdapters

public class MarkIlluminaAdapters
extends CommandLineProgram

Command line program to mark the location of adapter sequences. This also outputs a Histogram of metrics describing the clipped bases

Author:

Tim Fennell (adapted by mborkan@broadinstitute.org)

Field Summary

Fields

Modifier and Type	Field and Description
int	ADAPTER_TRUNCATION_LENGTH
java.util.List<IlluminaUtil.IlluminaAdapterPair>	ADAPTERS
java.lang.String	FIVE_PRIME_ADAPTER
java.io.File	INPUT
double	MAX_ERROR_RATE_PE
double	MAX_ERROR_RATE_SE
java.io.File	METRICS
int	MIN_MATCH_BASES_PE
int	MIN_MATCH_BASES_SE
int	NUM_ADAPTERS_TO_KEEP
java.io.File	OUTPUT
java.lang.Boolean	PAIRED_RUN
int	PRUNE_ADAPTER_LIST_AFTER_THIS_MANY_ADAPTERS_SEEN
java.lang.String	THREE_PRIME_ADAPTER

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
MarkIlluminaAdapters()

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")
public java.io.File INPUT

OUTPUT

@Option(doc="If output is not specified, just the metrics are generated",
        shortName="O",
        optional=true)
public java.io.File OUTPUT

METRICS

@Option(doc="Histogram showing counts of bases_clipped in how many reads",
        shortName="M")
public java.io.File METRICS

MIN_MATCH_BASES_SE

@Option(doc="The minimum number of bases to match over when clipping single-end reads.")
public int MIN_MATCH_BASES_SE

MIN_MATCH_BASES_PE

@Option(doc="The minimum number of bases to match over (per-read) when clipping paired-end reads.")
public int MIN_MATCH_BASES_PE

MAX_ERROR_RATE_SE

@Option(doc="The maximum mismatch error rate to tolerate when clipping single-end reads.")
public double MAX_ERROR_RATE_SE

MAX_ERROR_RATE_PE

@Option(doc="The maximum mismatch error rate to tolerate when clipping paired-end reads.")
public double MAX_ERROR_RATE_PE

PAIRED_RUN

@Option(doc="DEPRECATED. Whether this is a paired-end run. No longer used.",
        shortName="PE",
        optional=true)
public java.lang.Boolean PAIRED_RUN

ADAPTERS

@Option(doc="Which adapters sequences to attempt to identify and clip.")
public java.util.List<IlluminaUtil.IlluminaAdapterPair> ADAPTERS

FIVE_PRIME_ADAPTER

@Option(doc="For specifying adapters other than standard Illumina",
        optional=true)
public java.lang.String FIVE_PRIME_ADAPTER

THREE_PRIME_ADAPTER

@Option(doc="For specifying adapters other than standard Illumina",
        optional=true)
public java.lang.String THREE_PRIME_ADAPTER

ADAPTER_TRUNCATION_LENGTH

@Option(doc="Adapters are truncated to this length to speed adapter matching.  Set to a large number to effectively disable truncation.")
public int ADAPTER_TRUNCATION_LENGTH

PRUNE_ADAPTER_LIST_AFTER_THIS_MANY_ADAPTERS_SEEN

@Option(doc="If looking for multiple adapter sequences, then after having seen this many adapters, shorten the list of sequences. Keep the adapters that were found most frequently in the input so far. Set to -1 if the input has a heterogeneous mix of adapters so shortening is undesirable.",
        shortName="APT")
public int PRUNE_ADAPTER_LIST_AFTER_THIS_MANY_ADAPTERS_SEEN

NUM_ADAPTERS_TO_KEEP

@Option(doc="If pruning the adapter list, keep only this many adapter sequences when pruning the list (plus any adapters that were tied with the adapters being kept).")
public int NUM_ADAPTERS_TO_KEEP

Constructor Detail

MarkIlluminaAdapters

public MarkIlluminaAdapters()

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.