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add RunCoveredByNSamplesSites; changes in CoveredByNSamplesSites so it can work in parallel; also, move it to diagnostics

This commit is contained in:
Ami Levy-Moonshine 2013-01-10 21:26:49 -05:00
parent 15ca5015cd
commit fac0bce916
2 changed files with 24 additions and 55 deletions
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74
public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoveredByNSamplesSites.java → public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/CoveredByNSamplesSites.java
View File

@ -1,6 +1,7 @@
package org.broadinstitute.sting.gatk.walkers.coverage;
package org.broadinstitute.sting.gatk.walkers.diagnostics;
import ca.mcgill.mcb.pcingola.interval.Intron;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.ArgumentCollection;
import org.broadinstitute.sting.commandline.Output;
@ -52,10 +53,10 @@ import java.util.List;
*/
@By(DataSource.REFERENCE_ORDERED_DATA)
public class CoveredByNSamplesSites extends RodWalker<Pair<Integer,Integer>, Pair<Integer,Integer>> implements TreeReducible<Pair<Integer,Integer>> {
public class CoveredByNSamplesSites extends RodWalker<GenomeLoc, Integer> implements TreeReducible<Integer> {
@Output(fullName = "OutputIntervals", shortName = "out", doc = "Name of file for output intervals", required = true)
File intervalsFile;
PrintStream outputStream;
@ArgumentCollection
protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
@ -66,38 +67,18 @@ public class CoveredByNSamplesSites extends RodWalker<Pair<Integer,Integer>, Pai
@Argument(fullName = "precentageOfSamples", shortName = "percentage", doc = "only sites where at list percentageOfSamples of the samples have good coverage, will be emited", required = false)
double percentageOfSamples = 0.9;
private FileOutputStream outputStream;
@Override
public void initialize(){
if (! intervalsFile.getName().endsWith(".intervals")){
throw new UserException(String.format("Output interval file %s should be <name>.intervals", intervalsFile));
}
try{
outputStream = new FileOutputStream(intervalsFile);
if (!intervalsFile.exists()) {
intervalsFile.createNewFile();
}
}
catch (IOException e){
System.err.println(String.format("Problems with creating outputStream from %s",intervalsFile));
e.printStackTrace();
}
}
@Override
public Pair<Integer,Integer> map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
public GenomeLoc map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if ( tracker == null )
return new Pair<Integer, Integer>(0,0);
return null;
Collection<VariantContext> VCs = tracker.getValues(variantCollection.variants, context.getLocation());
if ( VCs.size() == 0 )
return new Pair<Integer, Integer>(0,0);
return null;
if(VCs.size() != 1)
throw new RuntimeException("there are more then one vc: "+VCs.size());
boolean emitSite = false;
List<GenomeLoc> outputIntervals = new ArrayList<GenomeLoc>();
for(VariantContext vc : VCs){
int coveredSamples = 0;
final GenotypesContext genotypes = vc.getGenotypes();
@ -108,49 +89,38 @@ public class CoveredByNSamplesSites extends RodWalker<Pair<Integer,Integer>, Pai
}
if((double)coveredSamples/numOfGenotypes > percentageOfSamples){
emitSite = true;
outputIntervals.add(ref.getLocus());
//System.out.println(ref.getLocus());
try{
String toPrint = ref.getLocus().toString() + "\n";
outputStream.write(toPrint.getBytes());
}catch (IOException e){
e.printStackTrace();
}
}
}
if (emitSite)
return new Pair<Integer, Integer>(1,1);
return ref.getLocus();
else
return new Pair<Integer, Integer>(1,0);
return null;
}
@Override
public Pair<Integer,Integer> reduceInit() { return new Pair<Integer, Integer>(0,0); }
public Integer reduceInit() { return 0; }
@Override
public Pair<Integer,Integer> reduce(Pair<Integer,Integer> value, Pair<Integer,Integer> sum) { return new Pair<Integer, Integer>(value.getFirst() + sum.getFirst(),value.getSecond()+sum.getSecond()); }
public Integer reduce(GenomeLoc value, Integer sum) {
if ( value != null ) {
outputStream.println(value);
sum++;
}
return sum;
}
@Override
public Pair<Integer,Integer> treeReduce(Pair<Integer,Integer> lhs, Pair<Integer,Integer> rhs) {
return new Pair<Integer, Integer>(lhs.getFirst() + rhs.getFirst(),lhs.getSecond() + rhs.getSecond());
public Integer treeReduce(Integer lhs, Integer rhs) {
return lhs + rhs;
}
/**
* Tell the user the number of sites processed and how many passed. Close out the new intervals file.
*
* @param result pair of the number of sites seen and number of sites passed the filter.
* @param result pair of *the number of sites seen and number of sites passed the filter.
*/
public void onTraversalDone(Pair<Integer,Integer> result) {
logger.info("Processed " + result.getFirst() + " variant sites and found "+ result.getSecond()+" sites that have "+(percentageOfSamples*100)+"% of the samples with at list "+minCoverage+" coverage.\n");
logger.info("All these sites were printed to the intervals file: "+intervalsFile.getAbsolutePath());
try{
outputStream.close();
}
catch (IOException e){
System.err.println("Couldn't close output steam properly");
e.printStackTrace();
}
public void onTraversalDone(Integer result) {
logger.info(result+" sites that have "+(percentageOfSamples*100)+"% of the samples with at list "+minCoverage+" coverage.\n");
}

5
public/scala/src/org/broadinstitute/sting/queue/extensions/gatk/CatVariantsGatherer.scala
View File

@ -1,9 +1,8 @@
package org.broadinstitute.sting.queue.extensions.gatk
import org.broadinstitute.sting.queue.function.{RetryMemoryLimit, JavaCommandLineFunction}
import org.broadinstitute.sting.queue.function.RetryMemoryLimit
import org.broadinstitute.sting.queue.function.scattergather.GatherFunction
import org.broadinstitute.sting.queue.util.ClassFieldCache
import org.broadinstitute.sting.gatk.io.stubs.VCFWriterArgumentTypeDescriptor
/**
* Created with IntelliJ IDEA.