Examples with PslAlign com.github.lindenb.jvarkit.util.ucsc.PslAlign used on opensource projects

Example 1 with PslAlign

use of com.github.lindenb.jvarkit.util.ucsc.PslAlign in project jvarkit by lindenb.

the class SamToPsl method toString.

private String toString(final PslAlign a, final SAMRecord rec) {
    if (this.output_bed12) {
        final StringBuilder b = new StringBuilder();
        // chrom - The name of the chromosome (e.g. chr3, chrY, chr2_random) or scaffold (e.g. scaffold10671).
        b.append(a.getTName());
        // chromStart - The starting position of the feature in the chromosome or scaffold. The first base in a chromosome is numbered 0.
        b.append('\t');
        b.append(a.getTStart());
        // chromEnd - The ending position of the feature in the chromosome or scaffold. The chromEnd base is not included in the display of the feature. For example, the first 100 bases of a chromosome are defined as chromStart=0, chromEnd=100, and span the bases numbered 0-99.
        b.append('\t');
        b.append(a.getTEnd());
        // name - Defines the name of the BED line. This label is displayed to the left of the BED line in the Genome Browser window when the track is open to full display mode or directly to the left of the item in pack mode.
        b.append('\t');
        b.append(a.getTName());
        // score - A score between 0 and 1000. If the track line useScore attribute is set to 1 for this annotation data set, the score value will determine the level of gray in which this feature is displayed (higher numbers = darker gray). This table shows the Genome Browser's translation of BED score values into shades of gray: shade
        b.append('\t');
        b.append((int) (((rec.getMappingQuality() >= 255 ? 0 : rec.getMappingQuality()) / 255.0)) * 1000);
        // strand - Defines the strand - either '+' or '-'.
        b.append('\t');
        b.append((char) a.getStrand());
        // thickStart - The starting position at which the feature is drawn thickly (for example, the start codon in gene displays).
        b.append('\t');
        b.append(a.getTStart());
        // thickEnd - The ending position at which the feature is drawn thickly (for example, the stop codon in gene displays).
        b.append('\t');
        b.append(a.getTEnd());
        // itemRgb - An RGB value of the form R,G,B (e.g. 255,0,0). If the track line itemRgb attribute is set to "On", this RBG value will determine the display color of the data contained in this BED line. NOTE: It is recommended that a simple color scheme (eight colors or less) be used with this attribute to avoid overwhelming the color resources of the Genome Browser and your Internet browser.
        b.append('\t');
        Color c = Color.BLACK;
        if (rec.getReadPairedFlag()) {
            c = Color.ORANGE;
            if (rec.getProperPairFlag())
                c = Color.GREEN;
        }
        b.append(c.getRed()).append(",").append(c.getGreen()).append(",").append(c.getBlue());
        // blockCount - The number of blocks (exons) in the BED line.
        b.append('\t');
        b.append(a.getBlockCount());
        // blockSizes - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount.
        b.append('\t');
        for (PslAlign.Block block : a.getBlocks()) {
            b.append(block.size());
            b.append(',');
        }
        // blockStarts - A comma-separated list of block starts. All of the blockStart positions should be calculated relative to chromStart. The number of items in this list should correspond to blockCount.
        b.append('\t');
        for (PslAlign.Block block : a.getBlocks()) {
            b.append(block.getTStart() - a.getTStart());
            b.append(',');
        }
        return b.toString();
    } else {
        return a.toString();
    }
}

Example 2 with PslAlign

use of com.github.lindenb.jvarkit.util.ucsc.PslAlign in project jvarkit by lindenb.

the class SamToPsl method scan.

private void scan(final SamReader in) {
    final SAMSequenceDictionary dict = in.getFileHeader().getSequenceDictionary();
    if (dict == null)
        throw new RuntimeException("Sequence dictionary missing...");
    final SAMRecordIterator iter = in.iterator();
    final SAMSequenceDictionaryProgress progress = new SAMSequenceDictionaryProgress(dict);
    while (iter.hasNext() && !this.out.checkError()) {
        final SAMRecord rec = progress.watch(iter.next());
        if (rec.getReadUnmappedFlag())
            continue;
        for (final PslAlign a : makePslAlign(rec, dict)) {
            out.println(toString(a, rec));
        }
    }
    progress.finish();
    iter.close();
}

Example 3 with PslAlign

use of com.github.lindenb.jvarkit.util.ucsc.PslAlign in project jvarkit by lindenb.

