Package htsjdk.tribble.readers

Examples of htsjdk.tribble.readers.AsciiLineReader.readLine()

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                        // Skip line
                        log.info("Skipping line (NumberFormatException) " + nextLine);
                    }
                }

                nextLine = reader.readLine();
            }

            // Loop complete
            ChromosomeData cd = new ChromosomeData(chrSummary.getName());
            cd.setProbes(probes.toArray(new String[]{}));
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        try {
            reader = ParsingUtils.openAsciiReader(locator);
            lineNumber = readHeader(reader);

            while ((nextLine = reader.readLine()) != null && (nextLine.trim().length() > 0)) {
                lineNumber++;
                String[] tokens = Globals.tabPattern.split(nextLine, -1);
                parseLine(parser, tokens);
            }
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        HashMap<String, PrintWriter> writers = new HashMap();
        try {
            String lastChr = "";
            reader = new AsciiLineReader(new FileInputStream(file));
            // Skip header
            reader.readLine();
            String nextLine;
            while ((nextLine = reader.readLine()) != null) {
                String[] tokens = Globals.tabPattern.split(nextLine, -1);
                String chr = tokens[chrCol];
                if (!chr.equals(lastChr)) {
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            String lastChr = "";
            reader = new AsciiLineReader(new FileInputStream(file));
            // Skip header
            reader.readLine();
            String nextLine;
            while ((nextLine = reader.readLine()) != null) {
                String[] tokens = Globals.tabPattern.split(nextLine, -1);
                String chr = tokens[chrCol];
                if (!chr.equals(lastChr)) {
                    closeWriters(writers);
                }
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            Map<String, List<htsjdk.tribble.Feature>> mutationMap = new LinkedHashMap();

            reader = ParsingUtils.openAsciiReader(locator);

            // Skip header - handled in codec
            while ((nextLine = reader.readLine()) != null) {
                if (nextLine.startsWith("#")) continue;
                else break;

            }
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                if (nextLine.startsWith("#")) continue;
                else break;

            }

            while ((nextLine = reader.readLine()) != null) {

                Mutation mut = codec.decode(nextLine);

                if (mut != null) {
                    String sampleId = mut.getSampleId();
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                + " -o %s -L 20:10,000,000-10,100,000 -nt 4",
                1, Arrays.asList("vcf.gz"), Arrays.asList(""));
        final File vcf = executeTest("testCompressedVCFOutputWithNT", spec).first.get(0);
        final AsciiLineReader reader = new AsciiLineReader(new BlockCompressedInputStream(vcf));
        int nLines = 0;
        while ( reader.readLine() != null )
            nLines++;
        Assert.assertTrue(nLines > 0);
    }

    // --------------------------------------------------------------------------------------------------------------
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