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Refactoring so that Unified Argument Collection doesn't use deprecated classes.

This commit is contained in:
Eric Banks 2012-04-09 13:45:17 -04:00
parent 6ddf2170b6
commit ea4300d583
3 changed files with 7 additions and 4 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoodsWithCorrectAlleleOrdering.java
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@ -72,6 +72,8 @@ import static java.lang.Math.pow;
*/
public class DiploidSNPGenotypeLikelihoodsWithCorrectAlleleOrdering implements Cloneable {
public final static double DEFAULT_PCR_ERROR_RATE = 1e-4;
protected final static int FIXED_PLOIDY = 2;
protected final static int MAX_PLOIDY = FIXED_PLOIDY + 1;
protected final static double ploidyAdjustment = log10(FIXED_PLOIDY);

4
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
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@ -45,7 +45,7 @@ public class UnifiedArgumentCollection {
* het = 1e-3, P(hom-ref genotype) = 1 - 3 * het / 2, P(het genotype) = het, P(hom-var genotype) = het / 2
*/
@Argument(fullName = "heterozygosity", shortName = "hets", doc = "Heterozygosity value used to compute prior likelihoods for any locus", required = false)
public Double heterozygosity = DiploidSNPGenotypePriors.HUMAN_HETEROZYGOSITY;
public Double heterozygosity = UnifiedGenotyperEngine.HUMAN_SNP_HETEROZYGOSITY;
/**
* The PCR error rate is independent of the sequencing error rate, which is necessary because we cannot necessarily
@ -53,7 +53,7 @@ public class UnifiedArgumentCollection {
* effectively acts as a cap on the base qualities.
*/
@Argument(fullName = "pcr_error_rate", shortName = "pcr_error", doc = "The PCR error rate to be used for computing fragment-based likelihoods", required = false)
public Double PCR_error = DiploidSNPGenotypeLikelihoods.DEFAULT_PCR_ERROR_RATE;
public Double PCR_error = DiploidSNPGenotypeLikelihoodsWithCorrectAlleleOrdering.DEFAULT_PCR_ERROR_RATE;
/**
* Specifies how to determine the alternate allele to use for genotyping

5
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
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@ -53,6 +53,9 @@ public class UnifiedGenotyperEngine {
public static final int DEFAULT_PLOIDY = 2;
public static final double HUMAN_SNP_HETEROZYGOSITY = 1e-3;
public static final double HUMAN_INDEL_HETEROZYGOSITY = 1e-4;
public enum OUTPUT_MODE {
/** produces calls only at variant sites */
EMIT_VARIANTS_ONLY,
@ -622,8 +625,6 @@ public class UnifiedGenotyperEngine {
}
public static final double HUMAN_SNP_HETEROZYGOSITY = 1e-3;
public static final double HUMAN_INDEL_HETEROZYGOSITY = 1e-4;
protected double getTheta( final GenotypeLikelihoodsCalculationModel.Model model ) {
if( model.name().contains("SNP") )
return HUMAN_SNP_HETEROZYGOSITY;