zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

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.
This commit is contained in:
Mark DePristo 2011-11-14 14:28:52 -05:00
parent 077397cb4b
commit 9b5c79b49d
6 changed files with 27 additions and 27 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
View File

@ -229,7 +229,7 @@ public class UnifiedGenotyperEngine {
VariantContext vcInput = UnifiedGenotyperEngine.getVCFromAllelesRod(tracker, ref, rawContext.getLocation(), false, logger, UAC.alleles); VariantContext vcInput = UnifiedGenotyperEngine.getVCFromAllelesRod(tracker, ref, rawContext.getLocation(), false, logger, UAC.alleles);
if ( vcInput == null ) if ( vcInput == null )
return 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 { } else {
// deal with bad/non-standard reference bases // deal with bad/non-standard reference bases

4
public/java/src/org/broadinstitute/sting/utils/variantcontext/InferredGeneticContext.java → public/java/src/org/broadinstitute/sting/utils/variantcontext/CommonInfo.java
View File

@ -11,7 +11,7 @@ import java.util.*;
* *
* @author depristo * @author depristo
*/ */
public final class InferredGeneticContext { final class CommonInfo {
public static final double NO_NEG_LOG_10PERROR = -1.0; public static final double NO_NEG_LOG_10PERROR = -1.0;
private static Set<String> NO_FILTERS = Collections.unmodifiableSet(new HashSet<String>()); private static Set<String> NO_FILTERS = Collections.unmodifiableSet(new HashSet<String>());
@ -22,7 +22,7 @@ public final class InferredGeneticContext {
private Set<String> filters = NO_FILTERS; private Set<String> filters = NO_FILTERS;
private Map<String, Object> attributes = NO_ATTRIBUTES; private Map<String, Object> attributes = NO_ATTRIBUTES;
public InferredGeneticContext(String name, double negLog10PError, Set<String> filters, Map<String, Object> attributes) { public CommonInfo(String name, double negLog10PError, Set<String> filters, Map<String, Object> attributes) {
this.name = name; this.name = name;
setNegLog10PError(negLog10PError); setNegLog10PError(negLog10PError);
if ( filters != null && ! filters.isEmpty() ) if ( filters != null && ! filters.isEmpty() )

6
public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java
View File

@ -17,8 +17,8 @@ public class Genotype {
public final static String PHASED_ALLELE_SEPARATOR = "|"; public final static String PHASED_ALLELE_SEPARATOR = "|";
public final static String UNPHASED_ALLELE_SEPARATOR = "/"; public final static String UNPHASED_ALLELE_SEPARATOR = "/";
protected InferredGeneticContext commonInfo; protected CommonInfo commonInfo;
public final static double NO_NEG_LOG_10PERROR = InferredGeneticContext.NO_NEG_LOG_10PERROR; public final static double NO_NEG_LOG_10PERROR = CommonInfo.NO_NEG_LOG_10PERROR;
protected List<Allele> alleles = null; // new ArrayList<Allele>(); protected List<Allele> alleles = null; // new ArrayList<Allele>();
protected Type type = null; protected Type type = null;
@ -32,7 +32,7 @@ public class Genotype {
public Genotype(String sampleName, List<Allele> alleles, double negLog10PError, Set<String> filters, Map<String, Object> attributes, boolean isPhased, double[] log10Likelihoods) { public Genotype(String sampleName, List<Allele> alleles, double negLog10PError, Set<String> filters, Map<String, Object> attributes, boolean isPhased, double[] log10Likelihoods) {
if ( alleles != null ) if ( alleles != null )
this.alleles = Collections.unmodifiableList(alleles); this.alleles = Collections.unmodifiableList(alleles);
commonInfo = new InferredGeneticContext(sampleName, negLog10PError, filters, attributes); commonInfo = new CommonInfo(sampleName, negLog10PError, filters, attributes);
if ( log10Likelihoods != null ) if ( log10Likelihoods != null )
commonInfo.putAttribute(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY, GenotypeLikelihoods.fromLog10Likelihoods(log10Likelihoods)); commonInfo.putAttribute(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY, GenotypeLikelihoods.fromLog10Likelihoods(log10Likelihoods));
filtersWereAppliedToContext = filters != null; filtersWereAppliedToContext = filters != null;

10
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
View File

@ -162,8 +162,8 @@ import java.util.*;
* @author depristo * @author depristo
*/ */
public class VariantContext implements Feature { // to enable tribble intergration public class VariantContext implements Feature { // to enable tribble intergration
protected InferredGeneticContext commonInfo = null; protected CommonInfo commonInfo = null;
public final static double NO_NEG_LOG_10PERROR = InferredGeneticContext.NO_NEG_LOG_10PERROR; 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_MAP_KEY = "_UNPARSED_GENOTYPE_MAP_";
public final static String UNPARSED_GENOTYPE_PARSER_KEY = "_UNPARSED_GENOTYPE_PARSER_"; public final static String UNPARSED_GENOTYPE_PARSER_KEY = "_UNPARSED_GENOTYPE_PARSER_";
public final static String ID_KEY = "ID"; public final static String ID_KEY = "ID";
@ -293,7 +293,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati
* @param alleles alleles * @param alleles alleles
*/ */
public VariantContext(String source, String contig, long start, long stop, Collection<Allele> alleles) { public VariantContext(String source, String contig, long start, long stop, Collection<Allele> 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 * @param genotypes genotypes
*/ */
public VariantContext(String source, String contig, long start, long stop, Collection<Allele> alleles, Collection<Genotype> genotypes) { public VariantContext(String source, String contig, long start, long stop, Collection<Allele> alleles, Collection<Genotype> 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); 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; filtersWereAppliedToContext = filters != null;
REFERENCE_BASE_FOR_INDEL = referenceBaseForIndel; REFERENCE_BASE_FOR_INDEL = referenceBaseForIndel;

