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Okay, all public->protected dependencies are gone except for the BQSR arguments. I'll need to think through this but should be able to make that work too.

This commit is contained in:
Eric Banks 2013-01-08 15:46:32 -05:00
parent 0841ce3de5
commit f0bd1b5ae5
6 changed files with 7 additions and 4 deletions
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0
public/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java → protected/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java
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1
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
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@ -37,6 +37,7 @@ import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.baq.BAQ;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
import org.broadinstitute.sting.utils.genotyper.DiploidGenotype;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;

8
public/java/src/org/broadinstitute/sting/gatk/examples/GATKPaperGenotyper.java
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@ -33,8 +33,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.gatk.walkers.TreeReducible;
import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine;
import org.broadinstitute.sting.gatk.walkers.genotyper.DiploidGenotype;
import org.broadinstitute.sting.utils.genotyper.DiploidGenotype;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
@ -50,6 +49,9 @@ import java.io.PrintStream;
*/
@DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} )
public class GATKPaperGenotyper extends LocusWalker<Integer,Long> implements TreeReducible<Long> {
public static final double HUMAN_SNP_HETEROZYGOSITY = 1e-3;
// the possible diploid genotype strings
private static enum GENOTYPE { AA, AC, AG, AT, CC, CG, CT, GG, GT, TT }
@ -73,7 +75,7 @@ public class GATKPaperGenotyper extends LocusWalker<Integer,Long> implements Tre
ReadBackedPileup pileup = context.getBasePileup().getPileupWithoutMappingQualityZeroReads();
double likelihoods[] = getReferencePolarizedPriors(ref.getBase(),
UnifiedGenotyperEngine.HUMAN_SNP_HETEROZYGOSITY,
HUMAN_SNP_HETEROZYGOSITY,
0.01);
// get the bases and qualities from the pileup
byte bases[] = pileup.getBases();

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotype.java → public/java/src/org/broadinstitute/sting/utils/genotyper/DiploidGenotype.java
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@ -23,7 +23,7 @@
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.walkers.genotyper;
package org.broadinstitute.sting.utils.genotyper;
import org.broadinstitute.variant.utils.BaseUtils;

0
protected/java/src/org/broadinstitute/sting/utils/recalibration/BQSRMode.java → public/java/src/org/broadinstitute/sting/utils/recalibration/BQSRMode.java
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0
protected/java/src/org/broadinstitute/sting/utils/recalibration/EventType.java → public/java/src/org/broadinstitute/sting/utils/recalibration/EventType.java
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