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Add a separate max alt alleles argument for indels that defaults to 2 instead of 3. PLEASE TAKE NOTE.

This commit is contained in:
Eric Banks 2012-10-04 13:52:14 -04:00
parent e13e61673b
commit c66ef17cd0
7 changed files with 23 additions and 16 deletions
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2
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyExactAFCalculation.java
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@ -47,7 +47,7 @@ public class GeneralPloidyExactAFCalculation extends ExactAFCalculation {
}
public GeneralPloidyExactAFCalculation(final int nSamples, final int maxAltAlleles, final int ploidy) {
super(nSamples, maxAltAlleles, false, null, null, null);
super(nSamples, maxAltAlleles, maxAltAlleles, null, null, null);
this.ploidy = ploidy;
}

10
public/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java
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@ -59,6 +59,16 @@ public class StandardCallerArgumentCollection {
@Argument(fullName = "max_alternate_alleles", shortName = "maxAltAlleles", doc = "Maximum number of alternate alleles to genotype", required = false)
public int MAX_ALTERNATE_ALLELES = 3;
/**
* If there are more than this number of alternate alleles presented to the genotyper (either through discovery or GENOTYPE_GIVEN ALLELES),
* then only this many alleles will be used. Note that genotyping sites with many alternate alleles is both CPU and memory intensive and it
* scales exponentially based on the number of alternate alleles. Unless there is a good reason to change the default value, we highly recommend
* that you not play around with this parameter.
*/
@Advanced
@Argument(fullName = "max_alternate_alleles_for_indels", shortName = "maxAltAllelesForIndels", doc = "Maximum number of alternate alleles to genotype for indels only", required = false)
public int MAX_ALTERNATE_ALLELES_FOR_INDELS = 2;
@Hidden
@Argument(shortName = "logExactCalls", doc="x", required=false)
public File exactCallsLog = null;

8
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/AlleleFrequencyCalculation.java
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@ -63,7 +63,7 @@ public abstract class AlleleFrequencyCalculation implements Cloneable {
protected int nSamples;
protected int MAX_ALTERNATE_ALLELES_TO_GENOTYPE;
protected boolean CAP_MAX_ALTERNATE_ALLELES_FOR_INDELS;
protected int MAX_ALTERNATE_ALLELES_FOR_INDELS;
protected Logger logger;
protected PrintStream verboseWriter;
@ -74,12 +74,12 @@ public abstract class AlleleFrequencyCalculation implements Cloneable {
private PrintStream callReport = null;
protected AlleleFrequencyCalculation(final UnifiedArgumentCollection UAC, final int nSamples, final Logger logger, final PrintStream verboseWriter) {
this(nSamples, UAC.MAX_ALTERNATE_ALLELES, UAC.CAP_MAX_ALTERNATE_ALLELES_FOR_INDELS, UAC.exactCallsLog, logger, verboseWriter);
this(nSamples, UAC.MAX_ALTERNATE_ALLELES, UAC.MAX_ALTERNATE_ALLELES_FOR_INDELS, UAC.exactCallsLog, logger, verboseWriter);
}
protected AlleleFrequencyCalculation(final int nSamples,
final int maxAltAlleles,
final boolean capMaxAltsForIndels,
final int maxAltAllelesForIndels,
final File exactCallsLog,
final Logger logger,
final PrintStream verboseWriter) {
@ -88,7 +88,7 @@ public abstract class AlleleFrequencyCalculation implements Cloneable {
this.nSamples = nSamples;
this.MAX_ALTERNATE_ALLELES_TO_GENOTYPE = maxAltAlleles;
this.CAP_MAX_ALTERNATE_ALLELES_FOR_INDELS = capMaxAltsForIndels;
this.MAX_ALTERNATE_ALLELES_FOR_INDELS = maxAltAllelesForIndels;
this.logger = logger == null ? defaultLogger : logger;
this.verboseWriter = verboseWriter;
if ( exactCallsLog != null )

4
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidExactAFCalculation.java
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@ -38,7 +38,7 @@ public class DiploidExactAFCalculation extends ExactAFCalculation {
private final static double MAX_LOG10_ERROR_TO_STOP_EARLY = 6; // we want the calculation to be accurate to 1 / 10^6
public DiploidExactAFCalculation(final int nSamples, final int maxAltAlleles) {
super(nSamples, maxAltAlleles, false, null, null, null);
super(nSamples, maxAltAlleles, maxAltAlleles, null, null, null);
}
/**
@ -62,7 +62,7 @@ public class DiploidExactAFCalculation extends ExactAFCalculation {
@Override
protected VariantContext reduceScope(final VariantContext vc) {
final int myMaxAltAllelesToGenotype = CAP_MAX_ALTERNATE_ALLELES_FOR_INDELS && vc.getType().equals(VariantContext.Type.INDEL) ? 2 : MAX_ALTERNATE_ALLELES_TO_GENOTYPE;
final int myMaxAltAllelesToGenotype = vc.getType().equals(VariantContext.Type.INDEL) ? MAX_ALTERNATE_ALLELES_FOR_INDELS : MAX_ALTERNATE_ALLELES_TO_GENOTYPE;
// don't try to genotype too many alternate alleles
if ( vc.getAlternateAlleles().size() > myMaxAltAllelesToGenotype ) {

