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Merge pull request #460 from broadinstitute/mc_document_readclippingstats 

Better documentation for ReadClippingStats walker
This commit is contained in:
Eric Banks 2014-01-01 16:00:40 -08:00
parent 154bab0849 d1febb89c8
commit ece346689c
1 changed files with 31 additions and 23 deletions
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54
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStats.java
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@ -26,8 +26,8 @@
package org.broadinstitute.sting.gatk.walkers.qc;
import net.sf.samtools.CigarElement;
import net.sf.samtools.CigarOperator;
import net.sf.samtools.SAMReadGroupRecord;
import org.broadinstitute.sting.commandline.Advanced;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.CommandLineGATK;
@ -48,39 +48,53 @@ import java.io.PrintStream;
import java.util.Arrays;
/**
* Read clipping statistics for all reads.
*
* Walks over the input reads, printing out statistics about the read length, number of clipping events, and length
* of the clipping to the output stream.
*
* Note: Ignores N's in the Cigar string.
*
* <h3>Input</h3>
* One or more BAM files
*
* <h3>Output</h3>
* A simple tabulated text file with read length and clipping statistics for every read (or every N reads if the "skip"
* option is used)
*
* User: depristo
* Date: May 5, 2010
* Time: 12:16:41 PM
*/
/**
* Walks over the input reads, printing out statistics about the read length, number of clipping events, and length
* of the clipping to the output stream.
*/
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )
@Requires({DataSource.READS})
public class ReadClippingStats extends ReadWalker<ReadClippingStats.ReadClippingInfo,Integer> {
@Output
protected PrintStream out;
@Argument(fullName="mappedOnly", shortName="mo", doc="when this flag is set (default), statistics will be collected "+
"on mapped reads only, while unmapped reads will be discarded", required=false)
protected boolean MAPPED_ONLY = true;
/**
* when this flag is set (default), statistics will be collected on unmapped reads as well. The default behavior
* is to ignore unmapped reads."
*/
@Argument(fullName="include_unmapped", shortName="u", doc="Include unmapped reads in the analysis", required=false)
protected boolean INCLUDE_UNMAPPED = false;
@Argument(fullName="skip", shortName="skip", doc="When provided, only every skip reads are analyzed", required=false)
/**
* print every read whose read number is divisible by SKIP. READ_NUMBER % SKIP == 0. First read in the file has read number = 1,
* second is 2, third is 3, ... A value of 1 means print every read. A value of 1000 means print every 1000th read.
*/
@Advanced
@Argument(fullName="skip", shortName="skip", doc="Do not print all reads, skip some.", required=false)
protected int SKIP = 1;
// public void initialize() {
//
// }
public class ReadClippingInfo {
SAMReadGroupRecord rg;
int readLength, nClippingEvents, nClippedBases;
}
public ReadClippingInfo map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker metaDataTracker) {
if ( AlignmentUtils.isReadUnmapped(read) && MAPPED_ONLY)
if ( AlignmentUtils.isReadUnmapped(read) && !INCLUDE_UNMAPPED)
return null;
ReadClippingInfo info = new ReadClippingInfo();
@ -89,24 +103,21 @@ public class ReadClippingStats extends ReadWalker<ReadClippingStats.ReadClipping
if ( info.rg == null ) throw new UserException.ReadMissingReadGroup(read);
for ( CigarElement elt : read.getCigar().getCigarElements() ) {
if ( elt.getOperator() != CigarOperator.N )
switch ( elt.getOperator()) {
case H : // ignore hard clips
case S : // soft clip
info.nClippingEvents++;
info.nClippedBases += elt.getLength();
// note the fall through here
break;
case M :
case D : // deletion w.r.t. the reference
case P : // ignore pads
case I : // insertion w.r.t. the reference
info.readLength += elt.getLength(); // Unless we have a reference skip, the read gets longer
break;
case N : // reference skip (looks and gets processed just like a "deletion", just different logical meaning)
break;
default : throw new IllegalStateException("Case statement didn't deal with cigar op: " + elt.getOperator());
}
info.readLength = read.getReadLength();
}
return info; //To change body of implemented methods use File | Settings | File Templates.
@ -137,13 +148,10 @@ public class ReadClippingStats extends ReadWalker<ReadClippingStats.ReadClipping
id, info.readLength, info.nClippingEvents, info.nClippedBases,
100.0 * MathUtils.ratio(info.nClippedBases, info.readLength));
}
return sum + 1; //To change body of implemented methods use File | Settings | File Templates.
return sum + 1;
} else {
return sum;
}
}
public void onTraversalDone(Integer result) {
}
}