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

Alleles now hash correctly. 

Special thanks to Matt & Aaron.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2965 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-03-09 18:09:44 +00:00
parent e5475a7ba9
commit 0e360ea8af
2 changed files with 52 additions and 40 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

83
java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/Allele.java
View File

@ -121,23 +121,33 @@ public class Allele implements Comparable<Allele> {
}
/**
* Do the bases represent the null allele?
* @param bases bases representing an allele
* @return true if the bases represent the null allele
*/
public static boolean wouldBeNullAllele(byte[] bases) {
return (bases.length == 1 && bases[0] == '-') || bases.length == 0;
}
/** Do the bases represent the NO_CALL allele? */
/**
* @param bases bases representing an allele
* @return true if the bases represent the NO_CALL allele
*/
public static boolean wouldBeNoCallAllele(byte[] bases) {
return bases.length == 1 && bases[0] == '.';
}
/** Do the bases represent the null allele? */
/**
* @param bases bases representing an allele
* @return true if the bases represent the well formatted allele
*/
public static boolean acceptableAlleleBases(String bases) {
return acceptableAlleleBases(bases.getBytes());
}
/** Can we create an allele from bases, including NO_CALL and Null alleles? */
/**
* @param bases bases representing an allele
* @return true if the bases represent the well formatted allele
*/
public static boolean acceptableAlleleBases(byte[] bases) {
if ( wouldBeNullAllele(bases) || wouldBeNoCallAllele(bases) )
return true;
@ -154,8 +164,8 @@ public class Allele implements Comparable<Allele> {
/**
* @see Allele(byte[], boolean)
*
* @param bases
* @param isRef
* @param bases bases representing an allele
* @param isRef is this the reference allele?
*/
public Allele(String bases, boolean isRef) {
this(bases.getBytes(), isRef);
@ -164,14 +174,14 @@ public class Allele implements Comparable<Allele> {
/**
* Creates a non-Ref allele. @see Allele(byte[], boolean) for full information
*
* @param bases
* @param bases bases representing an allele
*/
public Allele(String bases) { this(bases, false); }
/**
* Creates a non-Ref allele. @see Allele(byte[], boolean) for full information
*
* @param bases
* @param bases bases representing an allele
*/
public Allele(byte[] bases) { this(bases, false); }
@ -181,22 +191,22 @@ public class Allele implements Comparable<Allele> {
//
// ---------------------------------------------------------------------------------------------------------
/** Returns true if this is the null allele */
//Returns true if this is the null allele
public boolean isNull() { return isNull; }
/** Returns true if this is not the null allele */
// Returns true if this is not the null allele
public boolean isNonNull() { return ! isNull(); }
/** Returns true if this is the NO_CALL allele */
// Returns true if this is the NO_CALL allele
public boolean isNoCall() { return isNoCall; }
/** Returns true if this is the not the NO_CALL allele */
// Returns true if this is the not the NO_CALL allele
public boolean isCalled() { return ! isNoCall(); }
/** Returns true if this Allele is the reference allele */
// Returns true if this Allele is the reference allele
public boolean isReference() { return isRef; }
/** Returns true if this Allele is not the reference allele */
// Returns true if this Allele is not the reference allele
public boolean isNonReference() { return ! isReference(); }
/** Returns a nice string representation of this object */
// Returns a nice string representation of this object
public String toString() {
return (isNull() ? "-" : ( isNoCall() ? "." : new String(getBases()))) + (isReference() ? "*" : "");
}
@ -214,52 +224,55 @@ public class Allele implements Comparable<Allele> {
*
* @return true if these alleles are equal
*/
public boolean equals(Allele other) {
return equals(other, false);
public boolean equals(Object other) {
return ( ! (other instanceof Allele) ? false : equals((Allele)other, false) );
}
/**
* @return hash code
*/
public int hashCode() {
int hash = 1;
for (int i = 0; i < bases.length; i++)
hash += (i+1) * bases[i];
return hash;
}
/**
* Returns true if this and other are equal. If ignoreRefState is true, then doesn't require both alleles has the
* same ref tag
*
* @param other
* @param ignoreRefState
* @return
* @param other allele to compare to
* @param ignoreRefState if true, ignore ref state in comparison
* @return true if this and other are equal
*/
public boolean equals(Allele other, boolean ignoreRefState) {
return (isRef == other.isRef || ignoreRefState) && isNull == other.isNull && isNoCall == other.isNoCall && this.basesMatch(other.getBases());
return (isRef == other.isRef || ignoreRefState) && isNull == other.isNull && isNoCall == other.isNoCall && basesMatch(other.getBases());
}
/**
* Returns true if this Alelle contains the same bases as test, regardless of its reference status. Also handles
* Null and NO_CALL alleles
* @param test bases to test against
*
* @param test
* @return
* @return true if this Alelle contains the same bases as test, regardless of its reference status; handles Null and NO_CALL alleles
*/
public boolean basesMatch(byte[] test) { return bases == test || Arrays.equals(bases, test); }
/**
* Returns true if this Alelle contains the same bases as test, regardless of its reference status. Also handles
* Null and NO_CALL alleles
* @param test bases to test against
*
* @param test
* @return
* @return true if this Alelle contains the same bases as test, regardless of its reference status; handles Null and NO_CALL alleles
*/
public boolean basesMatch(String test) { return basesMatch(test.toUpperCase().getBytes()); }
/**
* Returns true if this Alelle contains the same bases as test, regardless of its reference status. Also handles
* Null and NO_CALL alleles
* @param test allele to test against
*
* @param test
* @return
* @return true if this Alelle contains the same bases as test, regardless of its reference status; handles Null and NO_CALL alleles
*/
public boolean basesMatch(Allele test) { return basesMatch(test.getBases()); }
/**
* Returns the length of this allele. Null and NO_CALL alleles have 0 length.
* @return
* @return the length of this allele. Null and NO_CALL alleles have 0 length.
*/
public int length() {
return bases.length;

