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In attempt to reuse: --pairCountsOutput is now optional, if not specified then only per-locus statistics is collected; --silent - do not echo results into stdout; --minMapQ - count only bases coming from reads mapped with specified quality or better; --blacklistedlanes - do not count reads/bases coming from specific lanes. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2761 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2010-02-01 22:05:19 +00:00
parent 2c4f709f6f
commit 4ddbaeed07
1 changed files with 37 additions and 21 deletions
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58
java/src/org/broadinstitute/sting/oneoffprojects/walkers/QualityScoreByStrandWalker.java
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@ -2,23 +2,22 @@ package org.broadinstitute.sting.oneoffprojects.walkers;
import java.io.IOException;
import org.broadinstitute.sting.utils.QualityUtils;
import org.broadinstitute.sting.utils.Pair;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.cmdLine.Argument;
import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.gatk.walkers.ReadFilters;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.playground.utils.PoolUtils;
import org.broadinstitute.sting.playground.gatk.walkers.poolseq.ReadOffsetQuad;
import sun.misc.Cache;
import org.broadinstitute.sting.gatk.filters.Platform454Filter;
import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter;
import org.broadinstitute.sting.gatk.filters.PlatformUnitFilter;
import org.broadinstitute.sting.gatk.filters.PlatformUnitFilterHelper;
import net.sf.samtools.SAMRecord;
import java.util.HashMap;
import java.io.PrintStream;
import java.io.PrintWriter;
/**
@ -35,15 +34,24 @@ import java.io.PrintWriter;
*
* @Author: Chris Hartl
*/
@ReadFilters({PlatformUnitFilter.class})
public class QualityScoreByStrandWalker extends LocusWalker<StrandedCounts,StrandedCounts> {
@Argument(fullName="readLength", shortName="rl", doc="Maximum length of the reads in the bam file", required=true)
int maxReadLength = -1;
@Argument(fullName="locusCountsOutput", shortName="lcf", doc="File to print locus count information to", required=true)
String locusOutput = null;
@Argument(fullName="pairCountsOutput", shortName="pcf", doc="File to print pair count information to", required=true)
@Argument(fullName="pairCountsOutput", shortName="pcf", doc="File to print pair count information to; when not specified pair count statistics is not collected", required=false)
String pairOutput = null;
@Argument(fullName="useCycle", shortName="c", doc="Use cycle directly rather than strand", required=false)
boolean useCycle = false;
@Argument(fullName="silent", shortName="s", doc="Don't echo results into stdout, just print them into the specified files.", required=false)
boolean silent= false;
@Argument(fullName="minMapQ",shortName="q",doc="Use only reads with mapping quality at or above this value.",required=false)
int MIN_MAPQ = -1;
@Argument(fullName="blacklistedLanes", shortName="BL",
doc="Name of lanes (platform units) that should be ignored. Reads coming from these lanes will never be seen "+
"by this application.", required=false)
PlatformUnitFilterHelper dummy;
public HashMap pairCache = new HashMap();
@ -63,10 +71,10 @@ public class QualityScoreByStrandWalker extends LocusWalker<StrandedCounts,Stran
}
public void updateCounts( StrandedCounts counts, AlignmentContext context, ReferenceContext ref ) {
ReadBackedPileup p = context.getPileup();
ReadBackedPileup p = context.getBasePileup().getMappingFilteredPileup(MIN_MAPQ);
for ( PileupElement e : p ) {
updateLocus(counts,e,ref);
updateReads(counts,e,ref);
if ( pairOutput != null ) updateReads(counts,e,ref);
}
}
@ -117,18 +125,26 @@ public class QualityScoreByStrandWalker extends LocusWalker<StrandedCounts,Stran
public void onTraversalDone(StrandedCounts finalCounts) {
try {
PrintWriter locusOut = new PrintWriter(locusOutput);
System.out.println("#$"); //delimeter
System.out.print(finalCounts.locusCountsAsString());
System.out.println("#$");
System.out.println("Unmatched reads="+pairCache.size());
System.out.println("#$");
locusOut.printf(finalCounts.locusCountsAsString());
PrintWriter pairOut = new PrintWriter(pairOutput);
pairOut.printf(finalCounts.pairCountsAsString());
System.out.println("#$");
System.out.print(finalCounts.pairCountsAsString());
System.out.print("#$");
if ( ! silent ) {
System.out.println("#$"); //delimeter
System.out.print(finalCounts.locusCountsAsString());
System.out.println("#$");
}
PrintWriter locusOut = new PrintWriter(locusOutput);
locusOut.print(finalCounts.locusCountsAsString());
locusOut.close();
if ( pairOutput != null ) {
if ( ! silent ) {
System.out.println("Unmatched reads="+pairCache.size());
System.out.println("#$");
System.out.println("#$");
System.out.print(finalCounts.pairCountsAsString());
System.out.print("#$");
}
PrintWriter pairOut = new PrintWriter(pairOutput);
pairOut.print(finalCounts.pairCountsAsString());
pairOut.close();
}
} catch ( IOException e ) {
throw new StingException("Outputfile could not be opened");
}