Package htsjdk.samtools.util

Examples of htsjdk.samtools.util.LineReader

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        InputStream is = null;
        try {
            URL url = new URL(getHeaderURL());
            is = HttpUtils.getInstance().openConnectionStream(url);

            LineReader reader = new BufferedLineReader(is);
            SAMTextHeaderCodec codec = new SAMTextHeaderCodec();
            header = codec.decode(reader, null);

        } catch (Exception ex) {
            log.info("Error loading header : " + ex.getMessage());
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            outputDir.deleteOnExit();
            // Create barcode.params with output files in the temp directory
            final File libraryParams = new File(outputDir, libraryParamsFile);
            libraryParams.deleteOnExit();
            final List<File> outputPrefixes = new ArrayList<File>();
            final LineReader reader = new BufferedLineReader(new FileInputStream(new File(testDataDir, libraryParamsFile)));
            final PrintWriter writer = new PrintWriter(libraryParams);
            final String header = reader.readLine();
            writer.println(header + "\tOUTPUT_PREFIX");
            while (true) {
                final String line = reader.readLine();
                if (line == null) {
                    break;
                }
                final String[] fields = line.split("\t");
                final File outputPrefix = new File(outputDir, StringUtil.join("", Arrays.copyOfRange(fields, 0, concatNColumnFields)));
                outputPrefixes.add(outputPrefix);
                writer.println(line + "\t" + outputPrefix);
            }
            writer.close();
            reader.close();

            runPicardCommandLine(new String[]{
                    "BASECALLS_DIR=" + baseCallsDir,
                    "LANE=" + lane,
                    "RUN_BARCODE=HiMom",
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        outputDir.deleteOnExit();
        // Create barcode.params with output files in the temp directory
        final File libraryParams = new File(outputDir, libraryParamsFile);
        libraryParams.deleteOnExit();
        final List<File> samFiles = new ArrayList<File>();
        final LineReader reader = new BufferedLineReader(new FileInputStream(new File(testDataDir, libraryParamsFile)));
        final PrintWriter writer = new PrintWriter(libraryParams);
        final String header = reader.readLine();
        writer.println(header + "\tOUTPUT");
        while (true) {
            final String line = reader.readLine();
            if (line == null) {
                break;
            }
            final String[] fields = line.split("\t");
            final File outputSam = new File(outputDir, StringUtil.join("", Arrays.copyOfRange(fields, 0, concatNColumnFields)) + ".sam");
            outputSam.deleteOnExit();
            samFiles.add(outputSam);
            writer.println(line + "\t" + outputSam);
        }
        writer.close();
        reader.close();

        runPicardCommandLine(new String[]{
                "BASECALLS_DIR=" + baseCallsDir,
                "LANE=" + lane,
                "RUN_BARCODE=HiMom",
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        viewSam.INPUT = inputSam;
        final PrintStream viewSamPrintStream = new PrintStream(viewSamOutputFile);
        // TODO - Should switch over to using invocation via new PicardCommandLine() - BUT the test here is accessing class members directly.
        Assert.assertEquals(viewSam.writeSamText(viewSamPrintStream), 0);
        viewSamPrintStream.close();
        final LineReader viewSamInputReader = new BufferedLineReader(new FileInputStream(viewSamOutputFile));
        Assert.assertEquals(viewSamInputReader.readLine(), oldVersionHeader);
    }
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Related Classes of htsjdk.samtools.util.LineReader

  • org.broad.igv.sam.reader.CGIAlignmentReader
  • picard.illumina.IlluminaBasecallsToFastqTest
  • picard.illumina.IlluminaBasecallsToSamTest
  • picard.sam.ViewSamTest
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