Examples of htsjdk.samtools.util.SortingCollection

htsjdk.samtools.util.SortingCollection




        BufferedReader reader = null;
        PrintWriter writer = null;


        SortingCollection cltn = getSortingCollection(maxRecords, tmpDir);
        try {
            reader = new BufferedReader(new FileReader(inputFile));
            writer = new PrintWriter(new BufferedWriter(new FileWriter(outputFile)));


            // Parse the header line
            String headerLine = reader.readLine();
            String[] tokens = headerLine.split("\t");


            //The sample names in a GCT file start at column 2,
            int sampleStart = 2;




            String nextLine = null;
            TrackType dataType = TrackType.GENE_EXPRESSION;
            while ((nextLine = reader.readLine()) != null) {


                // A gct row can map to multiple loci, normally this indicates a problem with the probe
                DataRow row = new DataRow(nextLine);
                String probe = row.getProbe();
                if (probe.startsWith("cg")) {
                    dataType = TrackType.DNA_METHYLATION;
                }


                List<Locus> loci = locusHelper.getLoci(probe, row.getDescription(), genome.getId());
                if (loci == null || loci.isEmpty()) {
                    System.out.println("No locus found for: " + probe + "  " + row.getDescription());
                } else {
                    for (Locus locus : loci) {
                        String igvLine = locus.getChr() + "\t" + locus.getStart() + "\t" + locus.getEnd() + "\t" + probe +
                                row.getData();
                        cltn.add(new SortableRecord(locus.getChr(), locus.getStart(), igvLine));
                    }
                }
            }


            writer.println("#type=" + dataType.toString());
            writer.print("Chr\tStart\tEnd\tProbe");
            for (int i = sampleStart; i < tokens.length; i++) {
                writer.print("\t" + tokens[i]);
            }
            writer.println();
            // Ouputput the sorted file
            CloseableIterator<SortableRecord> iter = cltn.iterator();
            while (iter.hasNext()) {
                SortableRecord al = iter.next();
                writer.println(al.getText());


            }

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        BufferedReader reader = null;
        PrintWriter writer = null;


        SortingCollection cltn = getSortingCollection(maxRecords, tmpDir);
        try {
            reader = new BufferedReader(new InputStreamReader(ParsingUtils.openInputStream(resourceLocator.getPath())));
            writer = new PrintWriter(new BufferedWriter(new FileWriter(outputFile)));


            ExpressionFileParser.FormatDescriptor formatDescriptor = ExpressionFileParser.parseHeader (reader, type, null);
            String [] dataHeadings = formatDescriptor.getDataHeaders();




            // Need a better way to determine type!
            String dataType = resourceLocator.getPath().contains("methylation") ? TrackType.DNA_METHYLATION.toString()
                    : TrackType.GENE_EXPRESSION.toString();


            writer.println("#type=" + dataType);
            writer.print("Chr\tStart\tEnd\tProbe");
            for (String s : dataHeadings) {
                writer.print("\t" + s);
            }
            writer.println();


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


                // A gct row can map to multiple loci, normally this indicates a problem with the probe
                DataRow row = new DataRow(nextLine, formatDescriptor);
                String probe = row.getProbe();
                List<Locus> loci = locusHelper.getLoci(probe, row.getDescription(), genome.getId());
                if (loci == null || loci.isEmpty()) {
                    log.warn("No locus found for: " + probe + "  " + row.getDescription());
                } else {
                    for (Locus locus : loci) {
                        String igvLine = locus.getChr() + "\t" + locus.getStart() + "\t" + locus.getEnd() + "\t" + probe +
                                "\t" + row.getData();
                        cltn.add(new SortableRecord(locus.getChr(), locus.getStart(), igvLine));
                    }
                }
            }




            // Ouputput the sorted file
            CloseableIterator<SortableRecord> iter = cltn.iterator();
            while (iter.hasNext()) {
                SortableRecord al = iter.next();
                writer.println(al.getText());


            }

View Full Code Here

            }
            writer = new PrintWriter(new BufferedWriter(rawWriter));


            SortableRecordCodec codec = new SortableRecordCodec();


            SortingCollection cltn = SortingCollection.newInstance(SortableRecord.class, codec, comparator, maxRecords, tmpDir);


            Parser parser = getParser();
            AsciiLineReader reader = new AsciiLineReader(fis);


            String firstDataRow = writeHeader(reader, writer);
            if (firstDataRow != null) {
                cltn.add(parser.createRecord(firstDataRow));
            }


            SortableRecord next = null;
            while ((next = parser.readNextRecord(reader)) != null) {
                cltn.add(next);
            }




            CloseableIterator<SortableRecord> iter = cltn.iterator();
            while (iter.hasNext()) {
                SortableRecord al = iter.next();
                writer.println(al.getText());


            }

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Related Classes of htsjdk.samtools.util.SortingCollection

org.broad.igv.tools.converters.GCTtoIGVConverter

org.broad.igv.tools.converters.MageTabToIGVConverter

org.broad.igv.tools.sort.Sorter

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