Package htsjdk.samtools

Examples of htsjdk.samtools.SAMFileWriter

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        final boolean presorted = inputSortOrder.equals(outputHeader.getSortOrder());
        log.info("Filtering [presorted=" + presorted + "] " + INPUT.getName() + " -> OUTPUT=" +
            OUTPUT.getName() + " [sortorder=" + outputHeader.getSortOrder().name() + "]");

        // create OUTPUT file
        final SAMFileWriter outputWriter = new SAMFileWriterFactory().makeSAMOrBAMWriter(outputHeader, presorted, OUTPUT);

        final ProgressLogger progress = new ProgressLogger(log, (int) 1e6, "Written");
       
        while (filteringIterator.hasNext()) {
            final SAMRecord rec = filteringIterator.next();
            outputWriter.addAlignment(rec);
            progress.record(rec);
        }

        filteringIterator.close();
        outputWriter.close();
        inputReader.close();
        log.info(new DecimalFormat("#,###").format(progress.getCount()) + " SAMRecords written to " + OUTPUT.getName());
    }
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    protected int doWork() {
        IOUtil.assertFileIsReadable(INPUT);
        IOUtil.assertFileIsWritable(OUTPUT);
        final SAMFileReader reader = new SAMFileReader(IOUtil.openFileForReading(INPUT));
        reader.getFileHeader().setSortOrder(SORT_ORDER);
        final SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(reader.getFileHeader(), false, OUTPUT);
      writer.setProgressLogger(
          new ProgressLogger(log, (int) 1e7, "Wrote", "records from a sorting collection"));

        final ProgressLogger progress = new ProgressLogger(log, (int) 1e7, "Read");
        for (final SAMRecord rec: reader) {
            writer.addAlignment(rec);
            progress.record(rec);
        }

        log.info("Finished reading inputs, merging and writing to output now.");

        reader.close();
        writer.close();
        return 0;
    }
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        header.setSortOrder(SORT_ORDER);
        final SAMFileWriterFactory samFileWriterFactory = new SAMFileWriterFactory();
        if (USE_THREADING) {
            samFileWriterFactory.setUseAsyncIo(true);
        }
        final SAMFileWriter out = samFileWriterFactory.makeSAMOrBAMWriter(header, presorted, OUTPUT);

        // Lastly loop through and write out the records
        final ProgressLogger progress = new ProgressLogger(log, PROGRESS_INTERVAL);
        while (iterator.hasNext()) {
            final SAMRecord record = iterator.next();
            out.addAlignment(record);
            progress.record(record);
        }

        log.info("Finished reading inputs.");
        out.close();
        return 0;
    }
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    protected int doWork() {
        IOUtil.assertFileIsReadable(INPUT);
        IOUtil.assertFileIsWritable(OUTPUT);
        final SAMFileReader reader = new SAMFileReader(INPUT);
        final SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(reader.getFileHeader(), true, OUTPUT);

        if  (CREATE_INDEX && writer.getFileHeader().getSortOrder() != SAMFileHeader.SortOrder.coordinate){
            throw new PicardException("Can't CREATE_INDEX unless sort order is coordinate");
        }

        final ProgressLogger progress = new ProgressLogger(Log.getInstance(SamFormatConverter.class));
        for (final SAMRecord rec : reader) {
            writer.addAlignment(rec);
            progress.record(rec);
        }
        reader.close();
        writer.close();
        return 0;
    }
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        final File alignedSam = File.createTempFile("aligned.", ".sam");
        alignedSam.deleteOnExit();
        final SAMFileHeader alignedHeader = new SAMFileHeader();
        alignedHeader.setSortOrder(SAMFileHeader.SortOrder.queryname);
        alignedHeader.setSequenceDictionary(new SAMFileReader(sequenceDict).getFileHeader().getSequenceDictionary());
        final SAMFileWriter alignedWriter = new SAMFileWriterFactory().makeSAMWriter(alignedHeader, true, alignedSam);
        for (int i = 0; i < Math.max(firstOfPair.size(), secondOfPair.size()); ++i) {
            final HitSpec firstHitSpec = firstOfPair.isEmpty()? null: firstOfPair.get(i);
            final HitSpec secondHitSpec = secondOfPair.isEmpty()? null: secondOfPair.get(i);
            final SAMRecord first = makeRead(alignedHeader, firstUnmappedRec, firstHitSpec, true, i);
            final SAMRecord second = makeRead(alignedHeader, secondUnmappedRec, secondHitSpec, false, i);
            if (first != null && second != null) SamPairUtil.setMateInfo(first, second, alignedHeader);
            if (first != null) {
                if (second == null) first.setMateUnmappedFlag(true);
                alignedWriter.addAlignment(first);
            }
            if (second != null) {
                if (first == null) second.setMateUnmappedFlag(true);
                alignedWriter.addAlignment(second);
            }
        }
        alignedWriter.close();

