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border case bug fixes 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@951 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-06-09 04:33:15 +00:00
parent fecba2cae5
commit b45b1d5f2b
2 changed files with 6 additions and 7 deletions
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11
java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IntervalCleanerWalker.java
View File

@ -539,7 +539,7 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
switch ( ce.getOperator() ) { switch ( ce.getOperator() ) {
case M: case M:
for (int k = 0 ; k < ce.getLength() ; k++, refIdx++, altIdx++ ) { for (int k = 0 ; k < ce.getLength() ; k++, refIdx++, altIdx++ ) {
if ( Character.toUpperCase(readStr.charAt(altIdx)) != Character.toUpperCase(reference.charAt(refIdx)) ) if ( refIdx < reference.length() && Character.toUpperCase(readStr.charAt(altIdx)) != Character.toUpperCase(reference.charAt(refIdx)) )
cleanedMismatchBases[refIdx] += (int)qualStr.charAt(altIdx) - 33; cleanedMismatchBases[refIdx] += (int)qualStr.charAt(altIdx) - 33;
} }
break; break;
@ -626,7 +626,6 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
// position, we will move insertion left, to the position right after CA. This way, while moving the indel across the repeat // position, we will move insertion left, to the position right after CA. This way, while moving the indel across the repeat
// on the ref, we can theoretically move it across a non-repeat on the read if the latter has a mismtach. // on the ref, we can theoretically move it across a non-repeat on the read if the latter has a mismtach.
while ( period < indel_length ) { // we will always get at least trivial period = indelStringLength while ( period < indel_length ) { // we will always get at least trivial period = indelStringLength
period = BaseUtils.sequencePeriod(indelString, period+1); period = BaseUtils.sequencePeriod(indelString, period+1);
@ -634,16 +633,16 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
if ( indel_length % period != 0 ) continue; // if indel sequence length is not a multiple of the period, it's not gonna work if ( indel_length % period != 0 ) continue; // if indel sequence length is not a multiple of the period, it's not gonna work
int newIndex = indelIndexOnRef; int newIndex = indelIndexOnRef;
while ( newIndex >= period ) { // let's see if there is a repeat, i.e. if we could also say that same bases at lower position are deleted while ( newIndex >= period ) { // let's see if there is a repeat, i.e. if we could also say that same bases at lower position are deleted
// lets check if bases [newIndex-period,newIndex) immediately preceding the indel on the ref // lets check if bases [newIndex-period,newIndex) immediately preceding the indel on the ref
// are the same as the currently checked period of the inserted sequence: // are the same as the currently checked period of the inserted sequence:
boolean match = true; boolean match = true;
for ( int testRefPos = newIndex - period, indelPos = 0 ; testRefPos < newIndex; testRefPos++, indelPos++) { for ( int testRefPos = newIndex - period, indelPos = 0 ; testRefPos < newIndex; testRefPos++, indelPos++) {
if ( Character.toUpperCase(refSeq.charAt(testRefPos)) != indelString.charAt(indelPos) ) { if ( Character.toUpperCase(refSeq.charAt(testRefPos)) != indelString.charAt(indelPos) || indelString.charAt(indelPos) == 'N' ) {
match = false; match = false;
break; break;
} }
@ -654,7 +653,7 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
} }
final int newDifference = indelIndexOnRef - newIndex; final int newDifference = indelIndexOnRef - newIndex;
if ( newDifference > difference ) difference = newDifference; // deletion should be moved 'difference' bases left if ( newDifference > difference ) difference = newDifference; // deletion should be moved 'difference' bases left
if ( period == 1 ) break; // we do not have to check all periods of homonucleotide sequences, we already if ( period == 1 ) break; // we do not have to check all periods of homonucleotide sequences, we already
// got maximum possible shift after checking period=1 above. // got maximum possible shift after checking period=1 above.

2
java/src/org/broadinstitute/sting/playground/indels/AlignmentUtils.java
View File

@ -123,7 +123,7 @@ public class AlignmentUtils {
switch ( ce.getOperator() ) { switch ( ce.getOperator() ) {
case M: case M:
for (int j = 0 ; j < ce.getLength() ; j++, refIndex++, readIdx++ ) { for (int j = 0 ; j < ce.getLength() ; j++, refIndex++, readIdx++ ) {
if ( Character.toUpperCase(readSeq.charAt(readIdx)) != Character.toUpperCase(refSeq.charAt(refIndex)) ) if ( refIndex < refSeq.length() && Character.toUpperCase(readSeq.charAt(readIdx)) != Character.toUpperCase(refSeq.charAt(refIndex)) )
mismatches++; mismatches++;
} }
break; break;