Package htsjdk.samtools

Examples of htsjdk.samtools.SAMFileWriterFactory

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        alignedIterator.close();

        // Write the records to the output file in specified sorted order,
        header.setSortOrder(this.sortOrder);
        final boolean presorted = this.sortOrder == SortOrder.coordinate;
        final SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(header, presorted, this.targetBamFile);
      writer.setProgressLogger(
          new ProgressLogger(log, (int) 1e7, "Wrote", "records from a sorting collection"));
        final ProgressLogger finalProgress = new ProgressLogger(log, 10000000, "Written in coordinate order to output", "records");

        for (final SAMRecord rec : sorted) {
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        }

        final SAMFileHeader header = new SAMFileHeader();
        header.setSortOrder(SAMFileHeader.SortOrder.queryname);
        header.addReadGroup(rg);
        return new SAMFileWriterWrapper(new SAMFileWriterFactory().makeSAMOrBAMWriter(header, true, output));
    }
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        final SAMFileHeader inHeader = in.getFileHeader();
        final SAMFileHeader outHeader = inHeader.clone();
        outHeader.setReadGroups(Arrays.asList(rg));
        if (SORT_ORDER != null) outHeader.setSortOrder(SORT_ORDER);

        final SAMFileWriter outWriter = new SAMFileWriterFactory().makeSAMOrBAMWriter(outHeader,
                                                                                      outHeader.getSortOrder() == inHeader.getSortOrder(),
                                                                                      OUTPUT);

        final ProgressLogger progress = new ProgressLogger(log);
        for (final SAMRecord read : in) {
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        IOUtil.assertDirectoryIsWritable(OUTPUT);

        SAMFileReader reader = new SAMFileReader(INPUT);
        Map<String, SAMFileWriter> libraryToWriter = new HashMap<String, SAMFileWriter>();
        Map<String, List<SAMReadGroupRecord>> libraryToRg = new HashMap<String, List<SAMReadGroupRecord>>();
        SAMFileWriterFactory factory = new SAMFileWriterFactory();
        String extension = reader.isBinary() ? ".bam" : ".sam";

        SAMFileHeader unknownHeader = reader.getFileHeader().clone();
        unknownHeader.setReadGroups(new ArrayList<SAMReadGroupRecord>());
        SAMFileWriter unknown = null;

        for (SAMReadGroupRecord rg : reader.getFileHeader().getReadGroups()) {
            String lib = rg.getLibrary();
            if (lib != null) {
                if (!libraryToRg.containsKey(lib)) {
                    libraryToRg.put(lib, new ArrayList<SAMReadGroupRecord>());
                }
                libraryToRg.get(lib).add(rg);
            }
            else {
                unknownHeader.addReadGroup(rg);
            }
        }

        if (libraryToRg.size() == 0) {
            log.error("No individual libraries are " +
                    "specified in the header of " + INPUT.getAbsolutePath());
            return NO_LIBRARIES_SPECIFIED_IN_HEADER;
        }

        for (Map.Entry<String, List<SAMReadGroupRecord>> entry : libraryToRg.entrySet()) {
            String lib = entry.getKey();
            SAMFileHeader header = reader.getFileHeader().clone();
            header.setReadGroups(entry.getValue());
            libraryToWriter.put(lib, factory.makeSAMOrBAMWriter(header, true,
                    new File(OUTPUT, IOUtil.makeFileNameSafe(lib) + extension)));
        }

        for (Iterator<SAMRecord> it = reader.iterator(); it.hasNext(); ) {
            SAMRecord sam = it.next();
            SAMReadGroupRecord rg = sam.getReadGroup();
            if (rg != null && rg.getLibrary() != null) {
                libraryToWriter.get(rg.getLibrary()).addAlignment(sam);
            }
            else {
                if (unknown == null) {
                    unknown = factory.makeSAMOrBAMWriter(unknownHeader, true,
                            new File(OUTPUT, "unknown" + extension));
                }
                unknown.addAlignment(sam);
            }
        }
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        return 0;
    }

    protected void createSamFileWriter(final SAMFileHeader header) {
        out = new SAMFileWriterFactory().makeSAMOrBAMWriter(header,
                  header.getSortOrder() == SortOrder.queryname, OUTPUT);

