Package htsjdk.tribble.readers

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

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            int nSkip = 10;
            while (nSkip-- > 0 && reader.readLine() != null) {
            }
            long startPos = reader.getPosition();

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

            if (lines == 0) {
                return defaultLength;
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        try {
            reader = ParsingUtils.openAsciiReader(file);
            String nextLine = null;

            //skip first row
            reader.readLine();

            //check second row for MAGE_TAB identifiers
            if ((nextLine = reader.readLine()) != null && (nextLine.contains("Reporter REF") ||
                    nextLine.contains("Composite Element REF") || nextLine.contains("Term Source REF") ||
                    nextLine.contains("CompositeElement REF") || nextLine.contains("TermSource REF") ||
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            //skip first row
            reader.readLine();

            //check second row for MAGE_TAB identifiers
            if ((nextLine = reader.readLine()) != null && (nextLine.contains("Reporter REF") ||
                    nextLine.contains("Composite Element REF") || nextLine.contains("Term Source REF") ||
                    nextLine.contains("CompositeElement REF") || nextLine.contains("TermSource REF") ||
                    nextLine.contains("Coordinates REF"))) {
                return true;
            }
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        try {
            reader = ParsingUtils.openAsciiReader(file);
            String nextLine = null;

            //skip first row
            reader.readLine();

            //check second row for MAGE_TAB identifiers
            if ((nextLine = reader.readLine()) != null && (nextLine.contains("Reporter REF") || nextLine.contains("Composite Element REF") || nextLine.contains("Term Source REF") || nextLine.contains("CompositeElement REF") || nextLine.contains("TermSource REF") || nextLine.contains("Coordinates REF"))) {
                int count = 0;
                // check if this mage_tab data matrix can be parsed by this class
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            //skip first row
            reader.readLine();

            //check second row for MAGE_TAB identifiers
            if ((nextLine = reader.readLine()) != null && (nextLine.contains("Reporter REF") || nextLine.contains("Composite Element REF") || nextLine.contains("Term Source REF") || nextLine.contains("CompositeElement REF") || nextLine.contains("TermSource REF") || nextLine.contains("Coordinates REF"))) {
                int count = 0;
                // check if this mage_tab data matrix can be parsed by this class
                while ((nextLine = reader.readLine()) != null && count < 5) {
                    nextLine = nextLine.trim();
                    if (nextLine.startsWith("SNP_A") || nextLine.startsWith("CN_")) {
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            //check second row for MAGE_TAB identifiers
            if ((nextLine = reader.readLine()) != null && (nextLine.contains("Reporter REF") || nextLine.contains("Composite Element REF") || nextLine.contains("Term Source REF") || nextLine.contains("CompositeElement REF") || nextLine.contains("TermSource REF") || nextLine.contains("Coordinates REF"))) {
                int count = 0;
                // check if this mage_tab data matrix can be parsed by this class
                while ((nextLine = reader.readLine()) != null && count < 5) {
                    nextLine = nextLine.trim();
                    if (nextLine.startsWith("SNP_A") || nextLine.startsWith("CN_")) {
                        return true;
                    }
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            } else {
                dataset.getTrackProperties().setWindowingFunction(WindowFunction.mean);
            }

            // Parse comments and directives, if any
            nextLine = reader.readLine();
            while (nextLine.startsWith("#") || (nextLine.trim().length() == 0)) {
                headerRows++;

                if (nextLine.length() > 0) {
                    parseDirective(nextLine, dataset);
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                headerRows++;

                if (nextLine.length() > 0) {
                    parseDirective(nextLine, dataset);
                }
                nextLine = reader.readLine();
            }

            if (chrColumn < 0) {
                setColumnDefaults();
            }
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            int chrRowCount = 0;

            // Update
            int updateCount = 5000;
            long lastPosition = 0;
            while ((nextLine = reader.readLine()) != null) {

                if (igv != null && ++count % updateCount == 0) {
                    igv.setStatusBarMessage("Loaded: " + count + " / " + estLineCount + " (est)");
                }
                // Distance since last sample
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            }

            // Begin loop through rows
            String chromosome = chrSummary.getName();
            boolean chromosomeStarted = false;
            String nextLine = reader.readLine();

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

                if (!nextLine.startsWith("#")) {
                    try {
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