6
public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
View File

@ -81,7 +81,7 @@ public class VariantContextUtils {
* @return VariantContext object * @return VariantContext object
*/ */
public static VariantContext toVC(String name, GenomeLoc loc, Collection<Allele> alleles) { public static VariantContext toVC(String name, GenomeLoc loc, Collection<Allele> 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 * @return VariantContext object
*/ */
public static VariantContext toVC(String name, GenomeLoc loc, Collection<Allele> alleles, Collection<Genotype> genotypes) { public static VariantContext toVC(String name, GenomeLoc loc, Collection<Allele> alleles, Collection<Genotype> 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); return pruneVariantContext(vc, null);
} }
private final static Map<String, Object> subsetAttributes(final InferredGeneticContext igc, final Collection<String> keysToPreserve) { private final static Map<String, Object> subsetAttributes(final CommonInfo igc, final Collection<String> keysToPreserve) {
Map<String, Object> attributes = new HashMap<String, Object>(keysToPreserve.size()); Map<String, Object> attributes = new HashMap<String, Object>(keysToPreserve.size());
for ( final String key : keysToPreserve ) { for ( final String key : keysToPreserve ) {
if ( igc.hasAttribute(key) ) if ( igc.hasAttribute(key) )

26
public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java
View File

@ -90,45 +90,45 @@ public class VariantContextUnitTest extends BaseTest {
// test INDELs // test INDELs
alleles = Arrays.asList(Aref, ATC); 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); Assert.assertEquals(vc.getType(), VariantContext.Type.INDEL);
alleles = Arrays.asList(ATCref, A); 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); Assert.assertEquals(vc.getType(), VariantContext.Type.INDEL);
alleles = Arrays.asList(Tref, TA, TC); 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); Assert.assertEquals(vc.getType(), VariantContext.Type.INDEL);
alleles = Arrays.asList(ATCref, A, AC); 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); Assert.assertEquals(vc.getType(), VariantContext.Type.INDEL);
alleles = Arrays.asList(ATCref, A, Allele.create("ATCTC")); 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); Assert.assertEquals(vc.getType(), VariantContext.Type.INDEL);
// test MIXED // test MIXED
alleles = Arrays.asList(TAref, T, TC); 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); Assert.assertEquals(vc.getType(), VariantContext.Type.MIXED);
alleles = Arrays.asList(TAref, T, AC); 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); Assert.assertEquals(vc.getType(), VariantContext.Type.MIXED);
alleles = Arrays.asList(ACref, ATC, AT); 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); Assert.assertEquals(vc.getType(), VariantContext.Type.MIXED);
alleles = Arrays.asList(Aref, T, symbolic); 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); Assert.assertEquals(vc.getType(), VariantContext.Type.MIXED);
// test SYMBOLIC // test SYMBOLIC
alleles = Arrays.asList(Tref, 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); Assert.assertEquals(vc.getType(), VariantContext.Type.SYMBOLIC);
} }
@ -199,7 +199,7 @@ public class VariantContextUnitTest extends BaseTest {
@Test @Test
public void testCreatingDeletionVariantContext() { public void testCreatingDeletionVariantContext() {
List<Allele> alleles = Arrays.asList(ATCref, del); List<Allele> 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.getChr(), delLoc);
Assert.assertEquals(vc.getStart(), delLocStart); Assert.assertEquals(vc.getStart(), delLocStart);
@ -226,7 +226,7 @@ public class VariantContextUnitTest extends BaseTest {
@Test @Test
public void testCreatingInsertionVariantContext() { public void testCreatingInsertionVariantContext() {
List<Allele> alleles = Arrays.asList(delRef, ATC); List<Allele> 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.getChr(), insLoc);
Assert.assertEquals(vc.getStart(), insLocStart); Assert.assertEquals(vc.getStart(), insLocStart);
@ -514,7 +514,7 @@ public class VariantContextUnitTest extends BaseTest {
@Test(dataProvider = "getAlleles") @Test(dataProvider = "getAlleles")
public void testMergeAlleles(GetAllelesTest cfg) { public void testMergeAlleles(GetAllelesTest cfg) {
final List<Allele> altAlleles = cfg.alleles.subList(1, cfg.alleles.size()); final List<Allele> 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.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"); Assert.assertEquals(vc.getNAlleles(), cfg.alleles.size(), "VC getNAlleles not the same as input alleles size");