@Override public RandSamRecord decode() { int r; try { r = this.binaryCodec.readInt(); } catch (Exception e) { return null; } RandSamRecord o = new RandSamRecord(); o.rand_index = r; o.samRecord = this.bamRecordCodec.decode(); return o; }
@Override public int doWork(String[] args) { boolean compressed = false; int maxRecordsInRAM = 100000; long count = -1L; File fileout = null; com.github.lindenb.jvarkit.util.cli.GetOpt opt = new com.github.lindenb.jvarkit.util.cli.GetOpt(); int c; while ((c = opt.getopt(args, getGetOptDefault() + "o:n:N:T:b")) != -1) { switch (c) { case 'b': compressed = true; break; case 'N': maxRecordsInRAM = Integer.parseInt(opt.getOptArg()); break; case 'n': count = Long.parseLong(opt.getOptArg()); break; case 'o': fileout = new File(opt.getOptArg()); break; case 'T': this.addTmpDirectory(new File(opt.getOptArg())); break; default: { switch (handleOtherOptions(c, opt, null)) { case EXIT_FAILURE: return -1; case EXIT_SUCCESS: return 0; default: break; } } } } if (count < -1L) // -1 == infinite { error("Bad count:" + count); return -1; } SamReader samReader = null; SAMRecordIterator iter = null; SAMFileWriter samWriter = null; Random random = new Random(); CloseableIterator<RandSamRecord> iter2 = null; try { SamFileReaderFactory.setDefaultValidationStringency(ValidationStringency.SILENT); if (opt.getOptInd() == args.length) { info("Reading from stdin"); samReader = SamFileReaderFactory.mewInstance().openStdin(); } else if (opt.getOptInd() + 1 == args.length) { File filename = new File(args[opt.getOptInd()]); info("Reading from " + filename); samReader = SamFileReaderFactory.mewInstance().open(filename); } else { error("Illegal number of arguments."); return -1; } SAMFileHeader header = samReader.getFileHeader(); header = header.clone(); header.setSortOrder(SortOrder.unsorted); header.addComment("Processed with " + getProgramName() + " : " + getProgramCommandLine()); SAMFileWriterFactory sfw = new SAMFileWriterFactory(); sfw.setCreateIndex(false); sfw.setCreateMd5File(false); if (fileout == null) { if (compressed) { samWriter = sfw.makeBAMWriter(header, true, System.out); } else { samWriter = sfw.makeSAMWriter(header, true, System.out); } } else { samWriter = sfw.makeSAMOrBAMWriter(header, true, fileout); this.addTmpDirectory(fileout); } iter = samReader.iterator(); SAMSequenceDictionaryProgress progress = new SAMSequenceDictionaryProgress(samReader.getFileHeader().getSequenceDictionary()); SortingCollection<RandSamRecord> sorter = SortingCollection.newInstance( RandSamRecord.class, new RandSamRecordCodec(header), new RandSamRecordComparator(), maxRecordsInRAM, getTmpDirectories()); sorter.setDestructiveIteration(true); while (iter.hasNext()) { RandSamRecord r = new RandSamRecord(); r.rand_index = random.nextInt(); r.samRecord = progress.watch(iter.next()); sorter.add(r); } iter.close(); iter = null; sorter.doneAdding(); iter2 = sorter.iterator(); if (count == -1) { while (iter2.hasNext()) { samWriter.addAlignment(iter2.next().samRecord); } } else { while (iter2.hasNext() && count > 0) { samWriter.addAlignment(iter2.next().samRecord); count--; } } iter2.close(); iter2 = null; sorter.cleanup(); progress.finish(); } catch (Exception e) { error(e); return -1; } finally { CloserUtil.close(iter); CloserUtil.close(iter2); CloserUtil.close(samReader); CloserUtil.close(samWriter); } return 0; }