Examples with SAMTagAndValue htsjdk.samtools.SAMRecord.SAMTagAndValue used on opensource projects

Example 1 with SAMTagAndValue

use of htsjdk.samtools.SAMRecord.SAMTagAndValue in project polyGembler by c-zhou.

the class SAMtools method run.

@Override
public void run() {
    // TODO Auto-generated method stub
    final SamReaderFactory factory = SamReaderFactory.makeDefault().enable(SamReaderFactory.Option.INCLUDE_SOURCE_IN_RECORDS, SamReaderFactory.Option.VALIDATE_CRC_CHECKSUMS).validationStringency(ValidationStringency.SILENT);
    final SamReader inputSam = factory.open(new File(mySamFile));
    samHeader = inputSam.getFileHeader();
    samHeader.setSortOrder(SortOrder.unsorted);
    SAMRecordIterator iter = inputSam.iterator();
    Set<Entry<String, String>> attr = samHeader.getAttributes();
    List<SAMReadGroupRecord> rgs = samHeader.getReadGroups();
    SAMReadGroupRecord rg = new SAMReadGroupRecord("cz1");
    rg.setSample("cz1");
    samHeader.addReadGroup(rg);
    // samHeader.setAttribute("RG", "cz1");
    final SAMFileWriter outSam = new SAMFileWriterFactory().makeSAMOrBAMWriter(samHeader, true, new File(myOutput));
    for (int i = 0; i < 100; i++) {
        SAMRecord record = iter.next();
        List<SAMTagAndValue> tags = record.getAttributes();
        record.setAttribute("RG", "cz1");
        List<SAMTagAndValue> tags2 = record.getAttributes();
        outSam.addAlignment(record);
    }
    myLogger.info("exit...");
    try {
        inputSam.close();
    } catch (IOException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
    outSam.close();
}

Example 2 with SAMTagAndValue

use of htsjdk.samtools.SAMRecord.SAMTagAndValue in project gridss by PapenfussLab.

the class SplitReadIdentificationHelper method convertToSupplementaryAlignmentRecord.

private static void convertToSupplementaryAlignmentRecord(SAMRecord primary, SAMRecord supplementary) {
    supplementary.setReadName(primary.getReadName());
    supplementary.setMateAlignmentStart(primary.getMateAlignmentStart());
    supplementary.setMateReferenceIndex(primary.getMateReferenceIndex());
    supplementary.setReadPairedFlag(primary.getReadPairedFlag());
    if (primary.getReadPairedFlag()) {
        supplementary.setProperPairFlag(primary.getProperPairFlag());
        supplementary.setFirstOfPairFlag(primary.getFirstOfPairFlag());
        supplementary.setSecondOfPairFlag(primary.getSecondOfPairFlag());
        supplementary.setMateUnmappedFlag(primary.getMateUnmappedFlag());
        supplementary.setMateNegativeStrandFlag(primary.getMateNegativeStrandFlag());
    }
    supplementary.setNotPrimaryAlignmentFlag(primary.getNotPrimaryAlignmentFlag());
    supplementary.setDuplicateReadFlag(primary.getDuplicateReadFlag());
    supplementary.setReadFailsVendorQualityCheckFlag(primary.getReadFailsVendorQualityCheckFlag());
    supplementary.setSupplementaryAlignmentFlag(true);
    // attributes not already set by the supplementary alignment
    for (SAMTagAndValue attr : primary.getAttributes()) {
        if (supplementary.getAttribute(attr.tag) == null) {
            supplementary.setAttribute(attr.tag, attr.value);
        }
    }
}

Example 3 with SAMTagAndValue

use of htsjdk.samtools.SAMRecord.SAMTagAndValue in project gridss by PapenfussLab.

the class CollectTagMetrics method acceptRead.

@Override
protected void acceptRead(final SAMRecord rec, final ReferenceSequence ref) {
    for (SAMTagAndValue attr : rec.getAttributes()) {
        String tag = attr.tag;
        TagSummaryMetrics metric = tags.get(tag);
        if (metric == null) {
            metric = new TagSummaryMetrics();
            metric.TAG = tag;
            metric.COUNT = 0;
            tags.put(tag, metric);
        }
        metric.COUNT++;
    }
}

Example 4 with SAMTagAndValue

use of htsjdk.samtools.SAMRecord.SAMTagAndValue in project jvarkit by lindenb.

the class BWAMemNOp method doWork.

