Package htsjdk.samtools.util

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

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            // Actually to the reverting of the remaining records
            revertSamRecord(rec);

            if (sanitizing) sorter.add(rec);
            else out.addAlignment(rec);
            progress.record(rec);
        }

        ////////////////////////////////////////////////////////////////////////////
        // Now if we're sanitizing, clean up the records and write them to the output
        ////////////////////////////////////////////////////////////////////////////
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                            quals[i] -= SolexaQualityConverter.ILLUMINA_TO_PHRED_SUBTRAHEND;
                        }
                        rec.setBaseQualities(quals);
                    }
                    out.addAlignment(rec);
                    sanitizerProgress.record(rec);
                }
            }

            out.close();
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        final ProgressLogger progress = new ProgressLogger(Log.getInstance(ReplaceSamHeader.class));
        for (final SAMRecord rec : recordReader) {
            rec.setHeader(replacementHeader);
            writer.addAlignment(rec);
            progress.record(rec);
        }
        writer.close();
        recordReader.close();
    }
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                                            SequenceUtil.countInsertedBases(rec) + SequenceUtil.countDeletedBases(rec);
                        }
                    }
                }

                progress.record(rec);
            }

            log.info("Processed reference sequence: " + ref.getName());
        }
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            for (final SinglePassSamProgram program : programs) {
                program.acceptRead(rec, ref);
            }

            progress.record(rec);

            // See if we need to terminate early?
            if (stopAfter > 0 && progress.getCount() >= stopAfter) {
                break;
            }
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        for ( ; freader.hasNext()  ; readCount++) {
            final FastqRecord frec = freader.next();
            final SAMRecord srec = createSamRecord(header, getReadName(frec.getReadHeader(), false) , frec, false) ;
            srec.setReadPairedFlag(false);
            writer.addAlignment(srec);
            progress.record(srec);
        }

        writer.close();
        return readCount;
    }
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                record.setBaseQualities(record.getOriginalBaseQualities());
                record.setOriginalBaseQualities(null);
                numOriginalQualitiesRestored++;
            }
            if (!foundPairedMappedReads && record.getReadPairedFlag() && !record.getReadUnmappedFlag()) foundPairedMappedReads = true;
            revertingProgress.record(record);
            sorter.add(record);
        }
        CloserUtil.close(in);
        log.info("Reverted the original base qualities for " + numOriginalQualitiesRestored + " records");
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        final SamPairUtil.SetMateInfoIterator sorterIterator = new SamPairUtil.SetMateInfoIterator(sorter.iterator(), true);
        final ProgressLogger sorterProgress = new ProgressLogger(log, 1000000, " mate cigars added");
        while (sorterIterator.hasNext()) {
            final SAMRecord record = sorterIterator.next();
            out.addAlignment(record);
            sorterProgress.record(record);
        }
        sorterIterator.close();
        CloserUtil.close(out);
        log.info("Updated " + sorterIterator.getNumMateCigarsAdded() + " records with mate cigar");
        if (!foundPairedMappedReads) log.info("Did not find any paired mapped reads.");
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                }

                final Interval interval = new Interval(sequenceName, start, end, bedFeature.getStrand() == Strand.POSITIVE, name);
                intervalList.add(interval);

                progressLogger.record(sequenceName, start);
            }
            CloserUtil.close(bedReader);

            // Sort and write the output
            intervalList.uniqued().write(OUTPUT);
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            }

            // Then output the records, update progress and metrics
            for (final SAMRecord r : new SAMRecord[] {rec, rec2}) {
                if (r != null) {
                    progress.record(r);
                    if (out != null) out.addAlignment(r);

                    final Integer clip = rec.getIntegerAttribute(ReservedTagConstants.XT);
                    if (clip != null) histo.increment(rec.getReadLength() - clip + 1);
                }
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