zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Bugfix for unnecessary optimization 

-- don't cache the ref bytes
This commit is contained in:
Mark DePristo 2012-01-16 18:49:58 -05:00
parent f2b0575dee
commit 62801e430a
1 changed files with 3 additions and 5 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

8
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
View File

@ -522,7 +522,7 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec {
if ( allele == null || allele.length() == 0 ) if ( allele == null || allele.length() == 0 )
generateException("Empty alleles are not permitted in VCF records", lineNo); generateException("Empty alleles are not permitted in VCF records", lineNo);
if ( allele.length() > MAX_EXPLICIT_ALLELE_SIZE ) if ( MAX_EXPLICIT_ALLELE_SIZE != -1 && allele.length() > MAX_EXPLICIT_ALLELE_SIZE )
generateException(String.format("Allele detected with length %d, exceeding max size %d. Please remove this from the VCF file before continuing", allele.length(), MAX_EXPLICIT_ALLELE_SIZE), lineNo); generateException(String.format("Allele detected with length %d, exceeding max size %d. Please remove this from the VCF file before continuing", allele.length(), MAX_EXPLICIT_ALLELE_SIZE), lineNo);
if ( isSymbolicAllele(allele) ) { if ( isSymbolicAllele(allele) ) {
@ -576,13 +576,12 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec {
public static int computeForwardClipping(List<Allele> unclippedAlleles, String ref) { public static int computeForwardClipping(List<Allele> unclippedAlleles, String ref) {
boolean clipping = true; boolean clipping = true;
final byte ref0 = ref.getBytes()[0];
for ( Allele a : unclippedAlleles ) { for ( Allele a : unclippedAlleles ) {
if ( a.isSymbolic() ) if ( a.isSymbolic() )
continue; continue;
if ( a.length() < 1 || (a.getBases()[0] != ref0) ) { if ( a.length() < 1 || (a.getBases()[0] != ref.getBytes()[0]) ) {
clipping = false; clipping = false;
break; break;
} }
@ -594,7 +593,6 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec {
protected static int computeReverseClipping(List<Allele> unclippedAlleles, String ref, int forwardClipping, int lineNo) { protected static int computeReverseClipping(List<Allele> unclippedAlleles, String ref, int forwardClipping, int lineNo) {
int clipping = 0; int clipping = 0;
boolean stillClipping = true; boolean stillClipping = true;
final byte[] refBytes = ref.getBytes();
while ( stillClipping ) { while ( stillClipping ) {
for ( Allele a : unclippedAlleles ) { for ( Allele a : unclippedAlleles ) {
@ -610,7 +608,7 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec {
stillClipping = false; stillClipping = false;
else if ( ref.length() == clipping ) else if ( ref.length() == clipping )
generateException("bad alleles encountered", lineNo); generateException("bad alleles encountered", lineNo);
else if ( a.getBases()[a.length()-clipping-1] != refBytes[ref.length()-clipping-1] ) else if ( a.getBases()[a.length()-clipping-1] != ref.getBytes()[ref.length()-clipping-1] )
stillClipping = false; stillClipping = false;
} }
if ( stillClipping ) if ( stillClipping )