Package htsjdk.samtools

Examples of htsjdk.samtools.SAMRecord

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            }
        }

        @Override
        public SAMRecordsForCluster decode() {
            final SAMRecord zerothRecord = bamCodec.decode();
            if (zerothRecord == null) return null;
            final SAMRecordsForCluster ret = new SAMRecordsForCluster(numRecords);
            ret.records[0] = zerothRecord;
            for (int i = 1; i < numRecords; ++i) {
                ret.records[i] = bamCodec.decode();
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     */
    private List<SAMRecord> fetchByReadName(final PeekableIterator<SAMRecord> iterator) {
        final List<SAMRecord> out = new LinkedList<SAMRecord>();

        if (iterator.hasNext()) {
            final SAMRecord first = iterator.next();
            out.add(first);

            while (iterator.hasNext() && iterator.peek().getReadName().equals(first.getReadName())) {
                out.add(iterator.next());
            }
        }

        return out;
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            final int refLength = refBases.length;
            final int lastWindowStart = refLength - WINDOW_SIZE;

            final byte[] gc = calculateAllGcs(refBases, windowsByGc, lastWindowStart);
            while (iterator.hasNext() && iterator.peek().getReferenceIndex() == ref.getContigIndex()) {
                final SAMRecord rec = iterator.next();

                if (!rec.getReadPairedFlag() || rec.getFirstOfPairFlag()) ++this.totalClusters;

                if (!rec.getReadUnmappedFlag()) {
                    final int pos = rec.getReadNegativeStrandFlag() ? rec.getAlignmentEnd() - WINDOW_SIZE : rec.getAlignmentStart();
                    ++this.totalAlignedReads;

                    if (pos > 0) {
                        final int windowGc = gc[pos];

                        if (windowGc >= 0) {
                            ++readsByGc[windowGc];
                            basesByGc[windowGc]  += rec.getReadLength();
                            errorsByGc[windowGc] +=
                                    SequenceUtil.countMismatches(rec, refBases, IS_BISULFITE_SEQUENCED) +
                                            SequenceUtil.countInsertedBases(rec) + SequenceUtil.countDeletedBases(rec);
                        }
                    }
                }

                progress.record(rec);
            }

            log.info("Processed reference sequence: " + ref.getName());
        }

        // Finish up the reads, presumably all unaligned
        while (iterator.hasNext()) {
            final SAMRecord rec = iterator.next();
            if (!rec.getReadPairedFlag() || rec.getFirstOfPairFlag()) ++this.totalClusters;

        }

        /////////////////////////////////////////////////////////////////////////////
        // Synthesize the normalized coverage metrics and write it all out to a file
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                                             final int index2,
                                             final int stricterMinMatchBases) {

        // Save all the data about the read where we found the adapter match
        final int matchedIndex = index1 == NO_MATCH ? index2 : index1;
        final SAMRecord matchedRead = index1 == NO_MATCH ? read2 : read1;


        // If it still matches with a stricter minimum matched bases, then
        // clip both reads
        if (matchedRead.getReadLength() - matchedIndex >= stricterMinMatchBases) {
            if (read1.getReadBases().length > matchedIndex) {
                read1.setAttribute(ReservedTagConstants.XT, matchedIndex + 1);
            }
            if (read2.getReadBases().length > matchedIndex) {
                read2.setAttribute(ReservedTagConstants.XT, matchedIndex + 1);
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    /**
     * Creates a new SAM record from the basecall data
     */
    private SAMRecord createSamRecord(final ReadData readData, final String readName, final boolean isPf, final boolean firstOfPair, final String unmatchedBarcode) {
        final SAMRecord sam = new SAMRecord(null);
        sam.setReadName(readName);
        sam.setReadBases(readData.getBases());
        sam.setBaseQualities(readData.getQualities());

        // Flag values
        sam.setReadPairedFlag(isPairedEnd);
        sam.setReadUnmappedFlag(true);
        sam.setReadFailsVendorQualityCheckFlag(!isPf);
        if (isPairedEnd) {
            sam.setMateUnmappedFlag(true);
            sam.setFirstOfPairFlag(firstOfPair);
            sam.setSecondOfPairFlag(!firstOfPair);
        }

        if (filters.filterOut(sam)) {
            sam.setAttribute(ReservedTagConstants.XN, 1);
        }

        if (this.readGroupId != null) {
            sam.setAttribute(SAMTag.RG.name(), readGroupId);
        }

