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) {
return new VCFHeader(new HashSet<VCFHeaderLine>(), vc.getGenotypes().getSampleNamesSorted());
return new VCFHeader(new HashSet<VCFHeaderLine>(), vc.getGenotypes().getSampleNamesOrderedByName());
}
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"})
Operation operation; // set automatically by framework
@Param({"OF_GENOTYPES", "OF_SAMPLES"})
@Param({"OF_SAMPLES"})
SubContextOp subContextOp; // set automatically by framework
private String INPUT_STRING;
@ -60,7 +60,6 @@ public class VariantContextBenchmark extends SimpleBenchmark {
}
public enum SubContextOp {
OF_GENOTYPES,
OF_SAMPLES
}
@ -91,7 +90,7 @@ public class VariantContextBenchmark extends SimpleBenchmark {
codec.readHeader(lineReader);
int counter = 0;
List<String> samples = null;
Set<String> samples = null;
while (counter++ < linesToRead ) {
String line = lineReader.readLine();
if ( line == null )
@ -99,7 +98,7 @@ public class VariantContextBenchmark extends SimpleBenchmark {
VariantContext vc = (VariantContext)codec.decode(line);
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)
@ -119,13 +118,10 @@ public class VariantContextBenchmark extends SimpleBenchmark {
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;
switch ( subop ) {
case OF_GENOTYPES:
sub = vc.subContextFromGenotypes(vc.getGenotypes(samples).values(), vc.getAlleles());
break;
case OF_SAMPLES:
sub = vc.subContextFromSamples(samples, vc.getAlleles());
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);
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 vc1 = vc.subContextFromGenotypes(Arrays.asList(g1));
VariantContext vc23 = vc.subContextFromGenotypes(Arrays.asList(g2, g3));
VariantContext vc4 = vc.subContextFromGenotypes(Arrays.asList(g4));
VariantContext vc14 = vc.subContextFromGenotypes(Arrays.asList(g1, g4));
VariantContext vc5 = vc.subContextFromGenotypes(Arrays.asList(g5));
VariantContext vc12 = vc.subContextFromSamples(new HashSet<String>(Arrays.asList(g1.getSampleName(),g2.getSampleName())));
VariantContext vc1 = vc.subContextFromSamples(new HashSet<String>(Arrays.asList(g1.getSampleName())));
VariantContext vc23 = vc.subContextFromSamples(new HashSet<String>(Arrays.asList(g2.getSampleName(), g3.getSampleName())));
VariantContext vc4 = vc.subContextFromSamples(new HashSet<String>(Arrays.asList(g4.getSampleName())));
VariantContext vc14 = vc.subContextFromSamples(new HashSet<String>(Arrays.asList(g1.getSampleName(), g4.getSampleName())));
VariantContext vc5 = vc.subContextFromSamples(new HashSet<String>(Arrays.asList(g5.getSampleName())));
Assert.assertTrue(vc12.isPolymorphic());
Assert.assertTrue(vc23.isPolymorphic());