Examples with VcfList com.github.lindenb.jvarkit.tools.vcflist.VcfList used on opensource projects

Example 1 with VcfList

use of com.github.lindenb.jvarkit.tools.vcflist.VcfList in project jvarkit by lindenb.

the class VcfEpistatis01 method doWork.

@Override
public int doWork(final List<String> args) {
    if (this.number_of_jobs < 1) {
        LOG.error("bad number of jobs");
        return -1;
    }
    try {
        final int variantsCount;
        final List<VariantContext> inMemoryVariants;
        final File vcfFile = new File(oneAndOnlyOneFile(args));
        final File tmpIndexFile;
        if (vcfFile.equals(this.outputFile)) {
            LOG.error("input == output");
            return -1;
        }
        VCFFileReader vcfFileReader = new VCFFileReader(vcfFile, false);
        final VCFHeader header = vcfFileReader.getFileHeader();
        final Pedigree pedigree;
        if (this.pedigreeFile != null) {
            pedigree = new Pedigree.Parser().parse(this.pedigreeFile);
        } else {
            pedigree = new Pedigree.Parser().parse(header);
        }
        pedigree.verifyPersonsHaveUniqueNames();
        final Map<String, Integer> sample2index = header.getSampleNameToOffset();
        final int[] caseIndexes = pedigree.getAffected().stream().filter(P -> sample2index.containsKey(P.getId())).mapToInt(P -> sample2index.get(P.getId())).sorted().toArray();
        final int[] ctrlIndexes = new ArrayList<>(pedigree.getUnaffected()).stream().filter(P -> sample2index.containsKey(P.getId())).mapToInt(P -> sample2index.get(P.getId())).sorted().toArray();
        if (caseIndexes.length == 0 || ctrlIndexes.length == 0) {
            LOG.error("empty ped or no case/ctrl");
            vcfFileReader.close();
            return -1;
        }
        if (this.load_variants_in_memory) {
            LOG.info("loading variants in memory");
            tmpIndexFile = null;
            final CloseableIterator<VariantContext> iter2 = vcfFileReader.iterator();
            inMemoryVariants = Collections.unmodifiableList(iter2.stream().filter(this.variantFilter).filter(// should fix https://github.com/samtools/htsjdk/issues/1026 ?
            V -> V.getGenotypes().stream().filter(G -> G.isCalled()).count() > 0).collect(Collectors.toList()));
            variantsCount = inMemoryVariants.size();
            iter2.close();
        } else {
            tmpIndexFile = File.createTempFile("epistatsis", VcfOffsetsIndexFactory.INDEX_EXTENSION);
            tmpIndexFile.deleteOnExit();
            new VcfOffsetsIndexFactory().setLogger(LOG).setPredicate(variantFilter).indexVcfFile(vcfFile, tmpIndexFile);
            final VcfList tmpList = VcfList.fromFile(vcfFile, tmpIndexFile);
            variantsCount = tmpList.size();
            tmpList.close();
            inMemoryVariants = null;
        }
        vcfFileReader.close();
        LOG.info("Number of variants: " + variantsCount);
        Result bestResult = null;
        int x = this.start_index_at;
        while (x + 1 < variantsCount) {
            final List<Runner> runners = new Vector<>(this.number_of_jobs);
            while (x + 1 < variantsCount && runners.size() < this.number_of_jobs) {
                LOG.info("starting " + x + "/" + variantsCount);
                runners.add(new Runner(inMemoryVariants == null ? VcfList.fromFile(vcfFile, tmpIndexFile) : new Vector<>(inMemoryVariants), x, caseIndexes, ctrlIndexes));
                ++x;
            }
            final ExecutorService execSvc;
            if (this.number_of_jobs == 1) {
                execSvc = null;
            } else {
                execSvc = Executors.newFixedThreadPool(this.number_of_jobs);
                ;
            }
            if (this.number_of_jobs == 1) {
                runners.get(0).call();
            } else {
                execSvc.invokeAll(runners);
            }
            if (execSvc != null) {
                execSvc.shutdown();
                execSvc.awaitTermination(10000L, TimeUnit.DAYS);
                execSvc.shutdownNow();
            }
            runners.stream().mapToLong(R -> R.duration).min().ifPresent(D -> {
                LOG.info("That took " + (D / 1000f) + " seconds.");
            });
            for (final Runner r : runners) {
                final Result rez = r.result;
                if (rez == null)
                    continue;
                if (bestResult == null || bestResult.score < rez.score) {
                    bestResult = rez;
                    if (this.output_score) {
                        final PrintWriter pw = super.openFileOrStdoutAsPrintWriter(this.outputFile);
                        pw.println(bestResult.score + "\t" + bestResult.toString());
                        pw.flush();
                        pw.close();
                    } else {
                        final VariantContextWriter w = openVariantContextWriter(this.outputFile);
                        final VCFHeader header2 = new VCFHeader(header);
                        header2.addMetaDataLine(new VCFHeaderLine(VcfEpistatis01.class.getName(), bestResult.toString()));
                        w.writeHeader(header2);
                        w.add(bestResult.ctx1);
                        w.add(bestResult.ctx2);
                        w.close();
                    }
                }
            }
            LOG.info("best: " + bestResult);
        }
        if (tmpIndexFile != null)
            tmpIndexFile.delete();
        return 0;
    } catch (final Exception err) {
        err.printStackTrace();
        LOG.error(err);
        return -1;
    } finally {
    }
}

Example 2 with VcfList

use of com.github.lindenb.jvarkit.tools.vcflist.VcfList in project jvarkit by lindenb.

the class TestNg01 method testVcfFileOffsets.

@Test(dataProvider = "all_vcfs")
public void testVcfFileOffsets(final String path) throws IOException {
    final File vcfFile = new File(path);
    VcfOffsetsIndexFactory factory = new VcfOffsetsIndexFactory();
    final File indexFile = factory.indexVcfFile(vcfFile);
    Assert.assertTrue(indexFile.exists());
    final VcfList list = VcfList.fromFile(vcfFile);
    final List<Integer> positions = streamVcf(vcfFile).map(CTX -> CTX.getStart()).collect(Collectors.toList());
    Assert.assertEquals(positions.size(), list.size());
    Assert.assertNotNull(list.getHeader());
    for (int i = list.size() - 1; i >= 0; --i) {
        Assert.assertNotNull(list.get(i));
        Assert.assertEquals(list.get(i).getStart(), positions.get(i).intValue());
    }
    Assert.assertEquals((long) list.size(), streamVcf(vcfFile).count());
    list.close();
    Assert.assertTrue(indexFile.delete());
}