        // If it's a barcoded run and the read isn't assigned to a barcode, then add the barcode
        // that was read as an optional tag
        if (unmatchedBarcode != null) {
            sam.setAttribute(SAMTag.BC.name(), unmatchedBarcode);
        }

        return sam;
    }
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        int readCount = 0;
        final ProgressLogger progress = new ProgressLogger(LOG);
        for ( ; freader.hasNext()  ; readCount++) {
            final FastqRecord frec = freader.next();
            final SAMRecord srec = createSamRecord(header, getReadName(frec.getReadHeader(), false) , frec, false) ;
            srec.setReadPairedFlag(false);
            writer.addAlignment(srec);
            progress.record(srec);
        }

        writer.close();
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                barcode[i] = cluster.getRead(barcodeIndices[i]).getBases();
            }
            unmatchedBarcode = IlluminaUtil.barcodeSeqsToString(barcode).replace('.', 'N'); //TODO: This has a separator, where as in other places we do not use a separator
        }

        final SAMRecord firstOfPair = createSamRecord(
            cluster.getRead(templateIndices[0]), readName, cluster.isPf(), true,unmatchedBarcode);
        ret.records[0] = firstOfPair;

        SAMRecord secondOfPair = null;

        if(isPairedEnd) {
            secondOfPair  = createSamRecord(
                cluster.getRead(templateIndices[1]), readName, cluster.isPf(), false, unmatchedBarcode);
            ret.records[1] = secondOfPair;
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            final String frec1Name = getReadName(frec1.getReadHeader(), true);
            final String frec2Name = getReadName(frec2.getReadHeader(), true);
            final String baseName = getBaseName(frec1Name, frec2Name, freader1, freader2);

            final SAMRecord srec1 = createSamRecord(header, baseName, frec1, true) ;
            srec1.setFirstOfPairFlag(true);
            srec1.setSecondOfPairFlag(false);
            writer.addAlignment(srec1);
            progress.record(srec1);

            final SAMRecord srec2 = createSamRecord(header, baseName, frec2, true) ;
            srec2.setFirstOfPairFlag(false);
            srec2.setSecondOfPairFlag(true);
            writer.addAlignment(srec2);
            progress.record(srec2);
        }

        writer.close();
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        return readCount;
    }

    private SAMRecord createSamRecord(final SAMFileHeader header, final String baseName, final FastqRecord frec, final boolean paired) {
        final SAMRecord srec = new SAMRecord(header);
        srec.setReadName(baseName);
        srec.setReadString(frec.getReadString());
        srec.setReadUnmappedFlag(true);
        srec.setAttribute(ReservedTagConstants.READ_GROUP_ID, READ_GROUP_NAME);
        final byte[] quals = StringUtil.stringToBytes(frec.getBaseQualityString());
        convertQuality(quals, QUALITY_FORMAT);
        for (final byte qual : quals) {
            final int uQual = qual & 0xff;
            if (uQual < MIN_Q || uQual > MAX_Q) {
                throw new PicardException("Base quality " + uQual + " is not in the range " + MIN_Q + ".." +
                MAX_Q + " for read " + frec.getReadHeader());
            }
        }
        srec.setBaseQualities(quals);

        if (paired) {
            srec.setReadPairedFlag(true);
            srec.setMateUnmappedFlag(true);
        }
        return srec ;
    }
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         * 2. push record into SAMFileWriter to the output
         */
        final SamPairUtil.SetMateInfoIterator sorterIterator = new SamPairUtil.SetMateInfoIterator(sorter.iterator(), true);
        final ProgressLogger sorterProgress = new ProgressLogger(log, 1000000, " mate cigars added");
        while (sorterIterator.hasNext()) {
            final SAMRecord record = sorterIterator.next();
            out.addAlignment(record);
            sorterProgress.record(record);
        }
        sorterIterator.close();
        CloserUtil.close(out);
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Related Classes of htsjdk.samtools.SAMRecord

  • org.broad.igv.sam.PicardAlignment
  • org.broad.igv.sam.reader.SAMFileGroup$SamGroupIterator
  • org.broad.igv.sam.reader.SAMQueryIterator
  • org.broadinstitute.gatk.engine.datasources.reads.IntervalOverlapFilteringIterator
  • org.broadinstitute.gatk.engine.datasources.reads.IntervalOverlapFilteringIteratorUnitTest
  • org.broadinstitute.gatk.engine.datasources.reads.PicardBaselineBenchmark
  • org.broadinstitute.gatk.engine.datasources.reads.TheoreticalMinimaBenchmark
  • org.broadinstitute.gatk.engine.downsampling.DownsamplingReadsIterator
  • org.broadinstitute.gatk.engine.downsampling.PerSampleDownsamplingReadsIterator
  • org.broadinstitute.gatk.engine.downsampling.PerSampleDownsamplingReadsIteratorUnitTest$PerSampleDownsamplingReadsIteratorTest
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