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

This commit is contained in:
Ryan Poplin 2011-12-14 12:15:46 -05:00
parent 08e0889f0a 7648521718
commit 4c077f9155
5 changed files with 15 additions and 3 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
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@ -182,6 +182,8 @@ public class CountVariants extends VariantEvaluator implements StandardEval {
nHomDerived++;
}
break;
case MIXED:
break;
default:
throw new ReviewedStingException("BUG: Unexpected genotype type: " + g);

8
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
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@ -184,7 +184,6 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec {
* @return a feature, (not guaranteed complete) that has the correct start and stop
*/
public Feature decodeLoc(String line) {
lineNo++;
// 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;
@ -279,6 +278,8 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec {
builder.source(getName());
// increment the line count
// TODO -- because of the way the engine utilizes Tribble, we can parse a line multiple times (especially when
// TODO -- the first record is far along the contig) and the line counter can get out of sync
lineNo++;
// parse out the required fields
@ -594,6 +595,11 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec {
if ( a.isSymbolic() )
continue;
// we need to ensure that we don't reverse clip out all of the bases from an allele because we then will have the wrong
// position set for the VariantContext (although it's okay to forward clip it all out, because the position will be fine).
if ( a.length() - clipping == 0 )
return clipping - 1;
if ( a.length() - clipping <= forwardClipping || a.length() - forwardClipping == 0 )
stillClipping = false;
else if ( ref.length() == clipping )

2
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCF3Codec.java
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@ -120,6 +120,8 @@ public class VCF3Codec extends AbstractVCFCodec {
genotypeParts = new String[header.getColumnCount() - NUM_STANDARD_FIELDS];
int nParts = ParsingUtils.split(str, genotypeParts, VCFConstants.FIELD_SEPARATOR_CHAR);
if ( nParts != genotypeParts.length )
generateException("there are " + (nParts-1) + " genotypes while the header requires that " + (genotypeParts.length-1) + " genotypes be present for all records", lineNo);
ArrayList<Genotype> genotypes = new ArrayList<Genotype>(nParts);

2
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java
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@ -147,6 +147,8 @@ public class VCFCodec extends AbstractVCFCodec {
genotypeParts = new String[header.getColumnCount() - NUM_STANDARD_FIELDS];
int nParts = ParsingUtils.split(str, genotypeParts, VCFConstants.FIELD_SEPARATOR_CHAR);
if ( nParts != genotypeParts.length )
generateException("there are " + (nParts-1) + " genotypes while the header requires that " + (genotypeParts.length-1) + " genotypes be present for all records", lineNo);
ArrayList<Genotype> genotypes = new ArrayList<Genotype>(nParts);

4
public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
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@ -184,11 +184,11 @@ public class UserException extends ReviewedStingException {
public static class MalformedVCF extends UserException {
public MalformedVCF(String message, String line) {
super(String.format("The provided VCF file is malformed at line %s: %s", line, message));
super(String.format("The provided VCF file is malformed at approximately line %s: %s", line, message));
}
public MalformedVCF(String message, int lineNo) {
super(String.format("The provided VCF file is malformed at line number %d: %s", lineNo, message));
super(String.format("The provided VCF file is malformed at approximately line number %d: %s", lineNo, message));
}
}