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interim commit 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3240 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-04-22 13:44:45 +00:00
parent f0fe2ea530
commit 121163dd49
1 changed files with 4 additions and 3 deletions
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7
java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelDBRateWalker.java
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@ -27,6 +27,7 @@ import java.util.*;
* @Author chartl * @Author chartl
* @Date Apr 21, 2010 * @Date Apr 21, 2010
*/ */
@Reference(window=@Window(start=-40,stop=40))
public class IndelDBRateWalker extends RodWalker<OverlapTable,OverlapTabulator> { public class IndelDBRateWalker extends RodWalker<OverlapTable,OverlapTabulator> {
@Argument(fullName="indelWindow",doc="size of the window in which to look for indels; max 40",required=false) @Argument(fullName="indelWindow",doc="size of the window in which to look for indels; max 40",required=false)
@ -125,7 +126,7 @@ public class IndelDBRateWalker extends RodWalker<OverlapTable,OverlapTabulator>
} }
// step 3: see if there are any contexts left; if so then they must be within the window // step 3: see if there are any contexts left; if so then they must be within the window
if ( ! compContexts.isEmpty() ) { if ( ! compContexts.isEmpty() ) {
return nonEmptyOverlapTable(); return nonEmptyOverlapTable(ref);
} else { } else {
return emptyOverlapTable(); return emptyOverlapTable();
} }
@ -138,14 +139,14 @@ public class IndelDBRateWalker extends RodWalker<OverlapTable,OverlapTabulator>
return ot; return ot;
} }
public OverlapTable nonEmptyOverlapTable() { public OverlapTable nonEmptyOverlapTable(ReferenceContext ref) {
if ( vcfWriter != null ) { if ( vcfWriter != null ) {
int i = 0; int i = 0;
while ( i < compContexts.size() && compContexts.get(i).getLocation().isBefore(evalContexts.get(0).getLocation())) { while ( i < compContexts.size() && compContexts.get(i).getLocation().isBefore(evalContexts.get(0).getLocation())) {
vcfWriter.addRecord(VariantContextAdaptors.toVCF(compContexts.get(i),(char)compContexts.get(i).getReference().getBases()[0])); vcfWriter.addRecord(VariantContextAdaptors.toVCF(compContexts.get(i),(char)compContexts.get(i).getReference().getBases()[0]));
i++; i++;
} }
vcfWriter.addRecord(VariantContextAdaptors.toVCF(evalContexts.get(0),(char) evalContexts.get(0).getReference().getBases()[0])); vcfWriter.addRecord(VariantContextAdaptors.toVCF(evalContexts.get(0),ref.getBase()));
while ( i < compContexts.size() && compContexts.get(i).getLocation().distance(evalContexts.get(0).getLocation()) <= indelWindow) { while ( i < compContexts.size() && compContexts.get(i).getLocation().distance(evalContexts.get(0).getLocation()) <= indelWindow) {
vcfWriter.addRecord(VariantContextAdaptors.toVCF(compContexts.get(i),(char) compContexts.get(i).getReference().getBases()[0])); vcfWriter.addRecord(VariantContextAdaptors.toVCF(compContexts.get(i),(char) compContexts.get(i).getReference().getBases()[0]));
i++; i++;