Package htsjdk.samtools

Examples of htsjdk.samtools.SAMFileReader

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    }

    private void loadHeader() {

        InputStream is = null;
        SAMFileReader reader = null;
        try {
            is = ParsingUtils.openInputStreamGZ(new ResourceLocator(samFile));
            BufferedInputStream bis = new BufferedInputStream(is);
            SAMFileReader.setDefaultValidationStringency(ValidationStringency.SILENT);
            reader = new SAMFileReader(bis);
            header = reader.getFileHeader();
        } catch (IOException e) {
            log.error("Error loading header", e);
        } finally {
            try {
                if (is != null) {
                    is.close();
                }
                if (reader != null) {
                    reader.close();
                }

            } catch (Exception e) {

            }
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        FeatureIndex.TileDef seekPos = featureIndex.getTileDef(sequence, startTileNumber);

        if (seekPos != null) {
            // Skip to the start of the query interval and open a sam file reader
            SAMFileReader reader = getSAMFileReader(samFile, seekPos.getStartPosition());
            CloseableIterator<SAMRecord> iter = reader.iterator();
            return new SAMQueryIterator(sequence, start, end, contained, iter);
        }
        return EmptyAlignmentIterator.getInstance();
    }
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        return sequenceNames;

    }

    public CloseableIterator<PicardAlignment> iterator() {
        SAMFileReader reader = getSAMFileReader(samFile, -1);
        CloseableIterator<SAMRecord> iter = reader.iterator();
        return new SAMQueryIterator(iter);
    }
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        try {
            SeekableStream stream = IGVSeekableStreamFactory.getInstance().getStreamFor(samFile);
            if (startPosition >= 0) {
                stream.seek(startPosition);
            }
            SAMFileReader reader = new SAMFileReader(stream);
            reader.setValidationStringency(ValidationStringency.SILENT);

            //Need to keep the file source, if loading lazily
            //TODO Can't reload from SAM files. See SAMTextReader.getIterator
            //reader.enableFileSource(PicardAlignment.DEFAULT_LAZY_LOAD);
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    public SAMFileHeader getHeader() {
        if (samFiles.length == 0) {
            return null;
        }
        SAMFileReader reader = new SAMFileReader(samFiles[0]);
        SAMFileHeader header = reader.getFileHeader();
        reader.close();
        ;
        return header;
    }
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                }
                if (currentReader != null) {
                    currentReader.close();
                }
                if (idx < samFiles.length) {
                    currentReader = new SAMFileReader(samFiles[idx]);
                    currentIter = currentReader.iterator();
                    idx++;
                }
            }
            next = currentIter == null ? null : currentIter.next();
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            SeekableStream ss = new IGVSeekableBufferedStream(IGVSeekableStreamFactory.getInstance().getStreamFor(url), 128000);
            //SeekableStream ss = getSeekableStream(url);
            log.debug("Initializing SAMFileReader");

            reader = new SAMFileReader(ss, indexFile, false);
        } else {
            InputStream is = HttpUtils.getInstance().openConnectionStream(url);
            reader = new SAMFileReader(new BufferedInputStream(is));
        }

    }
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    SAMFileHeader header;

    public BAMFileReader(File bamFile) {
        try {
            File indexFile = findIndexFile(bamFile);
            reader = new SAMFileReader(bamFile, indexFile);
            reader.setValidationStringency(ValidationStringency.SILENT);
            loadHeader();
        } catch (Exception e) {
            MessageUtils.showMessage("Error loading SAM header: " + e.getMessage());
            e.printStackTrace();
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    public CloseableIterator<PicardAlignment> iterator() {
        try {
            if (reader == null) {
                InputStream is = HttpUtils.getInstance().openConnectionStream(url);
                reader = new SAMFileReader(new BufferedInputStream(is));
            }
            return new WrappedIterator(reader.iterator());
        } catch (IOException e) {
            log.error("Error creating iterator", e);
            throw new RuntimeException(e);
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    public CloseableIterator<PicardAlignment> query(String sequence, int start, int end, boolean contained) {
        try {
            if (reader == null) {
                SeekableStream ss = new IGVSeekableBufferedStream(IGVSeekableStreamFactory.getInstance().getStreamFor(url));
                reader = new SAMFileReader(ss, indexFile, false);
            }
            CloseableIterator<SAMRecord> iter = reader.query(sequence, start + 1, end, contained);
            return new WrappedIterator(iter);
        } catch (IOException e) {
            log.error("Error opening SAM reader", e);
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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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