net.sf.picard.analysis
Class MeanQualityByCycle

java.lang.Object
  extended by net.sf.picard.cmdline.CommandLineProgram
      extended by net.sf.picard.analysis.SinglePassSamProgram
          extended by 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