Package htsjdk.samtools.util

Examples of htsjdk.samtools.util.BufferedLineReader.readLine()

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            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;
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            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)));
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        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;
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        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");
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        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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