zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Bug fix in reverse trim alleles for the case of mixed records.

This commit is contained in:
Ryan Poplin 2012-04-27 16:21:02 -04:00
parent 1bbb156afa
commit 2b5dd28550
3 changed files with 15 additions and 18 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
View File

@ -642,7 +642,7 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec {
boolean stillClipping = true;
while ( stillClipping ) {
for ( Allele a : unclippedAlleles ) {
for ( final Allele a : unclippedAlleles ) {
if ( a.isSymbolic() )
continue;

4
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
View File

@ -160,7 +160,7 @@ import java.util.*;
*
* @author depristo
*/
public class VariantContext implements Feature { // to enable tribble intergration
public class VariantContext implements Feature { // to enable tribble integration
protected CommonInfo commonInfo = null;
public final static double NO_LOG10_PERROR = CommonInfo.NO_LOG10_PERROR;
@ -377,7 +377,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati
*
* Not currently supported:
*
* Heterozygous sequencea
* Heterozygous sequence
* The term heterozygous is used to specify a region detected by certain methods that do not
* resolve the polymorphism into a specific sequence motif. In these cases, a unique flanking
* sequence must be provided to define a sequence context for the variation.

27
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
View File

@ -620,8 +620,8 @@ public class VariantContextUtils {
String key = p.getKey();
// if we don't like the key already, don't go anywhere
if ( ! inconsistentAttributes.contains(key) ) {
boolean alreadyFound = attributes.containsKey(key);
Object boundValue = attributes.get(key);
final boolean alreadyFound = attributes.containsKey(key);
final Object boundValue = attributes.get(key);
final boolean boundIsMissingValue = alreadyFound && boundValue.equals(VCFConstants.MISSING_VALUE_v4);
if ( alreadyFound && ! boundValue.equals(p.getValue()) && ! boundIsMissingValue ) {
@ -802,17 +802,16 @@ public class VariantContextUtils {
return inputVC;
}
public static VariantContext reverseTrimAlleles(VariantContext inputVC) {
public static VariantContext reverseTrimAlleles( final VariantContext inputVC ) {
// see if we need to trim common reference base from all alleles
final int trimExtent = AbstractVCFCodec.computeReverseClipping(inputVC.getAlleles(), inputVC.getReference().getDisplayString().getBytes(), 0, true, -1);
if ( trimExtent <= 0 )
return inputVC;
if ( trimExtent <= 0 || inputVC.getAlleles().size() <= 1 )
return inputVC;
final List<Allele> alleles = new ArrayList<Allele>();
GenotypesContext genotypes = GenotypesContext.create();
Map<Allele, Allele> originalToTrimmedAlleleMap = new HashMap<Allele, Allele>();
final GenotypesContext genotypes = GenotypesContext.create();
final Map<Allele, Allele> originalToTrimmedAlleleMap = new HashMap<Allele, Allele>();
for (final Allele a : inputVC.getAlleles()) {
if (a.isSymbolic()) {
@ -820,8 +819,8 @@ public class VariantContextUtils {
originalToTrimmedAlleleMap.put(a, a);
} else {
// get bases for current allele and create a new one with trimmed bases
byte[] newBases = Arrays.copyOfRange(a.getBases(), 0, a.length()-trimExtent);
Allele trimmedAllele = Allele.create(newBases, a.isReference());
final byte[] newBases = Arrays.copyOfRange(a.getBases(), 0, a.length()-trimExtent);
final Allele trimmedAllele = Allele.create(newBases, a.isReference());
alleles.add(trimmedAllele);
originalToTrimmedAlleleMap.put(a, trimmedAllele);
}
@ -829,9 +828,8 @@ public class VariantContextUtils {
// now we can recreate new genotypes with trimmed alleles
for ( final Genotype genotype : inputVC.getGenotypes() ) {
List<Allele> originalAlleles = genotype.getAlleles();
List<Allele> trimmedAlleles = new ArrayList<Allele>();
final List<Allele> originalAlleles = genotype.getAlleles();
final List<Allele> trimmedAlleles = new ArrayList<Allele>();
for ( final Allele a : originalAlleles ) {
if ( a.isCalled() )
trimmedAlleles.add(originalToTrimmedAlleleMap.get(a));
@ -841,8 +839,7 @@ public class VariantContextUtils {
genotypes.add(Genotype.modifyAlleles(genotype, trimmedAlleles));
}
final VariantContextBuilder builder = new VariantContextBuilder(inputVC).stop(inputVC.getStart() + alleles.get(0).length());
return builder.alleles(alleles).genotypes(genotypes).make();
return new VariantContextBuilder(inputVC).stop(inputVC.getEnd() - trimExtent).alleles(alleles).genotypes(genotypes).make();
}
public static GenotypesContext stripPLs(GenotypesContext genotypes) {