@Override
public int doWork(List<String> args) {
    SamReader r = null;
    SAMFileWriter w = null;
    try {
        r = super.openSamReader(oneFileOrNull(args));
        SAMFileHeader header = r.getFileHeader();
        OtherCanonicalAlignFactory ocaf = new OtherCanonicalAlignFactory(header);
        w = writingBamArgs.openSAMFileWriter(outputFile, header, true);
        SAMRecordFactory samRecordFactory = new DefaultSAMRecordFactory();
        SAMRecordIterator iter = r.iterator();
        while (iter.hasNext()) {
            SAMRecord rec = iter.next();
            if (rec.getSupplementaryAlignmentFlag()) {
                continue;
            }
            if (rec.getReadUnmappedFlag()) {
                if (!print_only_spit_read)
                    w.addAlignment(rec);
                continue;
            }
            Cigar cigar1 = rec.getCigar();
            if (cigar1 == null || cigar1.isEmpty() || !(cigar1.getCigarElement(cigar1.numCigarElements() - 1).getOperator().equals(CigarOperator.S) || cigar1.getCigarElement(0).getOperator().equals(CigarOperator.S))) // last or first is soft clipping
            {
                if (!print_only_spit_read)
                    w.addAlignment(rec);
                continue;
            }
            rec.getAlignmentStart();
            List<OtherCanonicalAlign> xps = ocaf.getXPAligns(rec);
            if (xps.isEmpty()) {
                if (!print_only_spit_read)
                    w.addAlignment(rec);
                continue;
            }
            boolean found_one = false;
            for (OtherCanonicalAlign xp : xps) {
                if (!rec.getReferenceName().equals(xp.getReferenceName()))
                    continue;
                if (xp.getReadNegativeStrandFlag() != rec.getReadNegativeStrandFlag())
                    continue;
                Cigar cigar2 = xp.getCigar();
                if (cigar2 == null || cigar2.isEmpty()) {
                    continue;
                }
                SAMRecord newrec = null;
                List<CigarEvt> L1 = null;
                List<CigarEvt> L2 = null;
                if (cigar1.getCigarElement(cigar1.numCigarElements() - 1).getOperator().equals(CigarOperator.S) && cigar1.getCigarElement(cigar1.numCigarElements() - 1).getLength() >= this.min_soft_clip_length && cigar2.getCigarElement(0).getOperator().equals(CigarOperator.S) && cigar2.getCigarElement(0).getLength() >= this.min_soft_clip_length && rec.getAlignmentEnd() < xp.getAlignmentStart()) {
                    newrec = samRecordFactory.createSAMRecord(header);
                    int ref1 = rec.getAlignmentStart();
                    newrec.setAlignmentStart(ref1);
                    L1 = cigarEvents(0, ref1, cigar1);
                    L2 = cigarEvents(0, xp.getAlignmentStart(), cigar2);
                } else if (cigar2.getCigarElement(cigar2.numCigarElements() - 1).getOperator().equals(CigarOperator.S) && cigar2.getCigarElement(cigar2.numCigarElements() - 1).getLength() >= this.min_soft_clip_length && cigar1.getCigarElement(0).getOperator().equals(CigarOperator.S) && cigar1.getCigarElement(0).getLength() >= this.min_soft_clip_length && xp.getAlignmentEnd() < rec.getAlignmentStart()) {
                    newrec = samRecordFactory.createSAMRecord(header);
                    int ref1 = xp.getAlignmentStart();
                    newrec.setAlignmentStart(ref1);
                    L1 = cigarEvents(0, ref1, cigar2);
                    L2 = cigarEvents(0, rec.getAlignmentStart(), cigar1);
                }
                if (newrec == null)
                    continue;
                newrec.setFlags(rec.getFlags());
                newrec.setReadName(rec.getReadName());
                newrec.setReadBases(rec.getReadBases());
                newrec.setMappingQuality(rec.getMappingQuality());
                newrec.setReferenceIndex(rec.getReferenceIndex());
                newrec.setBaseQualities(rec.getBaseQualities());
                if (found_one) {
                    newrec.setNotPrimaryAlignmentFlag(true);
