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Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Ryan Poplin 2012-08-06 11:40:27 -04:00
parent 973d1d47ed 210db5ec27
commit afa70a13a9
2 changed files with 8 additions and 3 deletions
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4
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
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@ -114,11 +114,11 @@ public class UnifiedArgumentCollection {
* that you not play around with this parameter. * that you not play around with this parameter.
*/ */
@Advanced @Advanced
@Argument(fullName = "max_alternate_alleles", shortName = "maxAlleles", doc = "Maximum number of alternate alleles to genotype", required = false) @Argument(fullName = "max_alternate_alleles", shortName = "maxAltAlleles", doc = "Maximum number of alternate alleles to genotype", required = false)
public int MAX_ALTERNATE_ALLELES = 3; public int MAX_ALTERNATE_ALLELES = 3;
@Hidden @Hidden
@Argument(fullName = "cap_max_alternate_alleles_for_indels", shortName = "capMaxAllelesForIndels", doc = "Cap the maximum number of alternate alleles to genotype for indel calls at 2; overrides the --max_alternate_alleles argument; GSA production use only", required = false) @Argument(fullName = "cap_max_alternate_alleles_for_indels", shortName = "capMaxAltAllelesForIndels", doc = "Cap the maximum number of alternate alleles to genotype for indel calls at 2; overrides the --max_alternate_alleles argument; GSA production use only", required = false)
public boolean CAP_MAX_ALTERNATE_ALLELES_FOR_INDELS = false; public boolean CAP_MAX_ALTERNATE_ALLELES_FOR_INDELS = false;
// indel-related arguments // indel-related arguments

7
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
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@ -237,7 +237,12 @@ public abstract class AbstractVCFCodec extends AsciiFeatureCodec<VariantContext>
// parse out the required fields // parse out the required fields
final String chr = getCachedString(parts[0]); final String chr = getCachedString(parts[0]);
builder.chr(chr); builder.chr(chr);
int pos = Integer.valueOf(parts[1]); int pos = -1;
try {
pos = Integer.valueOf(parts[1]);
} catch (NumberFormatException e) {
generateException(parts[1] + " is not a valid start position in the VCF format");
}
builder.start(pos); builder.start(pos);
if ( parts[2].length() == 0 ) if ( parts[2].length() == 0 )