        // Merge aligned file with original unmapped file.
        final File mergedSam = File.createTempFile("merged.", ".sam");
        mergedSam.deleteOnExit();
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        final File alignedSam = File.createTempFile("aligned.", ".sam");
        alignedSam.deleteOnExit();
        final SAMFileHeader alignedHeader = new SAMFileHeader();
        alignedHeader.setSortOrder(SAMFileHeader.SortOrder.queryname);
        alignedHeader.setSequenceDictionary(new SAMFileReader(sequenceDict).getFileHeader().getSequenceDictionary());
        final SAMFileWriter alignedWriter = new SAMFileWriterFactory().makeSAMWriter(alignedHeader, true, alignedSam);
        for (int i = 0; i < hitSpecs.size(); ++i) {
            final HitSpec hitSpec = hitSpecs.get(i);
            final SAMRecord mappedRec = makeRead(alignedHeader, unmappedRec, hitSpec, i);
            if (mappedRec != null) {
                alignedWriter.addAlignment(mappedRec);
            }
        }
        alignedWriter.close();

        // Merge aligned file with original unmapped file.
        final File mergedSam = File.createTempFile("merged.", ".sam");
        mergedSam.deleteOnExit();
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        secondOfPair.setReadUnmappedFlag(true);
        secondOfPair.setReadPairedFlag(true);
        secondOfPair.setSecondOfPairFlag(true);
        SamPairUtil.setMateInfo(firstOfPair, secondOfPair, header);

        final SAMFileWriter unmappedWriter = factory.makeSAMWriter(header, false, unmappedSam);
        unmappedWriter.addAlignment(firstOfPair);
        unmappedWriter.addAlignment(secondOfPair);
        unmappedWriter.close();

        final File alignedSam = File.createTempFile("aligned.", ".sam");
        alignedSam.deleteOnExit();

        // Populate the header with SAMSequenceRecords
        header.getSequenceDictionary().addSequence(new SAMSequenceRecord("chr1", 1000000));

        // Create 2 alignments for each end of pair
        final SAMFileWriter alignedWriter = factory.makeSAMWriter(header, false, alignedSam);
        for (int i = 1; i <= 2; ++i) {
            final SAMRecord firstOfPairAligned = new SAMRecord(header);
            firstOfPairAligned.setReadName(firstOfPair.getReadName());
            firstOfPairAligned.setReadBases(firstOfPair.getReadBases());
            firstOfPairAligned.setBaseQualities(firstOfPair.getBaseQualities());
            firstOfPairAligned.setReferenceName("chr1");
            firstOfPairAligned.setAlignmentStart(i);
            firstOfPairAligned.setCigarString(cigar);
            firstOfPairAligned.setMappingQuality(100);
            firstOfPairAligned.setReadPairedFlag(true);
            firstOfPairAligned.setFirstOfPairFlag(true);
            firstOfPairAligned.setAttribute(SAMTag.HI.name(), i);

            final SAMRecord secondOfPairAligned = new SAMRecord(header);
            secondOfPairAligned.setReadName(secondOfPair.getReadName());
            secondOfPairAligned.setReadBases(secondOfPair.getReadBases());
            secondOfPairAligned.setBaseQualities(secondOfPair.getBaseQualities());
            secondOfPairAligned.setReferenceName("chr1");
            secondOfPairAligned.setAlignmentStart(i + 10);
            secondOfPairAligned.setCigarString(cigar);
            secondOfPairAligned.setMappingQuality(100);
            secondOfPairAligned.setReadPairedFlag(true);
            secondOfPairAligned.setSecondOfPairFlag(true);
            secondOfPairAligned.setAttribute(SAMTag.HI.name(), i);

            SamPairUtil.setMateInfo(firstOfPairAligned, secondOfPairAligned, header);

            alignedWriter.addAlignment(firstOfPairAligned);
            alignedWriter.addAlignment(secondOfPairAligned);
        }
        alignedWriter.close();

        doMergeAlignment(unmappedSam, Collections.singletonList(alignedSam),
                null, null, null, null,
                false, true, false, 1,
                "0", "1.0", "align!", "myAligner",
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            unmappedRecord.setReadName("theRead");
            unmappedRecord.setReadString("ACGTACGTACGTACGT");
            unmappedRecord.setBaseQualityString("5555555555555555");
            unmappedRecord.setReadUnmappedFlag(true);

            final SAMFileWriter unmappedWriter = factory.makeSAMWriter(header, false, unmappedSam);
            unmappedWriter.addAlignment(unmappedRecord);
            unmappedWriter.close();

            final File alignedSam = File.createTempFile("aligned.", ".sam");
            alignedSam.deleteOnExit();

            final String sequence = "chr1";
            // Populate the header with SAMSequenceRecords
            header.getSequenceDictionary().addSequence(new SAMSequenceRecord(sequence, 1000000));

