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Massive bugfixes 

-- Previous version was reading the size of the encoded genotypes vector for each genotype.  This only worked because I never wrote out genotype field values with > 15 elements.  Mauricio's killer DiagnoseTargets VCF uncovered the bug.  Unfortunately since symbolic allele clipping is still busted those tests are still diabled
-- GenotypeContext getMaxPloidy was returning -1 in the case where there are no genotypes, but the answer should be 0.
This commit is contained in:
Mark DePristo 2012-06-27 18:18:25 -04:00
parent 7144154f53
commit 64d7e93209
5 changed files with 25 additions and 21 deletions
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7
public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Decoder.java
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@ -136,6 +136,10 @@ public final class BCF2Decoder {
public final Object decodeTypedValue(final byte typeDescriptor) { public final Object decodeTypedValue(final byte typeDescriptor) {
final int size = decodeNumberOfElements(typeDescriptor); final int size = decodeNumberOfElements(typeDescriptor);
return decodeTypedValue(typeDescriptor, size);
}
public final Object decodeTypedValue(final byte typeDescriptor, final int size) {
final BCF2Type type = BCF2Utils.decodeType(typeDescriptor); final BCF2Type type = BCF2Utils.decodeType(typeDescriptor);
assert size >= 0; assert size >= 0;
@ -285,8 +289,7 @@ public final class BCF2Decoder {
} }
} }
public final int[] decodeIntArray(final byte typeDescriptor) { public final int[] decodeIntArray(final byte typeDescriptor, final int size) {
final int size = decodeNumberOfElements(typeDescriptor);
final BCF2Type type = BCF2Utils.decodeType(typeDescriptor); final BCF2Type type = BCF2Utils.decodeType(typeDescriptor);
return decodeIntArray(size, type, null); return decodeIntArray(size, type, null);
} }

