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Increasing the size of the active regions that are produced by the active probability integrator, more context is needed to call more complex events

This commit is contained in:
Ryan Poplin 2012-01-30 15:36:12 -05:00
parent 0e17cbbce9
commit abb91cf26b
3 changed files with 5 additions and 5 deletions
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6
public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseActiveRegions.java
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@ -216,7 +216,7 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
// band-pass filter the list of isActive probabilities and turn into active regions // band-pass filter the list of isActive probabilities and turn into active regions
private ArrayList<ActiveRegion> integrateActiveList( final ArrayList<Double> activeList, final GenomeLoc firstIsActiveStart, final int activeRegionExtension ) { private ArrayList<ActiveRegion> integrateActiveList( final ArrayList<Double> activeList, final GenomeLoc firstIsActiveStart, final int activeRegionExtension ) {
final double ACTIVE_PROB_THRESHOLD = 0.2; final double ACTIVE_PROB_THRESHOLD = 0.2; // BUGBUG: needs to be set-able by the walker author
final ArrayList<ActiveRegion> returnList = new ArrayList<ActiveRegion>(); final ArrayList<ActiveRegion> returnList = new ArrayList<ActiveRegion>();
if( activeList.size() == 0 ) { if( activeList.size() == 0 ) {
return returnList; return returnList;
@ -227,8 +227,8 @@ public class TraverseActiveRegions <M,T> extends TraversalEngine<M,T,ActiveRegio
} else { } else {
final Double[] activeProbArray = activeList.toArray(new Double[activeList.size()]); final Double[] activeProbArray = activeList.toArray(new Double[activeList.size()]);
final double[] filteredProbArray = new double[activeProbArray.length]; final double[] filteredProbArray = new double[activeProbArray.length];
final int FILTER_SIZE = 10; final int FILTER_SIZE = 50; // BUGBUG: needs to be set-able by the walker author
final int MAX_ACTIVE_REGION = 200; final int MAX_ACTIVE_REGION = 425; // BUGBUG: needs to be set-able by the walker author
for( int iii = 0; iii < activeProbArray.length; iii++ ) { for( int iii = 0; iii < activeProbArray.length; iii++ ) {
double maxVal = 0; double maxVal = 0;
for( int jjj = Math.max(0, iii-FILTER_SIZE); jjj < Math.min(activeList.size(), iii+FILTER_SIZE); jjj++ ) { for( int jjj = Math.max(0, iii-FILTER_SIZE); jjj < Math.min(activeList.size(), iii+FILTER_SIZE); jjj++ ) {

2
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
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@ -335,7 +335,7 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
if (ref.getWindow().getStop() < loc.getStop() + HAPLOTYPE_SIZE) if (ref.getWindow().getStop() < loc.getStop() + HAPLOTYPE_SIZE)
return null; return null;
if (!(priors instanceof DiploidIndelGenotypePriors)) if (!(priors instanceof DiploidIndelGenotypePriors))
throw new StingException("Only diploid-based Indel priors are supported in the DINDEL GL model"); throw new StingException("Only diploid-based Indel priors are supported in the INDEL GL model");
if (alleleList.isEmpty()) if (alleleList.isEmpty())
return null; return null;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java
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@ -15,7 +15,7 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContext;
* @Author chartl * @Author chartl
* @Date May 26, 2010 * @Date May 26, 2010
*/ */
@Analysis(name = "Indel length histograms", description = "Shows the distrbution of insertion/deletion event lengths (negative for deletion, positive for insertion)") @Analysis(name = "Indel length histograms", description = "Shows the distribution of insertion/deletion event lengths (negative for deletion, positive for insertion)")
public class IndelLengthHistogram extends VariantEvaluator { public class IndelLengthHistogram extends VariantEvaluator {
private static final int SIZE_LIMIT = 100; private static final int SIZE_LIMIT = 100;
@DataPoint(description="Histogram of indel lengths") @DataPoint(description="Histogram of indel lengths")