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Cleanup BCF2Codec 

-- Remove FORBID_SYMBOLIC global that is no longer necessary
-- all error handling goes via error() function
This commit is contained in:
Mark DePristo 2012-08-16 10:53:22 -04:00
parent 9dc694b2e9
commit 28c8e3e6d7
1 changed files with 3 additions and 7 deletions
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10
public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java
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@ -51,7 +51,6 @@ import java.util.Map;
*/ */
public final class BCF2Codec implements FeatureCodec<VariantContext> { public final class BCF2Codec implements FeatureCodec<VariantContext> {
final protected static Logger logger = Logger.getLogger(BCF2Codec.class); final protected static Logger logger = Logger.getLogger(BCF2Codec.class);
private final static boolean FORBID_SYMBOLICS = false;
private final static int ALLOWED_MAJOR_VERSION = 2; private final static int ALLOWED_MAJOR_VERSION = 2;
private final static int MIN_MINOR_VERSION = 1; private final static int MIN_MINOR_VERSION = 1;
@ -178,7 +177,7 @@ public final class BCF2Codec implements FeatureCodec<VariantContext> {
contigNames.add(contig.getID()); contigNames.add(contig.getID());
} }
} else { } else {
throw new UserException.MalformedBCF2("Didn't find any contig lines in BCF2 file header"); error("Didn't find any contig lines in BCF2 file header");
} }
// create the string dictionary // create the string dictionary
@ -271,7 +270,7 @@ public final class BCF2Codec implements FeatureCodec<VariantContext> {
final int nSamples = nFormatSamples & 0x00FFFFF; final int nSamples = nFormatSamples & 0x00FFFFF;
if ( header.getNGenotypeSamples() != nSamples ) if ( header.getNGenotypeSamples() != nSamples )
throw new UserException.MalformedBCF2("GATK currently doesn't support reading BCF2 files with " + error("GATK currently doesn't support reading BCF2 files with " +
"different numbers of samples per record. Saw " + header.getNGenotypeSamples() + "different numbers of samples per record. Saw " + header.getNGenotypeSamples() +
" samples in header but have a record with " + nSamples + " samples"); " samples in header but have a record with " + nSamples + " samples");
@ -343,9 +342,6 @@ public final class BCF2Codec implements FeatureCodec<VariantContext> {
if ( isRef ) ref = alleleBases; if ( isRef ) ref = alleleBases;
alleles.add(allele); alleles.add(allele);
if ( FORBID_SYMBOLICS && allele.isSymbolic() )
throw new ReviewedStingException("LIMITATION: GATK BCF2 codec does not yet support symbolic alleles");
} }
assert ref != null; assert ref != null;
@ -496,7 +492,7 @@ public final class BCF2Codec implements FeatureCodec<VariantContext> {
return gtFieldDecoders.getDecoder(field); return gtFieldDecoders.getDecoder(field);
} }
private final void error(final String message) throws RuntimeException { private void error(final String message) throws RuntimeException {
throw new UserException.MalformedBCF2(String.format("%s, at record %d with position %d:", message, recordNo, pos)); throw new UserException.MalformedBCF2(String.format("%s, at record %d with position %d:", message, recordNo, pos));
} }
} }