Package htsjdk.samtools

Examples of htsjdk.samtools.SAMFileReader

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    @Override
    protected int doWork() {
        IOUtil.assertFileIsReadable(INPUT);
        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);
            }
        }

        // Close the reader and writers
        reader.close();

        if (unknown != null) {
            unknown.close();
        }
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        // Open up the input
        boolean allQueryNameSorted = true;
        final List<SAMFileReader> readers = new ArrayList<SAMFileReader>();
        for (final File f : INPUT) {
            IOUtil.assertFileIsReadable(f);
            final SAMFileReader reader = new SAMFileReader(f);
            readers.add(reader);
            if (reader.getFileHeader().getSortOrder() != SortOrder.queryname) allQueryNameSorted = false;
        }

        // Decide where to write the fixed file - into the specified output file
        // or into a temporary file that will overwrite the INPUT file eventually
        if (OUTPUT != null) OUTPUT = OUTPUT.getAbsoluteFile();
        final boolean differentOutputSpecified = OUTPUT != null;

        if (differentOutputSpecified) {
            IOUtil.assertFileIsWritable(OUTPUT);
        }
        else if (INPUT.size() != 1) {
            throw new PicardException("Must specify either an explicit OUTPUT file or a single INPUT file to be overridden.");
        }
        else {
            final File soleInput = INPUT.get(0).getAbsoluteFile();
            final File dir       = soleInput.getParentFile().getAbsoluteFile();
            try {
                IOUtil.assertFileIsWritable(soleInput);
                IOUtil.assertDirectoryIsWritable(dir);
                OUTPUT = File.createTempFile(soleInput.getName() + ".being_fixed.", BamFileIoUtils.BAM_FILE_EXTENSION, dir);
            }
            catch (final IOException ioe) {
                throw new RuntimeIOException("Could not create tmp file in " + dir.getAbsolutePath());
            }
        }

        // Get the input records merged and sorted by query name as needed
        final PeekableIterator<SAMRecord> iterator;
        final SAMFileHeader header;

        {
            // Deal with merging if necessary
            final Iterator<SAMRecord> tmp;
            if (INPUT.size() > 1) {
                final List<SAMFileHeader> headers = new ArrayList<SAMFileHeader>(readers.size());
                for (final SAMFileReader reader : readers) {
                    headers.add(reader.getFileHeader());
                }
                final SortOrder sortOrder = (allQueryNameSorted? SortOrder.queryname: SortOrder.unsorted);
                final SamFileHeaderMerger merger = new SamFileHeaderMerger(sortOrder, headers, false);
                tmp = new MergingSamRecordIterator(merger, readers, false);
                header = merger.getMergedHeader();
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    protected int doWork() {
        IOUtil.assertFileIsReadable(INPUT);
        IOUtil.assertFileIsReadable(REFERENCE);
        IOUtil.assertFileIsWritable(OUTPUT);

        final SAMFileReader in = new SAMFileReader(INPUT);

        ReferenceSequenceFile reference = ReferenceSequenceFileFactory.getReferenceSequenceFile(REFERENCE);
        SAMSequenceDictionary refDict = reference.getSequenceDictionary();

        if (refDict == null) {
          log.error("No reference sequence dictionary found. Aborting.  You can create a sequence dictionary for the reference fasta using CreateSequenceDictionary.jar.");
          in.close();
          return 1;
        }

        printDictionary("SAM/BAM file", in.getFileHeader().getSequenceDictionary());
        printDictionary("Reference", refDict);
        Map<Integer, Integer> newOrder = buildSequenceDictionaryMap(refDict, in.getFileHeader().getSequenceDictionary());

        // has to be after we create the newOrder
        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
        in.close();
        return 0;
    }
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     * multiple BAM files.
     */
    private static void gatherNormally(final List<File> inputs, final File output, final boolean createIndex, final boolean createMd5) {
        final SAMFileHeader header;
        {
            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);
            CloserUtil.close(in);
        }

        out.close();
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        // Check if we can skip this file since it does not have OQ tags and the mate cigar tag is already there.
        final CanSkipSamFile skipSamFile = RevertOriginalBaseQualitiesAndAddMateCigar.canSkipSAMFile(INPUT, MAX_RECORDS_TO_EXAMINE, RESTORE_ORIGINAL_QUALITIES);
        log.info(skipSamFile.getMessage(MAX_RECORDS_TO_EXAMINE));
        if (skipSamFile.canSkip()) return 0;

        final SAMFileReader in = new SAMFileReader(INPUT, true);
        final SAMFileHeader inHeader = in.getFileHeader();

