Package htsjdk.tribble.readers

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

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            } else if (isLOHFileExt(resourceLocator.getPath())) {
                setTrackType(TrackType.LOH);
            }

            // Parse comments, if any
            nextLine = reader.readLine();
            while (nextLine.startsWith("#") || (nextLine.trim().length() == 0)) {
                if (nextLine.length() > 0) {
                    parseComment(nextLine);
                }
                nextLine = reader.readLine();
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            nextLine = reader.readLine();
            while (nextLine.startsWith("#") || (nextLine.trim().length() == 0)) {
                if (nextLine.length() > 0) {
                    parseComment(nextLine);
                }
                nextLine = reader.readLine();
            }
            parseHeader(nextLine.trim().split("\t"));

            setTrackParameters();
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            setTrackParameters();

            float[] dataArray = new float[getHeadings().length];


            while ((nextLine = reader.readLine()) != null && (nextLine.trim().length() > 0)) {
                String[] tokens = Globals.singleTabMultiSpacePattern.split(nextLine);
                int nTokens = tokens.length;
                if (nTokens == 0) {
                    continue;
                }
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        try {
            reader = ParsingUtils.openAsciiReader(locator);

            if (type == Type.EXPR) {
                reader.readLine(); // Skip header line
            }

            int position = -1;

            while ((nextLine = reader.readLine()) != null) {
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                reader.readLine(); // Skip header line
            }

            int position = -1;

            while ((nextLine = reader.readLine()) != null) {
                lineNumber++;

                if (nextLine.startsWith("#") || nextLine.startsWith("data") || nextLine.startsWith("browser") || nextLine.trim().length() == 0) {
                    continue;
                    // Skip
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        AsciiLineReader reader = null;

        try {
            reader = ParsingUtils.openAsciiReader(rl);

            String name = reader.readLine();
            String serverURL = reader.readLine();

            Map<String, ResourceLocator> locators = new LinkedHashMap();

            String nextLine = null;
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        try {
            reader = ParsingUtils.openAsciiReader(rl);

            String name = reader.readLine();
            String serverURL = reader.readLine();

            Map<String, ResourceLocator> locators = new LinkedHashMap();

            String nextLine = null;
            while ((nextLine = reader.readLine()) != null) {
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            String serverURL = reader.readLine();

            Map<String, ResourceLocator> locators = new LinkedHashMap();

            String nextLine = null;
            while ((nextLine = reader.readLine()) != null) {
                String[] tokens = nextLine.split("\t");
                String chr = tokens[0];
                String file = tokens[1];
                ResourceLocator loc = new ResourceLocator(file);
                locators.put(chr, loc);
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                is = new GZIPInputStream(is);
            }
            bufReader = new AsciiLineReader(is);

            String nextLine = "";
            while ((nextLine = bufReader.readLine()) != null) {
                String[] tokens = nextLine.split("\t");
                probes.add(tokens[0]);
            }

            return probes;
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            reader = openAsciiReader(new ResourceLocator(path));
            String nextLine;
            int lines = 0;
            // Skip the first 10 lines (headers, etc)
            int nSkip = 10;
            while (nSkip-- > 0 && reader.readLine() != null) {
            }
            long startPos = reader.getPosition();

            while ((nextLine = reader.readLine()) != null & lines < 100) {
                lines++;
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