            final SAMFileWriter alignedWriter = factory.makeSAMWriter(header, false, alignedSam);
            for (final MultipleAlignmentSpec spec : specs) {
                final SAMRecord alignedRecord = new SAMRecord(header);
                alignedRecord.setReadName(unmappedRecord.getReadName());
                alignedRecord.setReadBases(unmappedRecord.getReadBases());
                alignedRecord.setBaseQualities(unmappedRecord.getBaseQualities());
                alignedRecord.setReferenceName(sequence);
                alignedRecord.setAlignmentStart(1);
                alignedRecord.setReadNegativeStrandFlag(spec.reverseStrand);
                alignedRecord.setCigarString(spec.cigar);
                alignedRecord.setMappingQuality(spec.mapQ);
                if (spec.oneOfTheBest) {
                    alignedRecord.setAttribute(ONE_OF_THE_BEST_TAG, 1);
                }
                alignedWriter.addAlignment(alignedRecord);
            }
            alignedWriter.close();

            return new File[]{unmappedSam, alignedSam};
        } catch (IOException e) {
            throw new PicardException(e.getMessage(), e);
        }
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        secondUnmappedRead.setReadPairedFlag(true);
        secondUnmappedRead.setSecondOfPairFlag(true);



        final SAMFileWriter unmappedWriter = factory.makeSAMWriter(header, false, unmappedSam);
        unmappedWriter.addAlignment(firstUnmappedRead);
        unmappedWriter.addAlignment(secondUnmappedRead);
        unmappedWriter.close();

        final File alignedSam = File.createTempFile("aligned.", ".sam");
        alignedSam.deleteOnExit();

        final String sequence = "chr1";
        // Populate the header with SAMSequenceRecords
        header.getSequenceDictionary().addSequence(new SAMSequenceRecord(sequence, 1000000));

        final SAMFileWriter alignedWriter = factory.makeSAMWriter(header, false, alignedSam);

        addAlignmentsForBestFragmentMapqStrategy(alignedWriter, firstUnmappedRead, sequence, firstMapQs);
        addAlignmentsForBestFragmentMapqStrategy(alignedWriter, secondUnmappedRead, sequence, secondMapQs);
        alignedWriter.close();

        final File output = File.createTempFile("testBestFragmentMapqStrategy." + testName, ".sam");
        output.deleteOnExit();
        doMergeAlignment(unmappedSam, Collections.singletonList(alignedSam),
                null, null, null, null,
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        secondUnmappedRead.setReadPairedFlag(true);
        secondUnmappedRead.setSecondOfPairFlag(true);



        final SAMFileWriter unmappedWriter = factory.makeSAMWriter(header, false, unmappedSam);
        unmappedWriter.addAlignment(firstUnmappedRead);
        unmappedWriter.addAlignment(secondUnmappedRead);
        unmappedWriter.close();

        final File alignedSam = File.createTempFile("aligned.", ".sam");
        alignedSam.deleteOnExit();

        final SAMFileReader dictReader = new SAMFileReader(sequenceDict);
        header.setSequenceDictionary(dictReader.getFileHeader().getSequenceDictionary());
        dictReader.close();

        final SAMFileWriter alignedWriter = factory.makeSAMWriter(header, false, alignedSam);

        String expectedFirstPrimarySequence = null;
        int expectedFirstPrimaryAlignmentStart = -1;
        String expectedSecondPrimarySequence = null;
        int expectedSecondPrimaryAlignmentStart = -1;

        // Semi-randomly make the reads align to forward or reverse strand.
        boolean reverse = false;
        for (final MostDistantStrategyAlignmentSpec spec: firstEndSpecs) {
            addAlignmentForMostStrategy(alignedWriter, firstUnmappedRead, spec, reverse);
            reverse = !reverse;
            if (spec.expectedPrimary) {
                expectedFirstPrimarySequence = spec.sequence;
                expectedFirstPrimaryAlignmentStart = spec.alignmentStart;
            }
        }
        for (final MostDistantStrategyAlignmentSpec spec: secondEndSpecs) {
            addAlignmentForMostStrategy(alignedWriter, secondUnmappedRead, spec, reverse);
            reverse = !reverse;
            if (spec.expectedPrimary) {
                expectedSecondPrimarySequence = spec.sequence;
                expectedSecondPrimaryAlignmentStart = spec.alignmentStart;
            }
        }
        alignedWriter.close();


        final File output = File.createTempFile("testMostDistantStrategy." + testName, ".sam");
        output.deleteOnExit();
        doMergeAlignment(unmappedSam, Collections.singletonList(alignedSam),
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Related Classes of htsjdk.samtools.SAMFileWriter

  • org.broadinstitute.gatk.engine.datasources.reads.ReadProcessingBenchmark
  • org.broadinstitute.gatk.engine.datasources.reads.utilities.BAMTagRenamer
  • org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller
  • org.broadinstitute.gatk.tools.walkers.readutils.SplitSamFile
  • picard.analysis.CollectRnaSeqMetricsTest
  • picard.illumina.MarkIlluminaAdapters
  • picard.sam.AbstractAlignmentMerger
  • picard.sam.AddOrReplaceReadGroups
  • picard.sam.CleanSam
  • picard.sam.CreateSequenceDictionary
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