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

GenotypeMap -> GenotypeCollection part 3 

-- Test code actually builds
This commit is contained in:
Mark DePristo 2011-11-14 17:51:41 -05:00
parent f0234ab67f
commit 4ff8225d78
3 changed files with 11 additions and 15 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
public/java/test/org/broadinstitute/sting/gatk/walkers/qc/TestVariantContextWalker.java
View File

@ -117,7 +117,7 @@ public class TestVariantContextWalker extends RodWalker<Integer, Integer> {
} }
private static VCFHeader createVCFHeader(VariantContext vc) { private static VCFHeader createVCFHeader(VariantContext vc) {
return new VCFHeader(new HashSet<VCFHeaderLine>(), vc.getGenotypes().getSampleNamesSorted()); return new VCFHeader(new HashSet<VCFHeaderLine>(), vc.getGenotypes().getSampleNamesOrderedByName());
} }
public Integer reduceInit() { public Integer reduceInit() {

12
public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextBenchmark.java
View File

@ -49,7 +49,7 @@ public class VariantContextBenchmark extends SimpleBenchmark {
@Param({"READ", "READ_SUBSET"}) @Param({"READ", "READ_SUBSET"})
Operation operation; // set automatically by framework Operation operation; // set automatically by framework
@Param({"OF_GENOTYPES", "OF_SAMPLES"}) @Param({"OF_SAMPLES"})
SubContextOp subContextOp; // set automatically by framework SubContextOp subContextOp; // set automatically by framework
private String INPUT_STRING; private String INPUT_STRING;
@ -60,7 +60,6 @@ public class VariantContextBenchmark extends SimpleBenchmark {
} }
public enum SubContextOp { public enum SubContextOp {
OF_GENOTYPES,
OF_SAMPLES OF_SAMPLES
} }
@ -91,7 +90,7 @@ public class VariantContextBenchmark extends SimpleBenchmark {
codec.readHeader(lineReader); codec.readHeader(lineReader);
int counter = 0; int counter = 0;
List<String> samples = null; Set<String> samples = null;
while (counter++ < linesToRead ) { while (counter++ < linesToRead ) {
String line = lineReader.readLine(); String line = lineReader.readLine();
if ( line == null ) if ( line == null )
@ -99,7 +98,7 @@ public class VariantContextBenchmark extends SimpleBenchmark {
VariantContext vc = (VariantContext)codec.decode(line); VariantContext vc = (VariantContext)codec.decode(line);
if ( samples == null ) { if ( samples == null ) {
samples = new ArrayList<String>(vc.getSampleNames()).subList(0, nSamplesToTake); samples = new HashSet<String>(new ArrayList<String>(vc.getSampleNames()).subList(0, nSamplesToTake));
} }
if ( op == Operation.READ_SUBSET) if ( op == Operation.READ_SUBSET)
@ -119,13 +118,10 @@ public class VariantContextBenchmark extends SimpleBenchmark {
CaliperMain.main(VariantContextBenchmark.class, args); CaliperMain.main(VariantContextBenchmark.class, args);
} }
private static final void processOneVC(VariantContext vc, List<String> samples, SubContextOp subop) { private static final void processOneVC(VariantContext vc, Set<String> samples, SubContextOp subop) {
VariantContext sub; VariantContext sub;
switch ( subop ) { switch ( subop ) {
case OF_GENOTYPES:
sub = vc.subContextFromGenotypes(vc.getGenotypes(samples).values(), vc.getAlleles());
break;
case OF_SAMPLES: case OF_SAMPLES:
sub = vc.subContextFromSamples(samples, vc.getAlleles()); sub = vc.subContextFromSamples(samples, vc.getAlleles());
break; break;

12
public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java
View File

@ -431,12 +431,12 @@ public class VariantContextUnitTest extends BaseTest {
Genotype g5 = new Genotype("--", Arrays.asList(del, del), 10); Genotype g5 = new Genotype("--", Arrays.asList(del, del), 10);
VariantContext vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop , alleles, Arrays.asList(g1,g2,g3,g4,g5)); VariantContext vc = new VariantContext("test", snpLoc,snpLocStart, snpLocStop , alleles, Arrays.asList(g1,g2,g3,g4,g5));
VariantContext vc12 = vc.subContextFromGenotypes(Arrays.asList(g1,g2)); VariantContext vc12 = vc.subContextFromSamples(new HashSet<String>(Arrays.asList(g1.getSampleName(),g2.getSampleName())));
VariantContext vc1 = vc.subContextFromGenotypes(Arrays.asList(g1)); VariantContext vc1 = vc.subContextFromSamples(new HashSet<String>(Arrays.asList(g1.getSampleName())));
VariantContext vc23 = vc.subContextFromGenotypes(Arrays.asList(g2, g3)); VariantContext vc23 = vc.subContextFromSamples(new HashSet<String>(Arrays.asList(g2.getSampleName(), g3.getSampleName())));
VariantContext vc4 = vc.subContextFromGenotypes(Arrays.asList(g4)); VariantContext vc4 = vc.subContextFromSamples(new HashSet<String>(Arrays.asList(g4.getSampleName())));
VariantContext vc14 = vc.subContextFromGenotypes(Arrays.asList(g1, g4)); VariantContext vc14 = vc.subContextFromSamples(new HashSet<String>(Arrays.asList(g1.getSampleName(), g4.getSampleName())));
VariantContext vc5 = vc.subContextFromGenotypes(Arrays.asList(g5)); VariantContext vc5 = vc.subContextFromSamples(new HashSet<String>(Arrays.asList(g5.getSampleName())));
Assert.assertTrue(vc12.isPolymorphic()); Assert.assertTrue(vc12.isPolymorphic());
Assert.assertTrue(vc23.isPolymorphic()); Assert.assertTrue(vc23.isPolymorphic());