Examples with BedFeature org.broad.igv.bbfile.BedFeature used on opensource projects

Example 1 with BedFeature

use of org.broad.igv.bbfile.BedFeature in project jvarkit by lindenb.

the class VcfEnsemblReg method annotate.

private void annotate(Track track, File inf, File outf) throws IOException {
    boolean contained = false;
    LOG.info("Processing " + track.id + " (" + track.shortLabel + ") " + track.url);
    VcfIterator in = VCFUtils.createVcfIteratorFromFile(inf);
    VCFHeader header = in.getHeader();
    VCFInfoHeaderLine info = null;
    SeekableStream sstream = SeekableStreamFactory.getInstance().getStreamFor(track.url);
    BBFileReader bigFile = new BBFileReader(track.url.toString(), new SeekableStreamAdaptor(sstream));
    VariantContextWriter w1 = VCFUtils.createVariantContextWriter(outf);
    if (bigFile.isBigWigFile()) {
        info = new VCFInfoHeaderLine(track.id, 1, VCFHeaderLineType.Float, String.valueOf(track.longLabel) + " " + track.url);
    } else {
        info = new VCFInfoHeaderLine(track.id, 1, VCFHeaderLineType.String, String.valueOf(track.longLabel) + " " + track.url);
    }
    header.addMetaDataLine(info);
    w1.writeHeader(in.getHeader());
    while (in.hasNext()) {
        VariantContext ctx = in.next();
        String chrom = ctx.getContig();
        if (!chrom.startsWith("chr"))
            chrom = "chr" + chrom;
        if (!chrom.matches("(chrX|chrY|chr[0-9]|chr1[0-9]|chr2[12])")) {
            w1.add(ctx);
        } else if (bigFile.isBigWigFile()) {
            BigWigIterator iter = bigFile.getBigWigIterator(chrom, ctx.getStart() - 1, chrom, ctx.getStart(), contained);
            Float wigValue = null;
            while (iter != null && iter.hasNext() && wigValue == null) {
                WigItem item = iter.next();
                wigValue = item.getWigValue();
            }
            if (wigValue == null) {
                w1.add(ctx);
                continue;
            }
            VariantContextBuilder vcb = new VariantContextBuilder(ctx);
            vcb.attribute(track.id, wigValue);
            w1.add(vcb.make());
        } else {
            BigBedIterator iter = bigFile.getBigBedIterator(chrom, ctx.getStart() - 1, chrom, ctx.getStart(), contained);
            Set<String> bedValues = new HashSet<String>();
            while (iter != null && iter.hasNext()) {
                BedFeature item = iter.next();
                String[] rest = item.getRestOfFields();
                if (rest == null || rest.length != 6) {
                    System.err.println(track.id + " " + Arrays.toString(item.getRestOfFields()));
                    continue;
                }
                String color = null;
                if (track.parent != null) {
                    if (track.parent.startsWith("Segway_17SegmentationSummaries")) {
                        color = segway_17SegmentationSummaries(rest[5]);
                    } else if (track.parent.startsWith("ProjectedSegments")) {
                        color = projectedSegments(rest[5]);
                    } else if (track.parent.startsWith("RegBuildOverview")) {
                        color = regBuildOverview(rest[5]);
                    } else if (track.parent.startsWith("Segway_17CellSegments")) {
                        color = segway_17CellSegments(rest[5]);
                    } else {
                        System.err.println("Unknown parent:" + track.parent);
                    }
                }
                if (color == null)
                    continue;
                bedValues.add(rest[0] + "|" + color);
            }
            if (bedValues.isEmpty()) {
                w1.add(ctx);
                continue;
            }
            StringBuilder sb = new StringBuilder();
            for (String s : bedValues) {
                if (sb.length() != 0)
                    sb.append(",");
                sb.append(s);
            }
            VariantContextBuilder vcb = new VariantContextBuilder(ctx);
            vcb.attribute(track.id, sb.toString());
            w1.add(vcb.make());
        }
    }
    sstream.close();
    in.close();
    w1.close();
}

Example 2 with BedFeature

use of org.broad.igv.bbfile.BedFeature in project ASCIIGenome by dariober.

the class Utils method initRegionFromBigBed.

private static String initRegionFromBigBed(String bigBedFile) throws IOException {
    BBFileReader reader = new BBFileReader(bigBedFile);
    if (!reader.isBigBedFile()) {
        System.err.println("File " + bigBedFile + " is not bigBed.");
        throw new RuntimeException();
    }
    // Just get chrom to start with
    String region = reader.getChromosomeNames().get(0);
    for (String chrom : reader.getChromosomeNames()) {
        BigBedIterator iter = reader.getBigBedIterator(chrom, 0, chrom, Integer.MAX_VALUE, false);
        if (iter.hasNext()) {
            BedFeature x = (BedFeature) iter.next();
            region = x.getChromosome() + ":" + (x.getStartBase() + 1);
            reader.close();
            return region;
        }
    }
    reader.close();
    return region;
}