Examples of SortableRecord

Examples of org.broad.igv.tools.sort.SortableRecord

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                    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());

            }
        } finally {
            if (reader != null) {
                reader.close();
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Examples of org.broad.igv.tools.sort.SortableRecord

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                    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());

            }
        } finally {
            if (reader != null) {
                reader.close();
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