Package htsjdk.tribble.readers

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

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            Genome genome = GenomeManager.getInstance().getCurrentGenome();

            reader = ParsingUtils.openAsciiReader(locator);

            // Parse header
            reader.readLine();
            rowCounter++;

            // Parse data
            // parameters to track chromosome breaks. Used in wholeGenome case.
            GisticTrack track = new GisticTrack(locator);
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            // parameters to track chromosome breaks. Used in wholeGenome case.
            GisticTrack track = new GisticTrack(locator);
            track.setName(locator.getTrackName());
            List<GisticScore> scores = new ArrayList();

            nextLine = reader.readLine();
            rowCounter++;

            while ((nextLine != null) && (nextLine.length() > 0)) {
                String[] tokens = nextLine.split("\t");
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                }
                catch (Exception ex) {
                    log.error("Skipping line: " + nextLine, ex);
                }

                nextLine = reader.readLine();
                rowCounter++;
            }

            if (scores.isEmpty()) {
                throw new RuntimeException("No gistic scores were found.");
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            //We loop through, generating a new FastaSequenceIndexEntry
            //every time we see a new header line, or when the file ends.
            while (haveTasks) {
                line = reader.readLine();
                curLineNum++;

                if (line == null || line.startsWith(">")) {
                    //The last line can have a different number of bases/bytes
                    if (numInconsistentLines >= 2) {
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        try {
            reader = ParsingUtils.openAsciiReader(locator);

            // Parse columns line
            String headerLine = reader.readLine();
            if (!this.columns.parseHeader(headerLine))
                throw new ParserException("Error while parsing columns line.", 0, nextLine);

            gData.getDescriptionCache().setHeaderTokens(headerLine);
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            // Number of lines to cache after the hit (tries to estimate that half of the cache will be filled with data from data before the query data point, and half with data after the query data point
            int cacheAfter = cacheSize / 2;
            int cacheCounter = 0;

            while (cacheCounter < cacheAfter && (nextLine = reader.readLine()) != null && (nextLine.trim().length() > 0)) {

                nextLine = nextLine.trim();
                rowCounter++;

                if (rowCounter >= searchStartRow) {
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        GWASEntry lastEntry = null;

        try {
            reader = ParsingUtils.openAsciiReader(locator);

            String headerLine = reader.readLine();
            if (!this.columns.parseHeader(headerLine))
                throw new ParserException("Error while parsing columns line.", 0, nextLine);

            GWASData gData = new GWASData();
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            GWASData gData = new GWASData();

            int indexCounter = 0;

            while ((nextLine = reader.readLine()) != null && (nextLine.trim().length() > 0)) {

                nextLine = nextLine.trim();
                rowCounter++;

                GWASEntry entry = parseLine(nextLine, rowCounter);
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            String headerLine = null;

            // Skip header rows

            nextLine = reader.readLine();
            nextLine = reader.readLine();

            headerLine = reader.readLine();

            // Parse column headings
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            String headerLine = null;

            // Skip header rows

            nextLine = reader.readLine();
            nextLine = reader.readLine();

            headerLine = reader.readLine();

            // Parse column headings
            int skip = 1;
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