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Updating example active region walker integration test.

This commit is contained in:
Ryan Poplin 2012-07-30 21:26:16 -04:00
parent c2b57ee444
commit 3dabb90eb0
1 changed files with 1 additions and 2 deletions
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protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
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@ -379,7 +379,6 @@ public class GenotypingEngine {
} }
if( thisVC == null || nextVC == null ) { if( thisVC == null || nextVC == null ) {
continue; continue;
//throw new ReviewedStingException("StartPos TreeSet has an entry for an event that is found on no haplotype. start pos = " + thisStart + ", next pos = " + nextStart);
} }
if( isBiallelic ) { if( isBiallelic ) {
final double R2 = calculateR2LD( Math.pow(10.0, x11), Math.pow(10.0, x12), Math.pow(10.0, x21), Math.pow(10.0, x22) ); final double R2 = calculateR2LD( Math.pow(10.0, x11), Math.pow(10.0, x12), Math.pow(10.0, x21), Math.pow(10.0, x22) );
@ -441,7 +440,7 @@ public class GenotypingEngine {
altBases = ArrayUtils.addAll(altBases, nextVC.getAlternateAllele(0).getBases()); altBases = ArrayUtils.addAll(altBases, nextVC.getAlternateAllele(0).getBases());
int iii = 0; int iii = 0;
if( refBases.length == altBases.length ) { // special case of insertion + deletion of same length creates an MNP --> trim padding bases off the allele if( refBases.length == altBases.length ) { // insertion + deletion of same length creates an MNP --> trim common prefix bases off the beginning of the allele
while( iii < refBases.length && refBases[iii] == altBases[iii] ) { iii++; } while( iii < refBases.length && refBases[iii] == altBases[iii] ) { iii++; }
} }
final ArrayList<Allele> mergedAlleles = new ArrayList<Allele>(); final ArrayList<Allele> mergedAlleles = new ArrayList<Allele>();