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Bug fix for decode loc 

-- decodeLoc() wasn't skipping input header lines, so the system blew up when there was an = line being split.
This commit is contained in:
Mark DePristo 2011-11-04 13:20:54 -04:00
parent a340a1aeac
commit e99871f587
1 changed files with 12 additions and 5 deletions
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17
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
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@ -163,19 +163,26 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
*/ */
public Feature decodeLoc(String line) { public Feature decodeLoc(String line) {
lineNo++; lineNo++;
String[] locParts = new String[6];
// the same line reader is not used for parsing the header and parsing lines, if we see a #, we've seen a header line
if (line.startsWith(VCFHeader.HEADER_INDICATOR)) return null;
// our header cannot be null, we need the genotype sample names and counts
if (header == null) throw new ReviewedStingException("VCF Header cannot be null when decoding a record");
final 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);
if ( nParts != 6 ) if ( nParts != 6 )
throw new UserException.MalformedVCF("there aren't enough columns for line " + line, lineNo); throw new UserException.MalformedVCF("there aren't enough columns for line " + line, lineNo);
// get our alleles (because the end position depends on them) // get our alleles (because the end position depends on them)
String ref = getCachedString(locParts[3].toUpperCase()); final String ref = getCachedString(locParts[3].toUpperCase());
String alts = getCachedString(locParts[4].toUpperCase()); final String alts = getCachedString(locParts[4].toUpperCase());
List<Allele> alleles = parseAlleles(ref, alts, lineNo); final List<Allele> alleles = parseAlleles(ref, alts, lineNo);
// find out our location // find out our location
int start = Integer.valueOf(locParts[1]); final int start = Integer.valueOf(locParts[1]);
int stop = start; int stop = start;
// ref alleles don't need to be single bases for monomorphic sites // ref alleles don't need to be single bases for monomorphic sites