Examples with TabixVcfFileReader com.github.lindenb.jvarkit.util.vcf.TabixVcfFileReader used on opensource projects

Example 1 with TabixVcfFileReader

use of com.github.lindenb.jvarkit.util.vcf.TabixVcfFileReader in project jvarkit by lindenb.

the class FindAVariation method scan.

private void scan(final BufferedReader in) throws IOException {
    String line;
    while ((line = in.readLine()) != null) {
        if (line.isEmpty() || line.startsWith("#"))
            continue;
        final File f = new File(line);
        if (!f.isFile())
            continue;
        if (!f.canRead())
            continue;
        if (!VCFUtils.isVcfFile(f))
            continue;
        VcfIterator iter = null;
        if (VCFUtils.isTribbleVcfFile(f)) {
            VCFFileReader r = null;
            try {
                r = new VCFFileReader(f, true);
                final VCFHeader header = r.getFileHeader();
                for (final Mutation m : convertFromVcfHeader(f, header)) {
                    final CloseableIterator<VariantContext> iter2 = r.query(m.chrom, m.pos, m.pos);
                    while (iter2.hasNext()) {
                        final VariantContext ctx = iter2.next();
                        if (this.onlySnp) {
                            if (ctx.getStart() != m.pos || ctx.getEnd() != m.pos)
                                continue;
                        }
                        report(f, header, ctx, m);
                    }
                    CloserUtil.close(iter2);
                }
            } catch (final htsjdk.tribble.TribbleException.InvalidHeader err) {
                LOG.warn(f + "\t" + err.getMessage());
            } catch (final Exception err) {
                LOG.severe("cannot read " + f, err);
            } finally {
                CloserUtil.close(r);
            }
        } else if (VCFUtils.isTabixVcfFile(f)) {
            TabixVcfFileReader r = null;
            try {
                r = new TabixVcfFileReader(f.getPath());
                final VCFHeader header = r.getHeader();
                for (final Mutation m : convertFromVcfHeader(f, header)) {
                    final Iterator<VariantContext> iter2 = r.iterator(m.chrom, m.pos, m.pos);
                    while (iter2.hasNext()) {
                        final VariantContext ctx = iter2.next();
                        if (this.onlySnp) {
                            if (ctx.getStart() != m.pos || ctx.getEnd() != m.pos)
                                continue;
                        }
                        report(f, header, ctx, m);
                    }
                    CloserUtil.close(iter2);
                }
            } catch (final htsjdk.tribble.TribbleException.InvalidHeader err) {
                LOG.warn(f + "\t" + err.getMessage());
            } catch (final Exception err) {
                LOG.severe("cannot read " + f, err);
            } finally {
                CloserUtil.close(r);
            }
        } else if (!this.indexedOnly) {
            try {
                iter = VCFUtils.createVcfIteratorFromFile(f);
                final VCFHeader header = iter.getHeader();
                final Set<Mutation> mutlist = convertFromVcfHeader(f, iter.getHeader());
                while (iter.hasNext()) {
                    final VariantContext ctx = iter.next();
                    final Mutation m = new Mutation(ctx.getContig(), ctx.getStart());
                    for (final Mutation m2 : mutlist) {
                        if (m.equals(m2)) {
                            if (this.onlySnp) {
                                if (ctx.getStart() != m2.pos || ctx.getEnd() != m2.pos)
                                    continue;
                            }
                            report(f, header, ctx, m2);
                            break;
                        }
                    }
                }
            } catch (final htsjdk.tribble.TribbleException.InvalidHeader err) {
                LOG.warn(f + "\t" + err.getMessage());
            } catch (final Exception err) {
                LOG.severe("Error in " + f, err);
            } finally {
                CloserUtil.close(iter);
            }
        }
    }
}

Example 2 with TabixVcfFileReader

use of com.github.lindenb.jvarkit.util.vcf.TabixVcfFileReader in project jvarkit by lindenb.

the class VcfRemoveGenotypeIfInVcf method doWork.

@Override
public int doWork(List<String> args) {
    if (tabixFilePath == null) {
        LOG.error("Undefined VCF tabix  file");
        return -1;
    }
    try {
        LOG.info("Opening " + tabixFilePath);
        this.tabix = new TabixVcfFileReader(tabixFilePath);
        return doVcfToVcf(args, outputFile);
    } catch (Exception err) {
        LOG.error(err);
        return -1;
    } finally {
        CloserUtil.close(this.tabix);
    }
}

Example 3 with TabixVcfFileReader

use of com.github.lindenb.jvarkit.util.vcf.TabixVcfFileReader in project jvarkit by lindenb.

the class BamToSVG method readVariantFile.

private void readVariantFile(String vcf) throws IOException {
    LOG.info("Reading " + vcf);
    TabixVcfFileReader tfr = new TabixVcfFileReader(vcf);
    Iterator<VariantContext> iter = tfr.iterator(this.interval.chrom, this.interval.start, this.interval.end);
    while (iter.hasNext()) {
        VariantContext ctx = iter.next();
        this.pos2variant.add(ctx);
    }
    tfr.close();
}