                }
                found_one = true;
                for (SAMTagAndValue tav : rec.getAttributes()) {
                    if (tav.tag.equals(ocaf.getAttributeKey()))
                        continue;
                    if (tav.tag.equals("NM"))
                        continue;
                    newrec.setAttribute(tav.tag, tav.value);
                }
                if (rec.getReadPairedFlag() && !rec.getMateUnmappedFlag()) {
                    newrec.setMateAlignmentStart(rec.getMateAlignmentStart());
                    newrec.setMateReferenceIndex(rec.getMateReferenceIndex());
                    newrec.setInferredInsertSize(rec.getInferredInsertSize());
                }
                while (!L1.isEmpty() && (L1.get(L1.size() - 1).op.equals(CigarOperator.S) || L1.get(L1.size() - 1).op.equals(CigarOperator.D) || L1.get(L1.size() - 1).op.equals(CigarOperator.H))) {
                    L1.remove(L1.size() - 1);
                }
                while (!L2.isEmpty() && L2.get(0).read0 <= L1.get(L1.size() - 1).read0) {
                    L2.remove(0);
                }
                List<CigarElement> cigarElements = new ArrayList<CigarElement>();
                int i = 0;
                while (i < L1.size()) {
                    int j = i + 1;
                    while (j < L1.size() && L1.get(i).op.equals(L1.get(j).op)) {
                        j++;
                    }
                    cigarElements.add(new CigarElement(j - i, L1.get(i).op));
                    i = j;
                }
                // add 'N'
                cigarElements.add(new CigarElement((L2.get(0).ref1 - L1.get(L1.size() - 1).ref1) - 1, CigarOperator.N));
                i = 0;
                while (i < L2.size()) {
                    int j = i + 1;
                    while (j < L2.size() && L2.get(i).op.equals(L2.get(j).op)) {
                        j++;
                    }
                    cigarElements.add(new CigarElement(j - i, L2.get(i).op));
                    i = j;
                }
                // cleanup : case where  'S' is close to 'N'
                i = 0;
                while (i + 1 < cigarElements.size()) {
                    CigarElement ce1 = cigarElements.get(i);
                    CigarElement ce2 = cigarElements.get(i + 1);
                    if (i > 0 && ce1.getOperator().equals(CigarOperator.S) && ce2.getOperator().equals(CigarOperator.N)) {
                        cigarElements.set(i, new CigarElement(ce1.getLength(), CigarOperator.X));
                    } else if (i + 2 < cigarElements.size() && ce1.getOperator().equals(CigarOperator.N) && ce2.getOperator().equals(CigarOperator.S)) {
                        cigarElements.set(i + 1, new CigarElement(ce2.getLength(), CigarOperator.X));
                    }
                    i++;
                }
                newrec.setCigar(new Cigar(cigarElements));
                List<SAMValidationError> validations = newrec.isValid();
                if (validations != null) {
                    for (SAMValidationError err : validations) {
                        LOG.warning(err.getType() + ":" + err.getMessage());
                    }
                }
                w.addAlignment(newrec);
            }
            if (!found_one) {
                if (!print_only_spit_read)
                    w.addAlignment(rec);
            }
        }
        iter.close();
        return 0;
    } catch (Exception err) {
        LOG.error(err);
        return -1;
    } finally {
        CloserUtil.close(r);
        CloserUtil.close(w);
    }
}

Example 5 with SAMTagAndValue

use of htsjdk.samtools.SAMRecord.SAMTagAndValue in project jvarkit by lindenb.

the class BamStage method createMetaDataTable.

private TableView<SAMTagAndValue> createMetaDataTable() {
    final TableView<SAMTagAndValue> table = new TableView<>();
    table.getColumns().add(makeColumn("Key", O -> O.tag));
    table.getColumns().add(makeColumn("Value", O -> O.value));
    table.setPlaceholder(new Label("No Meta-data."));
    return table;
}