30
public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2GenotypeFieldDecoders.java
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@ -104,19 +104,17 @@ public class BCF2GenotypeFieldDecoders {
final String field, final String field,
final BCF2Decoder decoder, final BCF2Decoder decoder,
final byte typeDescriptor, final byte typeDescriptor,
final int numElements,
final GenotypeBuilder[] gbs); final GenotypeBuilder[] gbs);
} }
private class GTDecoder implements Decoder { private class GTDecoder implements Decoder {
@Override @Override
public void decode(final List<Allele> siteAlleles, final String field, final BCF2Decoder decoder, final byte typeDescriptor, final GenotypeBuilder[] gbs) { public void decode(final List<Allele> siteAlleles, final String field, final BCF2Decoder decoder, final byte typeDescriptor, final int numElements, final GenotypeBuilder[] gbs) {
// we have to do a bit of low-level processing here as we want to know the size upfronta if ( ENABLE_FASTPATH_GT && siteAlleles.size() == 2 && numElements == 2 && gbs.length >= MIN_SAMPLES_FOR_FASTPATH_GENOTYPES )
final int ploidy = decoder.decodeNumberOfElements(typeDescriptor);
if ( ENABLE_FASTPATH_GT && siteAlleles.size() == 2 && ploidy == 2 && gbs.length >= MIN_SAMPLES_FOR_FASTPATH_GENOTYPES )
fastBiallelicDiploidDecode(siteAlleles, decoder, typeDescriptor, gbs); fastBiallelicDiploidDecode(siteAlleles, decoder, typeDescriptor, gbs);
else { else {
generalDecode(siteAlleles, ploidy, decoder, typeDescriptor, gbs); generalDecode(siteAlleles, numElements, decoder, typeDescriptor, gbs);
} }
} }
@ -218,7 +216,7 @@ public class BCF2GenotypeFieldDecoders {
private class DPDecoder implements Decoder { private class DPDecoder implements Decoder {
@Override @Override
public void decode(final List<Allele> siteAlleles, final String field, final BCF2Decoder decoder, final byte typeDescriptor, final GenotypeBuilder[] gbs) { public void decode(final List<Allele> siteAlleles, final String field, final BCF2Decoder decoder, final byte typeDescriptor, final int numElements, final GenotypeBuilder[] gbs) {
for ( final GenotypeBuilder gb : gbs ) { for ( final GenotypeBuilder gb : gbs ) {
// the -1 is for missing // the -1 is for missing
gb.DP(decoder.decodeInt(typeDescriptor, -1)); gb.DP(decoder.decodeInt(typeDescriptor, -1));
@ -228,7 +226,7 @@ public class BCF2GenotypeFieldDecoders {
private class GQDecoder implements Decoder { private class GQDecoder implements Decoder {
@Override @Override
public void decode(final List<Allele> siteAlleles, final String field, final BCF2Decoder decoder, final byte typeDescriptor, final GenotypeBuilder[] gbs) { public void decode(final List<Allele> siteAlleles, final String field, final BCF2Decoder decoder, final byte typeDescriptor, final int numElements, final GenotypeBuilder[] gbs) {
for ( final GenotypeBuilder gb : gbs ) { for ( final GenotypeBuilder gb : gbs ) {
// the -1 is for missing // the -1 is for missing
gb.GQ(decoder.decodeInt(typeDescriptor, -1)); gb.GQ(decoder.decodeInt(typeDescriptor, -1));
@ -238,27 +236,27 @@ public class BCF2GenotypeFieldDecoders {
private class ADDecoder implements Decoder { private class ADDecoder implements Decoder {
@Override @Override
public void decode(final List<Allele> siteAlleles, final String field, final BCF2Decoder decoder, final byte typeDescriptor, final GenotypeBuilder[] gbs) { public void decode(final List<Allele> siteAlleles, final String field, final BCF2Decoder decoder, final byte typeDescriptor, final int numElements, final GenotypeBuilder[] gbs) {
for ( final GenotypeBuilder gb : gbs ) { for ( final GenotypeBuilder gb : gbs ) {
gb.AD(decoder.decodeIntArray(typeDescriptor)); gb.AD(decoder.decodeIntArray(typeDescriptor, numElements));
} }
} }
} }
private class PLDecoder implements Decoder { private class PLDecoder implements Decoder {
@Override @Override
public void decode(final List<Allele> siteAlleles, final String field, final BCF2Decoder decoder, final byte typeDescriptor, final GenotypeBuilder[] gbs) { public void decode(final List<Allele> siteAlleles, final String field, final BCF2Decoder decoder, final byte typeDescriptor, final int numElements, final GenotypeBuilder[] gbs) {
for ( final GenotypeBuilder gb : gbs ) { for ( final GenotypeBuilder gb : gbs ) {
gb.PL(decoder.decodeIntArray(typeDescriptor)); gb.PL(decoder.decodeIntArray(typeDescriptor, numElements));
} }
} }
} }
private class GenericDecoder implements Decoder { private class GenericDecoder implements Decoder {
@Override @Override
public void decode(final List<Allele> siteAlleles, final String field, final BCF2Decoder decoder, final byte typeDescriptor, final GenotypeBuilder[] gbs) { public void decode(final List<Allele> siteAlleles, final String field, final BCF2Decoder decoder, final byte typeDescriptor, final int numElements, final GenotypeBuilder[] gbs) {
for ( final GenotypeBuilder gb : gbs ) { for ( final GenotypeBuilder gb : gbs ) {
Object value = decoder.decodeTypedValue(typeDescriptor); Object value = decoder.decodeTypedValue(typeDescriptor, numElements);
if ( value != null ) { // don't add missing values if ( value != null ) { // don't add missing values
if ( value instanceof List && ((List)value).size() == 1) { if ( value instanceof List && ((List)value).size() == 1) {
// todo -- I really hate this, and it suggests that the code isn't completely right // todo -- I really hate this, and it suggests that the code isn't completely right
@ -275,9 +273,9 @@ public class BCF2GenotypeFieldDecoders {
private class FTDecoder implements Decoder { private class FTDecoder implements Decoder {
@Override @Override
public void decode(final List<Allele> siteAlleles, final String field, final BCF2Decoder decoder, final byte typeDescriptor, final GenotypeBuilder[] gbs) { public void decode(final List<Allele> siteAlleles, final String field, final BCF2Decoder decoder, final byte typeDescriptor, final int numElements, final GenotypeBuilder[] gbs) {
for ( final GenotypeBuilder gb : gbs ) { for ( final GenotypeBuilder gb : gbs ) {
Object value = decoder.decodeTypedValue(typeDescriptor); Object value = decoder.decodeTypedValue(typeDescriptor, numElements);
if ( value != null ) { // don't add missing values if ( value != null ) { // don't add missing values
gb.filters(value instanceof String ? Collections.singletonList((String)value) : (List<String>)value); gb.filters(value instanceof String ? Collections.singletonList((String)value) : (List<String>)value);
} }

