net.sf.picard.analysis
Class MeanQualityByCycle

java.lang.Object
  net.sf.picard.cmdline.CommandLineProgram
      net.sf.picard.analysis.SinglePassSamProgram
          net.sf.picard.analysis.MeanQualityByCycle

public class MeanQualityByCycle
extends SinglePassSamProgram

Program to generate a data table and chart of mean quality by cycle from a BAM file. Works best on a single lane/run of data, but can be applied to merged BAMs - the output may just be a little confusing.

Author:

Tim Fennell

Field Summary

boolean	ALIGNED_READS_ONLY
File	CHART_OUTPUT
boolean	PF_READS_ONLY
String	USAGE

Fields inherited from class net.sf.picard.analysis.SinglePassSamProgram

ASSUME_SORTED, INPUT, OUTPUT, REFERENCE_SEQUENCE, STOP_AFTER

Fields inherited from class net.sf.picard.cmdline.CommandLineProgram

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

Constructor Summary

MeanQualityByCycle()

Method Summary

protected void	acceptRead(SAMRecord rec, ReferenceSequence ref) Should be implemented by subclasses to accept SAMRecords one at a time.
protected void	finish() Should be implemented by subclasses to do one-time finalization work.
static void	main(String[] args) Required main method.
protected void	setup(SAMFileHeader header, File samFile) Should be implemented by subclasses to do one-time initialization work.

Methods inherited from class net.sf.picard.analysis.SinglePassSamProgram

doWork, makeItSo, usesNoRefReads

Methods inherited from class net.sf.picard.cmdline.CommandLineProgram

customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getProgramVersion, 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

USAGE

public final String USAGE

CHART_OUTPUT

@Option(shortName="CHART",
        doc="A file (with .pdf extension) to write the chart to.")
public File CHART_OUTPUT

ALIGNED_READS_ONLY

@Option(doc="If set to true, calculate mean quality over aligned reads only.")
public boolean ALIGNED_READS_ONLY

PF_READS_ONLY

@Option(doc="If set to true calculate mean quality over PF reads only.")
public boolean PF_READS_ONLY

Constructor Detail

MeanQualityByCycle

public MeanQualityByCycle()

Method Detail

main

public static void main(String[] args)

Required main method.

setup

protected void setup(SAMFileHeader header,
                     File samFile)

Description copied from class: SinglePassSamProgram

Should be implemented by subclasses to do one-time initialization work.

Specified by:

setup in class SinglePassSamProgram

acceptRead

protected void acceptRead(SAMRecord rec,
                          ReferenceSequence ref)

Description copied from class: SinglePassSamProgram

Should be implemented by subclasses to accept SAMRecords one at a time. If the read has a reference sequence and a reference sequence file was supplied to the program it will be passed as 'ref'. Otherwise 'ref' may be null.

Specified by:

acceptRead in class SinglePassSamProgram

finish

protected void finish()

Description copied from class: SinglePassSamProgram

Should be implemented by subclasses to do one-time finalization work.

Specified by:

finish in class SinglePassSamProgram