Package htsjdk.samtools.util

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

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        // progress logger!
        final ProgressLogger progress = new ProgressLogger(log, (int) 1e6, "Read");

        // Go through the records
        for (final SAMRecord record : new IterableAdapter<SAMRecord>(iterator)) {
            if (progress.record(record)) {
                iterator.logMemoryStats(log);
            }

            // Update the program record if necessary
            updateProgramRecord(record, chainedPgIds);
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    final RrbsMetricsCollector metricsCollector = new RrbsMetricsCollector(METRIC_ACCUMULATION_LEVEL, samReader.getFileHeader().getReadGroups(),
        C_QUALITY_THRESHOLD, NEXT_BASE_QUALITY_THRESHOLD, MINIMUM_READ_LENGTH, MAX_MISMATCH_RATE);

    for (final SAMRecord samRecord : samReader) {
      progressLogger.record(samRecord);
      if (!samRecord.getReadUnmappedFlag() && !isSequenceFiltered(samRecord.getReferenceName())) {
        final ReferenceSequence referenceSequence = refWalker.get(samRecord.getReferenceIndex());
        metricsCollector.acceptRecord(samRecord, referenceSequence);
      }
    }
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        final ProgressLogger progress = new ProgressLogger(log);
        for (final SAMRecord read : in) {
            read.setAttribute(SAMTag.RG.name(), RGID);
            outWriter.addAlignment(read);
            progress.record(read);
        }

        // cleanup
        in.close();
        outWriter.close();
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        log.info("Traversing query name sorted records and fixing up mate pair information.");
        final ProgressLogger progress = new ProgressLogger(log);
        while (iterator.hasNext()) {
            final SAMRecord record = iterator.next();
            out.addAlignment(record);
            progress.record(record);
        }
        iterator.close();

        if (header.getSortOrder() == SortOrder.queryname) {
            log.info("Closing output file.");
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        }

        final ProgressLogger progress = new ProgressLogger(Log.getInstance(SamFormatConverter.class));
        for (final SAMRecord rec : reader) {
            writer.addAlignment(rec);
            progress.record(rec);
        }
        reader.close();
        writer.close();
        return 0;
    }
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                }
            } else {
                writeRecord(currentRecord, null, fq.getUnpaired(), READ1_TRIM, READ1_MAX_BASES_TO_WRITE);
            }

            progress.record(currentRecord);
        }

        reader.close();

        // Close all the fastq writers being careful to close each one only once!
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        final ProgressLogger progress = new ProgressLogger(log, (int) 1e6, "Written");
       
        while (filteringIterator.hasNext()) {
            final SAMRecord rec = filteringIterator.next();
            outputWriter.addAlignment(rec);
            progress.record(rec);
        }

        filteringIterator.close();
        outputWriter.close();
        inputReader.close();
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            }

            while (variantIterator.hasNext()) {
                lastContext = variantIterator.next();
                out.add(lastContext);
                progress.record(lastContext.getChr(), lastContext.getStart());
            }

            lastFile = f;

            CloserUtil.close(variantIterator);
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        final CloseableIterator<VariantContext> iterator = reader.iterator();
      while (iterator.hasNext()) {
        final VariantContext full = iterator.next();
            final VariantContext site = subsetToSamplesWithOriginalAnnotations(full, SAMPLE);
            writer.add(site);
            progress.record(site.getChr(), site.getStart());
        }

      CloserUtil.close(iterator);
      CloserUtil.close(reader);
      writer.close();
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      else {
                if (STRICT) throw new IllegalStateException("Found a record with type " + context.getType().name());
                else incorrectVariantCount++;
            }

            progress.record(context.getChr(), context.getStart());
    }

        if (incorrectVariantCount > 0) {
            log.debug("Found " + incorrectVariantCount + " records that didn't match SNP or INDEL");
        }
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