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added filter based on concordance to another call set 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1432 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-08-18 15:16:30 +00:00
parent b2a18a9d61
commit 9b1d7921e8
1 changed files with 12 additions and 3 deletions
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15
java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IndelFilterWalker.java
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@ -10,7 +10,8 @@ import org.broadinstitute.sting.utils.cmdLine.Argument;
/** /**
* filter an indel callset based on given criteria * filter an indel callset based on given criteria
*/ */
@Requires(value={DataSource.REFERENCE},referenceMetaData={@RMD(name="indels",type=AllelicVariant.class)}) @Requires(value={DataSource.REFERENCE},referenceMetaData={@RMD(name="calls",type=AllelicVariant.class)})
@Allows(value={DataSource.REFERENCE},referenceMetaData={@RMD(name="calls",type=AllelicVariant.class),@RMD(name="otherindels",type=AllelicVariant.class)})
@Reference(window=@Window(start=-20,stop=20)) @Reference(window=@Window(start=-20,stop=20))
public class IndelFilterWalker extends RefWalker<Integer, Integer> { public class IndelFilterWalker extends RefWalker<Integer, Integer> {
@Argument(fullName="homopolymerRunMax", shortName="homopolMax", doc="filter indels within homopolymer runs greater than the given length (max 20)", required=false) @Argument(fullName="homopolymerRunMax", shortName="homopolMax", doc="filter indels within homopolymer runs greater than the given length (max 20)", required=false)
@ -21,6 +22,10 @@ public class IndelFilterWalker extends RefWalker<Integer, Integer> {
Integer SIZE_MAX = 100; Integer SIZE_MAX = 100;
@Argument(fullName="sizeMin", shortName="sizeMin", doc="filter indels less than a certain size", required=false) @Argument(fullName="sizeMin", shortName="sizeMin", doc="filter indels less than a certain size", required=false)
Integer SIZE_MIN = 0; Integer SIZE_MIN = 0;
@Argument(fullName="inOtherSet", shortName="inSet", doc="filter indels that DO NOT occur in the provided 2nd set", required=false)
Boolean IN_OTHER_SET = false;
@Argument(fullName="notInOtherSet", shortName="notInSet", doc="filter indels that DO occur in the provided 2nd set", required=false)
Boolean NOT_IN_OTHER_SET = false;
public void initialize() { public void initialize() {
if ( HOMOPOLYMER_MAX > 20 ) if ( HOMOPOLYMER_MAX > 20 )
@ -30,7 +35,7 @@ public class IndelFilterWalker extends RefWalker<Integer, Integer> {
public Integer reduceInit() { return 0; } public Integer reduceInit() { return 0; }
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
AllelicVariant indel = (AllelicVariant)tracker.lookup("indels", null); AllelicVariant indel = (AllelicVariant)tracker.lookup("calls", null);
if ( indel == null || !indel.isIndel() ) if ( indel == null || !indel.isIndel() )
return 0; return 0;
@ -42,6 +47,10 @@ public class IndelFilterWalker extends RefWalker<Integer, Integer> {
if ( homopol < HOMOPOLYMER_MIN || homopol > HOMOPOLYMER_MAX ) if ( homopol < HOMOPOLYMER_MIN || homopol > HOMOPOLYMER_MAX )
return 0; return 0;
AllelicVariant other = (AllelicVariant)tracker.lookup("otherIndels", null);
if ( (IN_OTHER_SET && other == null) || (NOT_IN_OTHER_SET && other != null) )
return 0;
out.println(indel); out.println(indel);
return 1; return 1;
} }
@ -76,7 +85,7 @@ public class IndelFilterWalker extends RefWalker<Integer, Integer> {
rightRun++; rightRun++;
} }
System.out.println(String.valueOf(bases) + ": " + leftRun + " / " + rightRun); //System.out.println(String.valueOf(bases) + ": " + leftRun + " / " + rightRun);
return Math.max(leftRun, rightRun); return Math.max(leftRun, rightRun);
} }
} }