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Slight code cleanup 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@421 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-04-14 22:21:36 +00:00
parent e6fb122d7d
commit 24722a442e
4 changed files with 8 additions and 5 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java
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@ -36,7 +36,7 @@ public class PileupWalker extends LocusWalker<Integer, Integer> {
} }
public Integer map(RefMetaDataTracker tracker, char ref, LocusContext context) { public Integer map(RefMetaDataTracker tracker, char ref, LocusContext context) {
ReadBackedPileup pileup = new ReadBackedPileup(context.getLocation(), ref, context); ReadBackedPileup pileup = new ReadBackedPileup(ref, context);
String bases = pileup.getBases(); String bases = pileup.getBases();
if ( bases.equals("") && FLAG_UNCOVERED_BASES ) { if ( bases.equals("") && FLAG_UNCOVERED_BASES ) {

2
java/src/org/broadinstitute/sting/gatk/walkers/ValidatingPileupWalker.java
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@ -20,7 +20,7 @@ public class ValidatingPileupWalker extends LocusWalker<Integer, ValidationStats
public boolean VERBOSE; public boolean VERBOSE;
public Integer map(RefMetaDataTracker tracker, char ref, LocusContext context) { public Integer map(RefMetaDataTracker tracker, char ref, LocusContext context) {
ReadBackedPileup pileup = new ReadBackedPileup(context.getLocation(), ref, context); ReadBackedPileup pileup = new ReadBackedPileup(ref, context);
rodSAMPileup truePileup = (rodSAMPileup)tracker.lookup("pileup", null); rodSAMPileup truePileup = (rodSAMPileup)tracker.lookup("pileup", null);
if ( truePileup == null ) if ( truePileup == null )

5
java/src/org/broadinstitute/sting/playground/gatk/walkers/AlleleFrequencyWalker.java
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@ -62,7 +62,8 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
this.initalize(); this.initalize();
// Convert context data into bases and 4-base quals // Convert context data into bases and 4-base quals
String bases = getBases(context); Pileup pileup = new ReadBackedPileup(ref, context);
String bases = pileup.getBases();
double quals[][] = getQuals(context); double quals[][] = getQuals(context);
//String[] indels = getIndels(context); //String[] indels = getIndels(context);
@ -143,6 +144,7 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
return alleleFreq; return alleleFreq;
} }
/*
static public String getBases (LocusContext context) static public String getBases (LocusContext context)
{ {
// Convert bases to CharArray // Convert bases to CharArray
@ -159,6 +161,7 @@ public class AlleleFrequencyWalker extends LocusWalker<AlleleFrequencyEstimate,
} }
return new String(bases); return new String(bases);
} }
*/
/* /*
static public String[] getIndels(LocusContext context) static public String[] getIndels(LocusContext context)

4
java/src/org/broadinstitute/sting/utils/ReadBackedPileup.java
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@ -19,8 +19,8 @@ public class ReadBackedPileup extends BasicPileup {
List<SAMRecord> reads; List<SAMRecord> reads;
List<Integer> offsets; List<Integer> offsets;
public ReadBackedPileup(GenomeLoc loc, char ref, LocusContext context ) { public ReadBackedPileup(char ref, LocusContext context ) {
this(loc, ref, context.getReads(), context.getOffsets()); this(context.getLocation(), ref, context.getReads(), context.getOffsets());
} }
public ReadBackedPileup(GenomeLoc loc, char ref, List<SAMRecord> reads, List<Integer> offsets ) { public ReadBackedPileup(GenomeLoc loc, char ref, List<SAMRecord> reads, List<Integer> offsets ) {