9
java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
View File

@ -227,9 +227,8 @@ public class VariantContextAdaptors {
String filters = vc.isFiltered() ? Utils.join(";", Utils.sorted(vc.getFilters())) : (filtersWereAppliedToContext ? VCFRecord.PASSES_FILTERS : VCFRecord.UNFILTERED);
// TODO - fixme: temporarily using Strings as keys because Alleles aren't hashing correctly
Map<String, VCFGenotypeEncoding> alleleMap = new HashMap<String, VCFGenotypeEncoding>();
alleleMap.put(Allele.NO_CALL.toString(), new VCFGenotypeEncoding(VCFGenotypeRecord.EMPTY_ALLELE)); // convenience for lookup
Map<Allele, VCFGenotypeEncoding> alleleMap = new HashMap<Allele, VCFGenotypeEncoding>();
alleleMap.put(Allele.NO_CALL, new VCFGenotypeEncoding(VCFGenotypeRecord.EMPTY_ALLELE)); // convenience for lookup
List<VCFGenotypeEncoding> vcfAltAlleles = new ArrayList<VCFGenotypeEncoding>();
for ( Allele a : vc.getAlleles() ) {
@ -271,7 +270,7 @@ public class VariantContextAdaptors {
vcfAltAlleles.add(encoding);
}
alleleMap.put(a.toString(), encoding);
alleleMap.put(a, encoding);
}
if ( vcfGenotypeAttributeKeys == null ) {
@ -288,7 +287,7 @@ public class VariantContextAdaptors {
List<VCFGenotypeEncoding> encodings = new ArrayList<VCFGenotypeEncoding>(g.getPloidy());
for ( Allele a : g.getAlleles() ) {
encodings.add(alleleMap.get(a.toString()));
encodings.add(alleleMap.get(a));
}
VCFGenotypeRecord.PHASE phasing = g.genotypesArePhased() ? VCFGenotypeRecord.PHASE.PHASED : VCFGenotypeRecord.PHASE.UNPHASED;