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Bug fix. decodeLoc() should update lineNo so you get meaningful line no when indexing 

due to malformed VCF files.
This commit is contained in:
Mark DePristo 2011-11-04 11:44:24 -04:00
parent 849c0757f2
commit a340a1aeac
1 changed files with 1 additions and 0 deletions
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public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
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@ -162,6 +162,7 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
* @return a feature, (not guaranteed complete) that has the correct start and stop * @return a feature, (not guaranteed complete) that has the correct start and stop
*/ */
public Feature decodeLoc(String line) { public Feature decodeLoc(String line) {
lineNo++;
String[] locParts = new String[6]; String[] locParts = new String[6];
int nParts = ParsingUtils.split(line, locParts, VCFConstants.FIELD_SEPARATOR_CHAR, true); int nParts = ParsingUtils.split(line, locParts, VCFConstants.FIELD_SEPARATOR_CHAR, true);