Package htsjdk.samtools.util

Examples of htsjdk.samtools.util.ProgressLogger.record()

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            final SAMRecord srec1 = createSamRecord(header, baseName, frec1, true) ;
            srec1.setFirstOfPairFlag(true);
            srec1.setSecondOfPairFlag(false);
            writer.addAlignment(srec1);
            progress.record(srec1);

            final SAMRecord srec2 = createSamRecord(header, baseName, frec2, true) ;
            srec2.setFirstOfPairFlag(false);
            srec2.setSecondOfPairFlag(true);
            writer.addAlignment(srec2);
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            final SAMRecord srec2 = createSamRecord(header, baseName, frec2, true) ;
            srec2.setFirstOfPairFlag(false);
            srec2.setSecondOfPairFlag(true);
            writer.addAlignment(srec2);
            progress.record(srec2);
        }

        writer.close();

        if (freader1.hasNext() || freader2.hasNext()) {
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                if (prs.read1 != null && prs.read2 != null && prs.qualityOk) {
                    sorter.add(prs);
                }

                progress.record(rec);
            }
        }

        log.info("Finished reading - moving on to scanning for duplicates.");
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                    if (quals[i] >= 20) metrics.PF_Q20_BASES++;
                    if (quals[i] >= 30) metrics.PF_Q30_BASES++;
                }
            }

            progress.record(rec);
        }
       
        metrics.READ_LENGTH = metrics.TOTAL_READS == 0 ? 0 : (int) (metrics.TOTAL_BASES / metrics.TOTAL_READS);
        metrics.Q20_EQUIVALENT_YIELD =  metrics.Q20_EQUIVALENT_YIELD / 20 ;
        metrics.PF_Q20_EQUIVALENT_YIELD = metrics.PF_Q20_EQUIVALENT_YIELD / 20 ;
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                if (rec.getReadUnmappedFlag() && 0 != rec.getMappingQuality()) {
                    rec.setMappingQuality(0);
                }

                writer.addAlignment(rec);
                progress.record(rec);
            }

            writer.close();
            it.close();
        }
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            if (keeper) {
                out.addAlignment(rec);
                ++kept;
            }

            progress.record(rec);
        }

        out.close();
        log.info("Finished! Kept " + kept + " out of " + total + " reads.");
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            if (!this.REMOVE_DUPLICATES || !rec.getDuplicateReadFlag()) {
                if (PROGRAM_RECORD_ID != null) {
                    rec.setAttribute(SAMTag.PG.name(), chainedPgIds.get(rec.getStringAttribute(SAMTag.PG.name())));
                }
                out.addAlignment(rec);
                progress.record(rec);
            }
        }

        // remember to close the inputs
        iterator.close();
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                }
            }

            // Print out some stats every 1m reads
            ++index;
            if (progress.record(rec)) {
                log.info("Tracking " + tmp.size() + " as yet unmatched pairs. " + tmp.sizeInRam() + " records in RAM.");
            }
        }

        log.info("Read " + index + " records. " + tmp.size() + " pairs never matched.");
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            final int depth = Math.min(readNames.size(), max);
            if (depth < readNames.size()) basesExcludedByCapping += readNames.size() - max;
            HistogramArray[depth]++;

            // Record progress and perhaps stop
            progress.record(info.getSequenceName(), info.getPosition());
            if (usingStopAfter && ++counter > stopAfter) break;
        }

        // Construct and write the outputs
        final Histogram<Integer> histo = new Histogram<Integer>("coverage", "count");
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                        rec.setAttribute(SAMTag.UQ.name(), SequenceUtil.sumQualitiesOfMismatches(rec, referenceBases, 0, bisulfiteSequence));
                    }
                }
            }
            writer.addAlignment(rec);
            finalProgress.record(rec);
        }
        writer.close();
        sorted.cleanup();

        log.info("Wrote " + aligned + " alignment records and " + (alignedReadsOnly ? 0 : unmapped) + " unmapped reads.");
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