4
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculation.java
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@ -45,8 +45,8 @@ abstract class ExactAFCalculation extends AlleleFrequencyCalculation {
super(UAC, nSamples, logger, verboseWriter);
}
protected ExactAFCalculation(final int nSamples, int maxAltAlleles, boolean capMaxAltsForIndels, File exactCallsLog, Logger logger, PrintStream verboseWriter) {
super(nSamples, maxAltAlleles, capMaxAltsForIndels, exactCallsLog, logger, verboseWriter);
protected ExactAFCalculation(final int nSamples, int maxAltAlleles, int maxAltAllelesForIndels, File exactCallsLog, Logger logger, PrintStream verboseWriter) {
super(nSamples, maxAltAlleles, maxAltAllelesForIndels, exactCallsLog, logger, verboseWriter);
}
/**

4
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/OptimizedDiploidExactAFCalculation.java
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@ -38,7 +38,7 @@ public class OptimizedDiploidExactAFCalculation extends ExactAFCalculation {
private final static double MAX_LOG10_ERROR_TO_STOP_EARLY = 6; // we want the calculation to be accurate to 1 / 10^6
public OptimizedDiploidExactAFCalculation(final int nSamples, final int maxAltAlleles) {
super(nSamples, maxAltAlleles, false, null, null, null);
super(nSamples, maxAltAlleles, maxAltAlleles, null, null, null);
}
/**
@ -62,7 +62,7 @@ public class OptimizedDiploidExactAFCalculation extends ExactAFCalculation {
@Override
protected VariantContext reduceScope(final VariantContext vc) {
final int myMaxAltAllelesToGenotype = CAP_MAX_ALTERNATE_ALLELES_FOR_INDELS && vc.getType().equals(VariantContext.Type.INDEL) ? 2 : MAX_ALTERNATE_ALLELES_TO_GENOTYPE;
final int myMaxAltAllelesToGenotype = vc.getType().equals(VariantContext.Type.INDEL) ? MAX_ALTERNATE_ALLELES_FOR_INDELS : MAX_ALTERNATE_ALLELES_TO_GENOTYPE;
// don't try to genotype too many alternate alleles
if ( vc.getAlternateAlleles().size() > myMaxAltAllelesToGenotype ) {

7
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
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@ -75,10 +75,6 @@ public class UnifiedArgumentCollection extends StandardCallerArgumentCollection
@Argument(fullName = "max_deletion_fraction", shortName = "deletions", doc = "Maximum fraction of reads with deletions spanning this locus for it to be callable [to disable, set to < 0 or > 1; default:0.05]", required = false)
public Double MAX_DELETION_FRACTION = 0.05;
@Hidden
@Argument(fullName = "cap_max_alternate_alleles_for_indels", shortName = "capMaxAltAllelesForIndels", doc = "Cap the maximum number of alternate alleles to genotype for indel calls at 2; overrides the --max_alternate_alleles argument; GSA production use only", required = false)
public boolean CAP_MAX_ALTERNATE_ALLELES_FOR_INDELS = false;
// indel-related arguments
/**
* A candidate indel is genotyped (and potentially called) if there are this number of reads with a consensus indel at a site.
@ -211,7 +207,7 @@ public class UnifiedArgumentCollection extends StandardCallerArgumentCollection
uac.INDEL_HAPLOTYPE_SIZE = INDEL_HAPLOTYPE_SIZE;
uac.alleles = alleles;
uac.MAX_ALTERNATE_ALLELES = MAX_ALTERNATE_ALLELES;
uac.CAP_MAX_ALTERNATE_ALLELES_FOR_INDELS = CAP_MAX_ALTERNATE_ALLELES_FOR_INDELS;
uac.MAX_ALTERNATE_ALLELES_FOR_INDELS = MAX_ALTERNATE_ALLELES_FOR_INDELS;
uac.GLmodel = GLmodel;
uac.TREAT_ALL_READS_AS_SINGLE_POOL = TREAT_ALL_READS_AS_SINGLE_POOL;
uac.referenceSampleRod = referenceSampleRod;
@ -239,6 +235,7 @@ public class UnifiedArgumentCollection extends StandardCallerArgumentCollection
this.GenotypingMode = SCAC.GenotypingMode;
this.heterozygosity = SCAC.heterozygosity;
this.MAX_ALTERNATE_ALLELES = SCAC.MAX_ALTERNATE_ALLELES;
this.MAX_ALTERNATE_ALLELES_FOR_INDELS = SCAC.MAX_ALTERNATE_ALLELES_FOR_INDELS;
this.OutputMode = SCAC.OutputMode;
this.STANDARD_CONFIDENCE_FOR_CALLING = SCAC.STANDARD_CONFIDENCE_FOR_CALLING;
this.STANDARD_CONFIDENCE_FOR_EMITTING = SCAC.STANDARD_CONFIDENCE_FOR_EMITTING;