3
public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2LazyGenotypesDecoder.java
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@ -77,9 +77,10 @@ class BCF2LazyGenotypesDecoder implements LazyGenotypesContext.LazyParser {
// the type of each element // the type of each element
final byte typeDescriptor = decoder.readTypeDescriptor(); final byte typeDescriptor = decoder.readTypeDescriptor();
final int numElements = decoder.decodeNumberOfElements(typeDescriptor);
final BCF2GenotypeFieldDecoders.Decoder fieldDecoder = codec.getGenotypeFieldDecoder(field); final BCF2GenotypeFieldDecoders.Decoder fieldDecoder = codec.getGenotypeFieldDecoder(field);
try { try {
fieldDecoder.decode(siteAlleles, field, decoder, typeDescriptor, builders); fieldDecoder.decode(siteAlleles, field, decoder, typeDescriptor, numElements, builders);
} catch ( ClassCastException e ) { } catch ( ClassCastException e ) {
throw new UserException.MalformedBCF2("BUG: expected encoding of field " + field throw new UserException.MalformedBCF2("BUG: expected encoding of field " + field
+ " inconsistent with the value observed in the decoded value"); + " inconsistent with the value observed in the decoded value");

5
public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java
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@ -58,7 +58,6 @@ public class GenotypeLikelihoods {
static { static {
// must be done before PLIndexToAlleleIndex // must be done before PLIndexToAlleleIndex
for ( int numAlleles = 1; numAlleles < NUM_LIKELIHOODS_CACHE_N_ALLELES; numAlleles++ ) { for ( int numAlleles = 1; numAlleles < NUM_LIKELIHOODS_CACHE_N_ALLELES; numAlleles++ ) {
//numLikelihoodCache[numAlleles] = new int[NUM_LIKELIHOODS_CACHE_PLOIDY];
for ( int ploidy = 1; ploidy < NUM_LIKELIHOODS_CACHE_PLOIDY; ploidy++ ) { for ( int ploidy = 1; ploidy < NUM_LIKELIHOODS_CACHE_PLOIDY; ploidy++ ) {
numLikelihoodCache[numAlleles][ploidy] = calcNumLikelihoods(numAlleles, ploidy); numLikelihoodCache[numAlleles][ploidy] = calcNumLikelihoods(numAlleles, ploidy);
} }
@ -364,11 +363,13 @@ public class GenotypeLikelihoods {
* S(N,1) = N (only way to have N integers add up to 1 is all-zeros except one element with a one. There are N of these vectors) * S(N,1) = N (only way to have N integers add up to 1 is all-zeros except one element with a one. There are N of these vectors)
* S(1,P) = 1 (only way to have 1 integer add to P is with that integer P itself). * S(1,P) = 1 (only way to have 1 integer add to P is with that integer P itself).
* *
* note that in the case where ploidy == 0 we assume that the ploidy actually == 2
*
* @param numAlleles Number of alleles (including ref) * @param numAlleles Number of alleles (including ref)
* @param ploidy Ploidy, or number of chromosomes in set * @param ploidy Ploidy, or number of chromosomes in set
* @return Number of likelihood elements we need to hold. * @return Number of likelihood elements we need to hold.
*/ */
@Requires({"ploidy > 0", "numAlleles > 0"}) @Requires({"ploidy >= 0", "numAlleles > 0"})
@Ensures("result > 0") @Ensures("result > 0")
public static int numLikelihoods(final int numAlleles, final int ploidy) { public static int numLikelihoods(final int numAlleles, final int ploidy) {
if ( numAlleles < NUM_LIKELIHOODS_CACHE_N_ALLELES if ( numAlleles < NUM_LIKELIHOODS_CACHE_N_ALLELES

1
public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypesContext.java
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@ -416,6 +416,7 @@ public class GenotypesContext implements List<Genotype> {
@Ensures("result >= 0") @Ensures("result >= 0")
public int getMaxPloidy() { public int getMaxPloidy() {
if ( maxPloidy == -1 ) { if ( maxPloidy == -1 ) {
maxPloidy = 0; // necessary in the case where there are no genotypes
for ( final Genotype g : getGenotypes() ) { for ( final Genotype g : getGenotypes() ) {
maxPloidy = Math.max(g.getPloidy(), maxPloidy); maxPloidy = Math.max(g.getPloidy(), maxPloidy);
} }