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notes for chartl 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1894 348d0f76-0448-11de-a6fe-93d51630548a
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depristo 2009-10-21 18:31:31 +00:00
parent 77863d4940
commit 15a1849758
1 changed files with 22 additions and 17 deletions
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7
java/src/org/broadinstitute/sting/playground/gatk/walkers/BaseTransitionTableCalculatorJavaWalker.java
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@ -60,7 +60,10 @@ public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<Referen
return 0; return 0;
} }
// todo -- emit table from map and reduce just sums
public ReferenceContextWindow map( RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context ) { public ReferenceContextWindow map( RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context ) {
// todo -- change to use windowed reference itself
// todo -- move up calculations into map not reduce
ReadBackedPileup pileup = new ReadBackedPileup(ref.getBase(),context); ReadBackedPileup pileup = new ReadBackedPileup(ref.getBase(),context);
refWindow.update(ref,pileup,baseIsUsable(tracker,ref,pileup,context)); refWindow.update(ref,pileup,baseIsUsable(tracker,ref,pileup,context));
@ -261,7 +264,6 @@ public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<Referen
} }
class BaseTransitionTable implements Comparable { class BaseTransitionTable implements Comparable {
private int[][] table; private int[][] table;
@ -310,6 +312,7 @@ class BaseTransitionTable implements Comparable {
ListIterator<Comparable> thisIter = this.conditions.listIterator(); ListIterator<Comparable> thisIter = this.conditions.listIterator();
ListIterator<Comparable> thatIter = t.conditions.listIterator(); ListIterator<Comparable> thatIter = t.conditions.listIterator();
while ( thisIter.next() == thatIter.next() ) { while ( thisIter.next() == thatIter.next() ) {
// todo -- compareTo
// do nothing // do nothing
} }
return thisIter.previous().compareTo(thatIter.previous()); return thisIter.previous().compareTo(thatIter.previous());
@ -325,6 +328,8 @@ class BaseTransitionTable implements Comparable {
for ( char observedBase : BaseUtils.BASES ) { for ( char observedBase : BaseUtils.BASES ) {
for ( char refBase : BaseUtils.BASES ) { for ( char refBase : BaseUtils.BASES ) {
// todo -- String.format please
// todo -- in these situations use StringBuilder
String outString = observedBase+"\t"+refBase; String outString = observedBase+"\t"+refBase;
for ( Comparable c : conditions ) { for ( Comparable c : conditions ) {
outString = outString+"\t"+c.toString(); outString = outString+"\t"+c.toString();