From 9b5c79b49de7976fb167fb2c74985e2a3dcd36be Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Mon, 14 Nov 2011 14:28:52 -0500 Subject: [PATCH] Renamed InferredGeneticContext to CommonInfo -- I have no idea why I named this InferredGeneticContext, a totally meaningless term -- Renamed to CommonInfo. -- Made package protected, as no one should use this outside of VariantContext and Genotype -- UGEngine was using IGC constant, but it's now using the public one in VariantContext. --- .../genotyper/UnifiedGenotyperEngine.java | 2 +- ...redGeneticContext.java => CommonInfo.java} | 4 +-- .../sting/utils/variantcontext/Genotype.java | 6 ++--- .../utils/variantcontext/VariantContext.java | 10 +++---- .../variantcontext/VariantContextUtils.java | 6 ++--- .../VariantContextUnitTest.java | 26 +++++++++---------- 6 files changed, 27 insertions(+), 27 deletions(-) rename public/java/src/org/broadinstitute/sting/utils/variantcontext/{InferredGeneticContext.java => CommonInfo.java} (98%) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java index bc9a5f65b..10bd7c8ae 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java @@ -229,7 +229,7 @@ public class UnifiedGenotyperEngine { VariantContext vcInput = UnifiedGenotyperEngine.getVCFromAllelesRod(tracker, ref, rawContext.getLocation(), false, logger, UAC.alleles); if ( vcInput == null ) return null; - vc = new VariantContext("UG_call", vcInput.getChr(), vcInput.getStart(), vcInput.getEnd(), vcInput.getAlleles(), InferredGeneticContext.NO_NEG_LOG_10PERROR, null, null, ref.getBase()); + vc = new VariantContext("UG_call", vcInput.getChr(), vcInput.getStart(), vcInput.getEnd(), vcInput.getAlleles(), VariantContext.NO_NEG_LOG_10PERROR, null, null, ref.getBase()); } else { // deal with bad/non-standard reference bases diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/InferredGeneticContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/CommonInfo.java similarity index 98% rename from public/java/src/org/broadinstitute/sting/utils/variantcontext/InferredGeneticContext.java rename to public/java/src/org/broadinstitute/sting/utils/variantcontext/CommonInfo.java index e7d9b3338..57edbbfcc 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/InferredGeneticContext.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/CommonInfo.java @@ -11,7 +11,7 @@ import java.util.*; * * @author depristo */ -public final class InferredGeneticContext { +final class CommonInfo { public static final double NO_NEG_LOG_10PERROR = -1.0; private static Set NO_FILTERS = Collections.unmodifiableSet(new HashSet()); @@ -22,7 +22,7 @@ public final class InferredGeneticContext { private Set filters = NO_FILTERS; private Map attributes = NO_ATTRIBUTES; - public InferredGeneticContext(String name, double negLog10PError, Set filters, Map attributes) { + public CommonInfo(String name, double negLog10PError, Set filters, Map attributes) { this.name = name; setNegLog10PError(negLog10PError); if ( filters != null && ! filters.isEmpty() ) diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java index eabd2dbad..28f2d85fc 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java @@ -17,8 +17,8 @@ public class Genotype { public final static String PHASED_ALLELE_SEPARATOR = "|"; public final static String UNPHASED_ALLELE_SEPARATOR = "/"; - protected InferredGeneticContext commonInfo; - public final static double NO_NEG_LOG_10PERROR = InferredGeneticContext.NO_NEG_LOG_10PERROR; + protected CommonInfo commonInfo; + public final static double NO_NEG_LOG_10PERROR = CommonInfo.NO_NEG_LOG_10PERROR; protected List alleles = null; // new ArrayList(); protected Type type = null; @@ -32,7 +32,7 @@ public class Genotype { public Genotype(String sampleName, List alleles, double negLog10PError, Set filters, Map attributes, boolean isPhased, double[] log10Likelihoods) { if ( alleles != null ) this.alleles = Collections.unmodifiableList(alleles); - commonInfo = new InferredGeneticContext(sampleName, negLog10PError, filters, attributes); + commonInfo = new CommonInfo(sampleName, negLog10PError, filters, attributes); if ( log10Likelihoods != null ) commonInfo.putAttribute(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY, GenotypeLikelihoods.fromLog10Likelihoods(log10Likelihoods)); filtersWereAppliedToContext = filters != null; diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java index 1766dc2bf..47b792e0b 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java @@ -162,8 +162,8 @@ import java.util.