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Merge branch 'master' of gsa2:/humgen/gsa-scr1/chartl/dev/unstable

This commit is contained in:
Chris Hartl 2013-01-10 14:35:59 -05:00
parent 31a5f88c4f f801cb3be5
commit 80dec72c53
9 changed files with 35 additions and 10 deletions
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2
build.xml
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@ -991,7 +991,7 @@
<!-- Maven install a package consisting of all supporting files. Don't call this target directly. Call one of the specific packaging targets below -->
<target name="mvninstall" depends="package" description="maven install a package into .m2/repository">
<property name="mvn.build.version" value="0.0.1" />
<property name="mvn.build.version" value="0.0.2" />
<!--
We should use the build version or better yet a git tag version, but tags are currently missing. Alternatively how do we then depend on the LATEST?
<property name="mvn.build.version" value="${build.version}" />

7
licensing/private_license.txt 100644
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@ -0,0 +1,7 @@
PRIVATE PRIVATE PRIVATE
This is a test license for the GATK
all files will abide to it
one license to rule them all
PRIVATE PRIVATE PRIVATE

7
licensing/protected_license.txt 100644
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@ -0,0 +1,7 @@
PROTECTED PROTECTED PROTECTED
This is a test license for the GATK
all files will abide to it
one license to rule them all
PROTECTED PROTECTED PROTECTED

7
licensing/public_license.txt 100644
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@ -0,0 +1,7 @@
PUBLIC PUBLIC PUBLIC
This is a test license for the GATK
all files will abide to it
one license to rule them all
PUBLIC PUBLIC PUBLIC

4
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
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@ -92,6 +92,7 @@ public class GenotypingEngine {
cleanUpSymbolicUnassembledEvents( haplotypes );
if( !in_GGA_mode && samples.size() >= 10 ) { // if not in GGA mode and have at least 10 samples try to create MNP and complex events by looking at LD structure
mergeConsecutiveEventsBasedOnLD( haplotypes, samples, haplotypeReadMap, startPosKeySet, ref, refLoc );
cleanUpSymbolicUnassembledEvents( haplotypes ); // the newly created merged events could be overlapping the unassembled events
}
if( in_GGA_mode ) {
for( final VariantContext compVC : activeAllelesToGenotype ) {
@ -261,7 +262,6 @@ public class GenotypingEngine {
return returnMap;
}
protected static void cleanUpSymbolicUnassembledEvents( final List<Haplotype> haplotypes ) {
final ArrayList<Haplotype> haplotypesToRemove = new ArrayList<Haplotype>();
for( final Haplotype h : haplotypes ) {
@ -269,7 +269,7 @@ public class GenotypingEngine {
if( vc.isSymbolic() ) {
for( final Haplotype h2 : haplotypes ) {
for( final VariantContext vc2 : h2.getEventMap().values() ) {
if( vc.getStart() == vc2.getStart() && vc2.isIndel() ) {
if( vc.getStart() == vc2.getStart() && (vc2.isIndel() || vc2.isMNP()) ) { // unfortunately symbolic alleles can't currently be combined with non-point events
haplotypesToRemove.add(h);
break;
}

7
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
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@ -136,6 +136,10 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
@Argument(fullName="gcpHMM", shortName="gcpHMM", doc="Flat gap continuation penalty for use in the Pair HMM", required = false)
protected int gcpHMM = 10;
@Advanced
@Argument(fullName="maxNumHaplotypesInPopulation", shortName="maxNumHaplotypesInPopulation", doc="Maximum number of haplotypes to consider for your population. This number will probably need to be increased when calling organisms with high heterozygosity.", required = false)
protected int maxNumHaplotypesInPopulation = 13;
@Advanced
@Argument(fullName="minKmer", shortName="minKmer", doc="Minimum kmer length to use in the assembly graph", required = false)
protected int minKmer = 11;
@ -414,7 +418,8 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
final Map<String, ArrayList<GATKSAMRecord>> perSampleFilteredReadList = splitReadsBySample( filteredReads );
// subset down to only the best haplotypes to be genotyped in all samples ( in GGA mode use all discovered haplotypes )
final ArrayList<Haplotype> bestHaplotypes = ( UG_engine.getUAC().GenotypingMode != GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ? likelihoodCalculationEngine.selectBestHaplotypes( haplotypes, stratifiedReadMap ) : haplotypes );
final ArrayList<Haplotype> bestHaplotypes = ( UG_engine.getUAC().GenotypingMode != GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES ?
likelihoodCalculationEngine.selectBestHaplotypes( haplotypes, stratifiedReadMap, maxNumHaplotypesInPopulation ) : haplotypes );
for( final VariantContext call : genotypingEngine.assignGenotypeLikelihoods( UG_engine,
bestHaplotypes,

4
protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
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@ -273,7 +273,7 @@ public class LikelihoodCalculationEngine {
@Requires({"haplotypes.size() > 0"})
@Ensures({"result.size() <= haplotypes.size()"})
public ArrayList<Haplotype> selectBestHaplotypes( final ArrayList<Haplotype> haplotypes, final Map<String, PerReadAlleleLikelihoodMap> stratifiedReadMap ) {
public ArrayList<Haplotype> selectBestHaplotypes( final ArrayList<Haplotype> haplotypes, final Map<String, PerReadAlleleLikelihoodMap> stratifiedReadMap, final int maxNumHaplotypesInPopulation ) {
final int numHaplotypes = haplotypes.size();
final Set<String> sampleKeySet = stratifiedReadMap.keySet();
@ -287,7 +287,7 @@ public class LikelihoodCalculationEngine {
int hap1 = 0;
int hap2 = 0;
//double bestElement = Double.NEGATIVE_INFINITY;
final int maxChosenHaplotypes = Math.min( 13, sampleKeySet.size() * 2 + 1 );
final int maxChosenHaplotypes = Math.min( maxNumHaplotypesInPopulation, sampleKeySet.size() * 2 + 1 );
while( bestHaplotypesIndexList.size() < maxChosenHaplotypes ) {
double maxElement = Double.NEGATIVE_INFINITY;
for( int iii = 0; iii < numHaplotypes; iii++ ) {

2
public/java/src/org/broadinstitute/variant/variantcontext/VariantContextUtils.java
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@ -710,7 +710,7 @@ public class VariantContextUtils {
for ( VariantContext vc : VCs ) {
// look at previous variant contexts of different type. If:
// a) otherVC has alleles which are subset of vc, remove otherVC from its list and add otherVC to vc's list
// a) otherVC has alleles which are subset of vc, remove otherVC from its list and add otherVC to vc's list
// b) vc has alleles which are subset of otherVC. Then, add vc to otherVC's type list (rather, do nothing since vc will be added automatically to its list)
// c) neither: do nothing, just add vc to its own list
boolean addtoOwnList = true;

5
public/packages/GATKEngine.xml
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@ -53,11 +53,10 @@
<file name="public/testdata/exampleFASTA.fasta.fai" />
<file name="public/testdata/exampleFASTA.dict" />
<!-- GATK sample code and build scripts -->
<file name="public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java" />
<file name="public/java/src/org/broadinstitute/sting/gatk/walkers/Pileup.java" />
<file name="public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReads.java" />
<file name="public/java/src/org/broadinstitute/sting/gatk/walkers/qc/Pileup.java" />
<file name="public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLoci.java" />
<file name="public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReads.java" />
<file name="public/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileup.java" />
<file name="public/java/src/org/broadinstitute/sting/gatk/walkers/readutils/PrintReads.java" />
</resources>
</package>