    }
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        SAMFileHeader outHeader = in.getFileHeader().clone();
        outHeader.setSequenceDictionary(refDict);

        log.info("Writing reads...");
        if (in.hasIndex()) {
            final SAMFileWriter out = new SAMFileWriterFactory().makeSAMOrBAMWriter(outHeader, true, OUTPUT);

            // write the reads in contig order
            for (final SAMSequenceRecord contig : refDict.getSequences() ) {
                final SAMRecordIterator it = in.query(contig.getSequenceName(), 0, 0, false);
                writeReads(out, it, newOrder, contig.getSequenceName());
            }
            // don't forget the unmapped reads
            writeReads( out, in.queryUnmapped(), newOrder, "unmapped" );
            out.close();
        }
        else {
            SAMFileWriter out = new SAMFileWriterFactory().makeSAMOrBAMWriter(outHeader, false, OUTPUT);
            writeReads(out, in.iterator(), newOrder, "All reads");
            out.close();
        }

        // cleanup
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            final SAMFileReader tmp = new SAMFileReader(inputs.get(0));
            header = tmp.getFileHeader();
            tmp.close();
        }

        final SAMFileWriter out = new SAMFileWriterFactory().setCreateIndex(createIndex).setCreateMd5File(createMd5).makeSAMOrBAMWriter(header, true, output);

        for (final File f : inputs) {
            log.info("Gathering " + f.getAbsolutePath());
            final SAMFileReader in = new SAMFileReader(f);
            for (final SAMRecord rec : in) out.addAlignment(rec);
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                    " already exists.  Delete this file and try again, or specify a different output file.");
        }
        final SAMSequenceDictionary sequences = makeSequenceDictionary(REFERENCE);
        final SAMFileHeader samHeader = new SAMFileHeader();
        samHeader.setSequenceDictionary(sequences);
        final SAMFileWriter samWriter = new SAMFileWriterFactory().makeSAMWriter(samHeader, false, OUTPUT);
        samWriter.close();
        return 0;
    }
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        final MostDistantStrategyAlignmentSpec[] firstEndSpecs,
        final MostDistantStrategyAlignmentSpec[] secondEndSpecs) throws Exception {

        final File unmappedSam = File.createTempFile("unmapped.", ".sam");
        unmappedSam.deleteOnExit();
        final SAMFileWriterFactory factory = new SAMFileWriterFactory();
        final SAMFileHeader header = new SAMFileHeader();
        header.setSortOrder(SAMFileHeader.SortOrder.queryname);

        final String readName = "theRead";
        final SAMRecord firstUnmappedRead = new SAMRecord(header);
        firstUnmappedRead.setReadName(readName);
        firstUnmappedRead.setReadString("ACGT");
        firstUnmappedRead.setBaseQualityString("5555");
        firstUnmappedRead.setReadUnmappedFlag(true);
        firstUnmappedRead.setMateUnmappedFlag(true);
        firstUnmappedRead.setReadPairedFlag(true);
        firstUnmappedRead.setFirstOfPairFlag(true);

        final SAMRecord secondUnmappedRead = new SAMRecord(header);
        secondUnmappedRead.setReadName(readName);
        secondUnmappedRead.setReadString("TCGA");
        secondUnmappedRead.setBaseQualityString("6666");
        secondUnmappedRead.setReadUnmappedFlag(true);
        secondUnmappedRead.setMateUnmappedFlag(true);
        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;
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    }

    private File createInputFile() {
        // Create the input file
        final File input = new File(outputDir, "input.sam");
        final SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(samRecordSetBuilder.getHeader(), true, input);
        for (final SAMRecord record : samRecordSetBuilder.getRecords()) {
            writer.addAlignment(record);
        }
        writer.close();
        return input;
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Related Classes of htsjdk.samtools.SAMFileWriterFactory

  • org.broadinstitute.gatk.engine.datasources.reads.ReadProcessingBenchmark
  • org.broadinstitute.gatk.engine.datasources.reads.utilities.BAMTagRenamer
  • picard.analysis.CollectRnaSeqMetricsTest
  • picard.illumina.IlluminaBasecallsToSam
  • picard.illumina.MarkIlluminaAdapters
  • picard.sam.AbstractAlignmentMerger
  • picard.sam.AddOrReplaceReadGroups
  • picard.sam.CleanSam
  • picard.sam.CreateSequenceDictionary
  • picard.sam.DownsampleSam
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