the class SamToPsl method makePslAlign.

private List<PslAlign> makePslAlign(SAMRecord rec, SAMSequenceDictionary dict) {
    final List<PslAlign> aligns = new ArrayList<PslAlign>();
    final PslAlign a = new PslAlign();
    a.setStrand(rec.getReadNegativeStrandFlag() ? '-' : '+');
    a.setQName(rec.getReadName() + (rec.getReadPairedFlag() ? (rec.getFirstOfPairFlag() ? "/1" : "/2") : "") + "_" + rec.getFlags());
    a.setTName(rec.getReferenceName());
    final SAMSequenceRecord ssr = dict.getSequence(rec.getReferenceIndex());
    if (ssr == null) {
        throw new RuntimeException("Cannot get SAMSequenceRecord dict for " + rec.getReferenceName());
    }
    a.setTSize(ssr.getSequenceLength());
    int qBaseInsert = 0;
    int tBaseInsert = 0;
    int readLength = 0;
    for (final CigarElement ce : rec.getCigar().getCigarElements()) {
        switch(ce.getOperator()) {
            case I:
                qBaseInsert += ce.getLength();
                readLength += ce.getLength();
                break;
            case N:
            case D:
                tBaseInsert += ce.getLength();
                break;
            // threw
            case M:
            case X:
            case EQ:
            case H:
            case S:
                {
                    readLength += ce.getLength();
                    break;
                }
            default:
                break;
        }
    }
    a.setQBaseInsert(qBaseInsert);
    a.setTBaseInsert(tBaseInsert);
    boolean treat_as_paired = this.handle_paired_reads;
    if (rec.getSupplementaryAlignmentFlag())
        treat_as_paired = false;
    if (rec.getReadPairedFlag()) {
        if (rec.getMateUnmappedFlag()) {
            treat_as_paired = false;
        } else {
            if (!rec.getMateReferenceIndex().equals(rec.getReferenceIndex())) {
                treat_as_paired = false;
            } else {
                if (rec.getReadNegativeStrandFlag() == rec.getMateNegativeStrandFlag())
                    treat_as_paired = false;
                if (rec.getAlignmentStart() <= rec.getMateAlignmentStart()) {
                    if (rec.getMateAlignmentStart() <= rec.getAlignmentEnd())
                        treat_as_paired = false;
                }
            }
        }
    } else {
        treat_as_paired = false;
    }
    if (!treat_as_paired) {
        a.setMatches(rec.getCigar().getReferenceLength());
        a.setQSize(readLength);
        a.setQEnd(readLength - (rec.getUnclippedEnd() - rec.getAlignmentEnd()));
        a.setTEnd(rec.getAlignmentEnd());
        final int readPos = rec.getAlignmentStart() - rec.getUnclippedStart();
        final int refPos = rec.getAlignmentStart() - 1;
        a.setQStart(readPos);
        a.setTStart(refPos);
        for (final Align ctg : scancigar(readPos, refPos, rec)) {
            a.addBlock(ctg.read0, ctg.ref0, ctg.len);
        }
    } else {
        a.setMatches(rec.getCigar().getReferenceLength() + 1);
        a.setQSize(readLength + 1);
        if (rec.getAlignmentStart() < rec.getMateAlignmentStart()) {
            a.setQEnd(readLength + 1);
            a.setTEnd(rec.getMateAlignmentStart());
            int readPos = rec.getAlignmentStart() - rec.getUnclippedStart();
            int refPos = rec.getAlignmentStart() - 1;
            a.setQStart(readPos);
            a.setTStart(refPos);
            for (final Align ctg : scancigar(readPos, refPos, rec)) {
                a.addBlock(ctg.read0, ctg.ref0, ctg.len);
            }
            a.addBlock(readLength, rec.getMateAlignmentStart() - 1, 1);
        } else {
            a.setQStart(0);
            a.setQEnd((readLength + 1) - (rec.getUnclippedEnd() - rec.getAlignmentEnd()));
            a.setTStart(rec.getMateAlignmentStart() - 1);
            a.setTEnd(rec.getAlignmentEnd());
            a.addBlock(0, rec.getMateAlignmentStart() - 1, 1);
            for (final Align ctg : scancigar(1, rec.getAlignmentStart(), rec)) {
                a.addBlock(ctg.read0, ctg.ref0, ctg.len);
            }
        }
    }
    aligns.add(a);
    return aligns;
}