        // Build the output writer based on the correct sort order
        final SAMFileHeader outHeader = inHeader.clone();
        if (null == SORT_ORDER) this.SORT_ORDER = inHeader.getSortOrder(); // same as the input
        outHeader.setSortOrder(SORT_ORDER);
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     * @param maxRecordsToExamine the maximum number of records to examine before quitting
     * @param revertOriginalBaseQualities true if we are to revert original base qualities, false otherwise
     * @return whether we can skip or not, and the explanation why.
     */
    public static CanSkipSamFile canSkipSAMFile(final File inputFile, final int maxRecordsToExamine, final boolean revertOriginalBaseQualities)  {
        final SAMFileReader in = new SAMFileReader(inputFile, true);
        final Iterator<SAMRecord> iterator = in.iterator();
        int numRecordsExamined = 0;
        CanSkipSamFile returnType = CanSkipSamFile.FOUND_NO_EVIDENCE;

        while (iterator.hasNext() && numRecordsExamined < maxRecordsToExamine) {
            final SAMRecord record = iterator.next();

            if (revertOriginalBaseQualities && null != record.getOriginalBaseQualities()) {
                // has OQ, break and return case #2
                returnType = CanSkipSamFile.CANNOT_SKIP_FOUND_OQ;
                break;
            }

            // check if mate pair and its mate is mapped
            if (record.getReadPairedFlag() && !record.getMateUnmappedFlag()) {
                if (null == SAMUtils.getMateCigar(record)) {
                    // has no MC, break and return case #2
                    returnType = CanSkipSamFile.CANNOT_SKIP_FOUND_NO_MC;
                    break;
                }
                else {
                    // has MC, previously checked that it does not have OQ, break and return case #1
                    returnType = CanSkipSamFile.CAN_SKIP;
                    break;
                }
            }

            numRecordsExamined++;
        }

        // no more records anyhow, so we can skip
        if (!iterator.hasNext() && CanSkipSamFile.FOUND_NO_EVIDENCE == returnType) {
            returnType = CanSkipSamFile.CAN_SKIP;
        }

        in.close();

        return returnType;
    }
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    /**
     * Writes the binary fastq file(s) to the output directory
     */
    public void writeBfqFiles() {

        final Iterator<SAMRecord> iterator = (new SAMFileReader(IOUtil.openFileForReading(this.bamFile))).iterator();

        // Filter out noise reads and reads that fail the quality filter
        final TagFilter tagFilter = new TagFilter(ReservedTagConstants.XN, 1);
        final FailsVendorReadQualityFilter qualityFilter = new FailsVendorReadQualityFilter();
        final WholeReadClippedFilter clippedFilter = new WholeReadClippedFilter();
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     * @return  the number of records in the Bam file
     */
    private int countWritableRecords() {
        int count = 0;
       
        SAMFileReader reader = new SAMFileReader(IOUtil.openFileForReading(this.bamFile));
        if(!reader.getFileHeader().getSortOrder().equals(SAMFileHeader.SortOrder.queryname)) {
          //this is a fix for issue PIC-274: It looks like BamToBfqWriter requires that the input BAM is queryname sorted,
          //but it doesn't check this early, nor produce an understandable error message."
          throw new PicardException("Input file (" + this.bamFile.getAbsolutePath() +") needs to be sorted by queryname.");
        }
        final PeekableIterator<SAMRecord> it = new PeekableIterator<SAMRecord>(reader.iterator());
        if (!this.pairedReads) {
            // Filter out noise reads and reads that fail the quality filter
            final List<SamRecordFilter> filters = new ArrayList<SamRecordFilter>();
            filters.add(new TagFilter(ReservedTagConstants.XN, 1));
            if (!this.includeNonPfReads) {
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        final LiftOver liftOver = new LiftOver(CHAIN);
        liftOver.setLiftOverMinMatch(MIN_LIFTOVER_PCT);

        final IntervalList fromIntervals = IntervalList.fromFile(INPUT);
        final SAMFileHeader toHeader = new SAMFileReader(SEQUENCE_DICTIONARY).getFileHeader();
        liftOver.validateToSequences(toHeader.getSequenceDictionary());
        final IntervalList toIntervals = new IntervalList(toHeader);
        boolean anyFailed = false;
        for (final Interval fromInterval : fromIntervals) {
            final Interval toInterval = liftOver.liftOver(fromInterval);
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     * @return program exit status.
     */
    @Override
    protected int doWork() {
        for (int i = 0; i < samFiles.size(); ++i) {
            samReaders[i] = new SAMFileReader(samFiles.get(i));
        }
        areEqual = compareHeaders();
        areEqual = compareAlignments() && areEqual;
        printReport();
        if (!areEqual) {
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Related Classes of htsjdk.samtools.SAMFileReader

  • org.broad.igv.cli_plugin.AlignmentDecoder
  • org.broad.igv.sam.reader.BAMFileReader
  • org.broad.igv.sam.reader.BAMHttpReader
  • org.broad.igv.sam.reader.SAMFileGroup
  • org.broad.igv.sam.reader.SAMFileGroup$SamGroupIterator
  • org.broad.igv.sam.reader.SAMReader
  • org.broad.igv.sam.SAMWriterTest
  • org.broadinstitute.gatk.engine.CommandLineGATKUnitTest
  • org.broadinstitute.gatk.engine.datasources.reads.GATKBAMIndexUnitTest
  • org.broadinstitute.gatk.engine.datasources.reads.PicardBaselineBenchmark
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