use of au.edu.wehi.idsv.VariantCaller in project gridss by PapenfussLab.
the class AllocateEvidenceTest method should_annotate_reads.
@Test
public void should_annotate_reads() throws IOException {
final ProcessingContext pc = getCommandlineContext();
pc.getVariantCallingParameters().minScore = 0;
pc.getVariantCallingParameters().minSize = 0;
createInput(RP(0, 1, 10), DP(0, 1, "5M5S", true, 1, 10, "5M", true), DP(0, 2, "5M5S", true, 1, 10, "5M", true));
SAMEvidenceSource ses = new SAMEvidenceSource(getContext(), input, null, 0);
ses.ensureMetrics();
File assemblyFile = new File(testFolder.getRoot(), "assembly.bam");
AssemblyEvidenceSource aes = new AssemblyEvidenceSource(pc, ImmutableList.of(ses), assemblyFile);
aes.assembleBreakends(null);
aes.ensureExtracted();
VariantCaller caller = new VariantCaller(pc, ImmutableList.of(ses), aes);
caller.callBreakends(output, MoreExecutors.newDirectExecutorService());
AllocateEvidence cmd = new AllocateEvidence();
cmd.INPUT_VCF = output;
cmd.setContext(pc);
cmd.setAssemblySource(aes);
cmd.setSamEvidenceSources(ImmutableList.of(ses));
cmd.OUTPUT_VCF = new File(testFolder.getRoot(), "annotated.vcf");
List<VariantContextDirectedBreakpoint> vcfs = Lists.newArrayList(Iterables.filter(getVcf(output, null), VariantContextDirectedBreakpoint.class));
// both breakends
assertEquals(2 * 1, vcfs.size());
assertSymmetrical(vcfs);
List<VariantContextDirectedBreakpoint> results = Lists.newArrayList(cmd.iterator(new AutoClosingIterator<>(vcfs.iterator()), MoreExecutors.newDirectExecutorService()));
assertSymmetrical(results);
assertEquals(vcfs.size(), results.size());
VariantContextDirectedBreakpoint e = results.get(0);
assertEquals(2, e.getBreakpointEvidenceCount());
assertEquals(2, e.getBreakendEvidenceCountSoftClip());
}
use of au.edu.wehi.idsv.VariantCaller in project gridss by PapenfussLab.
the class AllocateEvidenceTest method should_apply_filters.
@Test
public void should_apply_filters() throws IOException {
final ProcessingContext pc = getCommandlineContext();
pc.getVariantCallingParameters().minScore = 0;
pc.getVariantCallingParameters().minSize = 0;
createInput(RP(0, 1, 10), DP(0, 1, "5M5S", true, 1, 10, "5M", true));
SAMEvidenceSource ses = new SAMEvidenceSource(getContext(), input, null, 0);
ses.ensureMetrics();
File assemblyFile = new File(testFolder.getRoot(), "assembly.bam");
AssemblyEvidenceSource aes = new AssemblyEvidenceSource(pc, ImmutableList.of(ses), assemblyFile);
aes.assembleBreakends(null);
aes.ensureExtracted();
VariantCaller caller = new VariantCaller(pc, ImmutableList.of(ses), aes);
caller.callBreakends(output, MoreExecutors.newDirectExecutorService());
AllocateEvidence cmd = new AllocateEvidence();
cmd.INPUT_VCF = output;
cmd.setContext(pc);
cmd.setAssemblySource(aes);
cmd.setSamEvidenceSources(ImmutableList.of(ses));
cmd.OUTPUT_VCF = new File(testFolder.getRoot(), "annotated.vcf");
List<VariantContextDirectedBreakpoint> vcfs = Lists.newArrayList(Iterables.filter(getVcf(output, null), VariantContextDirectedBreakpoint.class));
// both breakends
assertEquals(2 * 1, vcfs.size());
assertSymmetrical(vcfs);
List<VariantContextDirectedBreakpoint> results = Lists.newArrayList(cmd.iterator(new AutoClosingIterator<>(vcfs.iterator()), MoreExecutors.newDirectExecutorService()));
assertSymmetrical(results);
// single read support
assertEquals(0, results.size());
}
use of au.edu.wehi.idsv.VariantCaller in project gridss by PapenfussLab.
the class IdentifyVariants method doWork.
@Override
public int doWork(ExecutorService threadpool) throws IOException, InterruptedException, ExecutionException {
IOUtil.assertFileIsWritable(OUTPUT_VCF);
VariantCaller caller = new VariantCaller(getContext(), getSamEvidenceSources(), getAssemblySource());
caller.callBreakends(OUTPUT_VCF, threadpool);
log.info("Raw variant calls written to " + OUTPUT_VCF);
return 0;
}
use of au.edu.wehi.idsv.VariantCaller in project gridss by PapenfussLab.
the class AllocateEvidenceTest method should_uniquely_assign.