*; * @author depristo */ public class VariantContext implements Feature { // to enable tribble intergration - protected InferredGeneticContext commonInfo = null; - public final static double NO_NEG_LOG_10PERROR = InferredGeneticContext.NO_NEG_LOG_10PERROR; + protected CommonInfo commonInfo = null; + public final static double NO_NEG_LOG_10PERROR = CommonInfo.NO_NEG_LOG_10PERROR; public final static String UNPARSED_GENOTYPE_MAP_KEY = "_UNPARSED_GENOTYPE_MAP_"; public final static String UNPARSED_GENOTYPE_PARSER_KEY = "_UNPARSED_GENOTYPE_PARSER_"; public final static String ID_KEY = "ID"; @@ -293,7 +293,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati * @param alleles alleles */ public VariantContext(String source, String contig, long start, long stop, Collection alleles) { - this(source, contig, start, stop, alleles, NO_GENOTYPES, InferredGeneticContext.NO_NEG_LOG_10PERROR, null, null, null, false); + this(source, contig, start, stop, alleles, NO_GENOTYPES, CommonInfo.NO_NEG_LOG_10PERROR, null, null, null, false); } /** @@ -307,7 +307,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati * @param genotypes genotypes */ public VariantContext(String source, String contig, long start, long stop, Collection alleles, Collection genotypes) { - this(source, contig, start, stop, alleles, genotypes, InferredGeneticContext.NO_NEG_LOG_10PERROR, null, null); + this(source, contig, start, stop, alleles, genotypes, CommonInfo.NO_NEG_LOG_10PERROR, null, null); } /** @@ -350,7 +350,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati attributes.remove(UNPARSED_GENOTYPE_PARSER_KEY); } - this.commonInfo = new InferredGeneticContext(source, negLog10PError, filters, attributes); + this.commonInfo = new CommonInfo(source, negLog10PError, filters, attributes); filtersWereAppliedToContext = filters != null; REFERENCE_BASE_FOR_INDEL = referenceBaseForIndel; diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java index 996628b23..37d8acbe2 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java @@ -81,7 +81,7 @@ public class VariantContextUtils { * @return VariantContext object */ public static VariantContext toVC(String name, GenomeLoc loc, Collection alleles) { - return new VariantContext (name, loc.getContig(), loc.getStart(), loc.getStop(), alleles, VariantContext.NO_GENOTYPES, InferredGeneticContext.NO_NEG_LOG_10PERROR, null, null); + return new VariantContext (name, loc.getContig(), loc.getStart(), loc.getStop(), alleles, VariantContext.NO_GENOTYPES, CommonInfo.NO_NEG_LOG_10PERROR, null, null); } /** @@ -93,7 +93,7 @@ public class VariantContextUtils { * @return VariantContext object */ public static VariantContext toVC(String name, GenomeLoc loc, Collection alleles, Collection genotypes) { - return new VariantContext(name, loc.getContig(), loc.getStart(), loc.getStop(), alleles, genotypes, InferredGeneticContext.NO_NEG_LOG_10PERROR, null, null); + return new VariantContext(name, loc.getContig(), loc.getStart(), loc.getStop(), alleles, genotypes, CommonInfo.NO_NEG_LOG_10PERROR, null, null); } /** @@ -330,7 +330,7 @@ public class VariantContextUtils { return pruneVariantContext(vc, null); } - private final static Map subsetAttributes(final InferredGeneticContext igc, final Collection keysToPreserve) { + private final static Map subsetAttributes(final CommonInfo igc, final Collection keysToPreserve) { Map attributes = new HashMap(keysToPreserve.size()); for ( final String key : keysToPreserve ) { if ( igc.hasAttribute(key) ) diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java index 092bd362e..77980267c 100755 --- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java @@ -90,45 +90,45 @@ public class VariantContextUnitTest extends BaseTest { // test INDELs alleles = Arrays.asList(Aref, ATC); - vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles, null, InferredGeneticContext.NO_NEG_LOG_10PERROR, null, null, (byte)'A'); + vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles, null, CommonInfo.NO_NEG_LOG_10PERROR, null, null, (byte)'A'); Assert.assertEquals(vc.getType(), VariantContext.Type.INDEL); alleles = Arrays.asList(ATCref, A); - vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop+2, alleles, null, InferredGeneticContext.NO_NEG_LOG_10PERROR, null, null, (byte)'A'); + vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop+2, alleles, null, CommonInfo.NO_NEG_LOG_10PERROR, null, null, (byte)'A'); Assert.assertEquals(vc.getType(), VariantContext.Type.INDEL); alleles = Arrays.asList(Tref, TA, TC); - vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles, null, InferredGeneticContext.NO_NEG_LOG_10PERROR, null, null, (byte)'A'); + vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles, null, CommonInfo.NO_NEG_LOG_10PERROR, null, null, (byte)'A'); Assert.assertEquals(vc.getType(), VariantContext.Type.INDEL); alleles = Arrays.asList(ATCref, A, AC); - vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop+2, alleles, null, InferredGeneticContext.NO_NEG_LOG_10PERROR, null, null, (byte)'A'); + vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop+2, alleles, null, CommonInfo.NO_NEG_LOG_10PERROR, null, null, (byte)'A'); Assert.assertEquals(vc.getType(), VariantContext.Type.INDEL); alleles = Arrays.asList(ATCref, A, Allele.create("ATCTC")); - vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop+2, alleles, null, InferredGeneticContext.NO_NEG_LOG_10PERROR, null, null, (byte)'A'); + vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop+2, alleles, null, CommonInfo.NO_NEG_LOG_10PERROR, null, null, (byte)'A'); Assert.assertEquals(vc.getType(), VariantContext.Type.INDEL); // test MIXED alleles = Arrays.asList(TAref, T, TC); - vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop+1, alleles, null, InferredGeneticContext.NO_NEG_LOG_10PERROR, null, null, (byte)'A'); + vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop+1, alleles, null, CommonInfo.NO_NEG_LOG_10PERROR, null, null, (byte)'A'); Assert.assertEquals(vc.getType(), VariantContext.Type.MIXED); alleles = Arrays.asList(TAref, T, AC); - vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop+1, alleles, null, InferredGeneticContext.NO_NEG_LOG_10PERROR, null, null, (byte)'A'); + vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop+1, alleles, null, CommonInfo.NO_NEG_LOG_10PERROR, null, null, (byte)'A'); Assert.assertEquals(vc.getType(), VariantContext.Type.MIXED); alleles = Arrays.asList(ACref, ATC, AT); - vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop+1, alleles, null, InferredGeneticContext.NO_NEG_LOG_10PERROR, null, null, (byte)'A'); + vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop+1, alleles, null, CommonInfo.NO_NEG_LOG_10PERROR, null, null, (byte)'A'); Assert.assertEquals(vc.getType(), VariantContext.Type.MIXED); alleles = Arrays.asList(Aref, T, symbolic); - vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles, null, InferredGeneticContext.NO_NEG_LOG_10PERROR, null, null, (byte)'A'); + vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles, null, CommonInfo.NO_NEG_LOG_10PERROR, null, null, (byte)'A'); Assert.assertEquals(vc.getType(), VariantContext.Type.MIXED); // test SYMBOLIC alleles = Arrays.asList(Tref, symbolic); - vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles, null, InferredGeneticContext.NO_NEG_LOG_10PERROR, null, null, (byte)'A'); + vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop, alleles, null, CommonInfo.NO_NEG_LOG_10PERROR, null, null, (byte)'A'); Assert.assertEquals(vc.getType(), VariantContext.Type.SYMBOLIC); } @@ -199,7 +199,7 @@ public class VariantContextUnitTest extends BaseTest { @Test public void testCreatingDeletionVariantContext() { List alleles = Arrays.asList(ATCref, del); - VariantContext vc = new VariantContext("test", delLoc, delLocStart, delLocStop, alleles, null, InferredGeneticContext.NO_NEG_LOG_10PERROR, null, null, (byte)'A'); + VariantContext vc = new VariantContext("test", delLoc, delLocStart, delLocStop, alleles, null, CommonInfo.NO_NEG_LOG_10PERROR, null, null, (byte)'A'); Assert.assertEquals(vc.getChr(), delLoc); Assert.assertEquals(vc.getStart(), delLocStart); @@ -226,7 +226,7 @@ public class VariantContextUnitTest extends BaseTest { @Test public void testCreatingInsertionVariantContext() { List alleles = Arrays.asList(delRef, ATC); - VariantContext vc = new VariantContext("test", insLoc, insLocStart, insLocStop, alleles, null, InferredGeneticContext.NO_NEG_LOG_10PERROR, null, null, (byte)'A'); + VariantContext vc = new VariantContext("test", insLoc, insLocStart, insLocStop, alleles, null, CommonInfo.NO_NEG_LOG_10PERROR, null, null, (byte)'A'); Assert.assertEquals(vc.getChr(), insLoc); Assert.assertEquals(vc.getStart(), insLocStart); @@ -514,7 +514,7 @@ public class VariantContextUnitTest extends BaseTest { @Test(dataProvider = "getAlleles") public void testMergeAlleles(GetAllelesTest cfg) { final List altAlleles = cfg.alleles.subList(1, cfg.alleles.size()); - final VariantContext vc = new VariantContext("test", snpLoc, snpLocStart, snpLocStop, cfg.alleles, null, InferredGeneticContext.NO_NEG_LOG_10PERROR, null, null, (byte)'A'); + final VariantContext vc = new VariantContext("test", snpLoc, snpLocStart, snpLocStop, cfg.alleles, null, CommonInfo.NO_NEG_LOG_10PERROR, null, null, (byte)'A'); Assert.assertEquals(vc.getAlleles(), cfg.alleles, "VC alleles not the same as input alleles"); Assert.assertEquals(vc.getNAlleles(), cfg.alleles.size(), "VC getNAlleles not the same as input alleles size");