@Test
public void should_uniquely_assign() throws IOException, InterruptedException, ExecutionException {
final int fragSize = 4;
final int testSize = 64;
final List<SAMRecord> in = new ArrayList<SAMRecord>();
final ProcessingContext pc = getCommandlineContext();
pc.getVariantCallingParameters().writeFiltered = true;
pc.getVariantCallingParameters().minScore = 0;
StubSAMEvidenceSource ses = new StubSAMEvidenceSource(pc, input, 0, 0, fragSize);
for (int i = 1; i < testSize; i++) {
for (int j = 1; j < testSize; j++) {
SAMRecord[] dp = withReadName(String.format("read-%d-%d", i, j), DP(0, i, "1M", true, 1, j, "1M", false));
ses.evidence.add(NonReferenceReadPair.create(dp[0], dp[1], ses));
ses.evidence.add(NonReferenceReadPair.create(dp[1], dp[0], ses));
in.add(dp[0]);
in.add(dp[1]);
}
}
StubAssemblyEvidenceSource aes = new StubAssemblyEvidenceSource(pc);
aes.fragSize = fragSize;
Collections.sort(ses.evidence, DirectedEvidenceOrder.ByNatural);
createInput(in);
VariantCaller vc = new VariantCaller(pc, ImmutableList.<SAMEvidenceSource>of(ses), aes);
ExecutorService threadpool = Executors.newSingleThreadExecutor();
vc.callBreakends(output, threadpool);
threadpool.shutdown();
AllocateEvidence cmd = new AllocateEvidence();
cmd.INPUT_VCF = output;
cmd.setContext(pc);
cmd.setAssemblySource(aes);
cmd.setSamEvidenceSources(ImmutableList.of(ses));
cmd.OUTPUT_VCF = new File(testFolder.getRoot(), "annotated.vcf");
cmd.ASSEMBLY = new File(testFolder.getRoot(), "assembly.bam");
// to shut up the command-line parsing
createBAM(cmd.ASSEMBLY, SortOrder.coordinate, Collections.emptyList());
cmd.doWork(null);
// List<IdsvVariantContext> annotated = getVcf(new File(testFolder.getRoot(), "out.vcf"), null);
List<IdsvVariantContext> rawcalls = getVcf(output, null);
List<IdsvVariantContext> calls = getVcf(cmd.OUTPUT_VCF, null);
assertSymmetrical(rawcalls.stream().map(x -> (VariantContextDirectedBreakpoint) x).collect(Collectors.toList()));
assertSymmetrical(calls.stream().map(x -> (VariantContextDirectedBreakpoint) x).collect(Collectors.toList()));
// with no filtering, annotation should not change call set
double expectedEvidence = 0;
for (DirectedEvidence e : ses.evidence) {
DiscordantReadPair bp = (DiscordantReadPair) e;
expectedEvidence += bp.getBreakpointQual();
}
double annotatedEvidence = 0;
for (IdsvVariantContext e : calls) {
annotatedEvidence += e.getPhredScaledQual();
}
double rawEvidence = rawcalls.stream().mapToDouble(e -> e.getPhredScaledQual()).sum();
// unique assignment must result in the evidence total being, at most, the same
assertTrue(annotatedEvidence <= rawEvidence);
// each piece of evidence should be assigned to a single breakpoint so totals should match
int rpCalls = calls.stream().mapToInt(v -> ((VariantContextDirectedBreakpoint) v).getBreakpointEvidenceCount()).sum();
assertEquals(ses.evidence.size(), rpCalls);
// floating point truncation on VCF is severe!
assertEquals(expectedEvidence, annotatedEvidence, 20);
}
use of au.edu.wehi.idsv.VariantCaller in project gridss by PapenfussLab.
the class AllocateEvidenceTest method should_filter_if_insufficient_reads.
@Test
public void should_filter_if_insufficient_reads() throws IOException {
final ProcessingContext pc = getCommandlineContext();
pc.getVariantCallingParameters().minScore = 0;
pc.getVariantCallingParameters().minSize = 0;
pc.getVariantCallingParameters().minReads = 3;
createInput(RP(0, 1, 10), DP(0, 1, "5M5S", true, 1, 10, "5M", true));
SAMEvidenceSource ses = new SAMEvidenceSource(getContext(), input, null, 0);
ses.ensureMetrics();
File assemblyFile = new File(testFolder.getRoot(), "assembly.bam");
AssemblyEvidenceSource aes = new AssemblyEvidenceSource(pc, ImmutableList.of(ses), assemblyFile);
aes.assembleBreakends(null);
aes.ensureExtracted();
VariantCaller caller = new VariantCaller(pc, ImmutableList.of(ses), aes);
caller.callBreakends(output, MoreExecutors.newDirectExecutorService());
AllocateEvidence cmd = new AllocateEvidence();
cmd.INPUT_VCF = output;
cmd.setContext(pc);
cmd.setAssemblySource(aes);
cmd.setSamEvidenceSources(ImmutableList.of(ses));
cmd.OUTPUT_VCF = new File(testFolder.getRoot(), "annotated.vcf");
List<VariantContextDirectedBreakpoint> vcfs = Lists.newArrayList(Iterables.filter(getVcf(output, null), VariantContextDirectedBreakpoint.class));
List<VariantContextDirectedBreakpoint> results = Lists.newArrayList(cmd.iterator(new AutoClosingIterator<>(vcfs.iterator()), MoreExecutors.newDirectExecutorService()));
assertEquals(2, vcfs.size());
assertEquals(0, results.size());
}
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