Package htsjdk.samtools.util

Examples of htsjdk.samtools.util.ProgressLogger

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                targetIntervals,
                getProbeIntervals(),
                getProbeSetName()
        );

        final ProgressLogger progress = new ProgressLogger(log);
        for (final SAMRecord record : reader) {
            collector.acceptRecord(record, null);
            progress.record(record);
        }

        // Write the output file
        final MetricsFile<METRIC, Integer> metrics = getMetricsFile();
        collector.finish();
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    this.CREATE_INDEX = true;
  }

    @Override
    protected int doWork() {
        final ProgressLogger progress = new ProgressLogger(LOG, 10000);
       
        IOUtil.assertFileIsReadable(INPUT);
        IOUtil.assertFileIsWritable(OUTPUT);

      final VCFFileReader reader = new VCFFileReader(INPUT, REQUIRE_INDEX);
      final VCFHeader header = new VCFHeader(reader.getFileHeader());
      final SAMSequenceDictionary sequenceDictionary = header.getSequenceDictionary();
      if (CREATE_INDEX && sequenceDictionary == null) {
        throw new PicardException("A sequence dictionary must be available in the input file when creating indexed output.");
      }

        final VariantContextWriterBuilder builder = new VariantContextWriterBuilder()
                .setOutputFile(OUTPUT)
                .setReferenceDictionary(sequenceDictionary);
        if (CREATE_INDEX)
            builder.setOption(Options.INDEX_ON_THE_FLY);
        else
            builder.unsetOption(Options.INDEX_ON_THE_FLY);
        final VariantContextWriter writer = builder.build();
        writer.writeHeader(header);
      final CloseableIterator<VariantContext> iterator = reader.iterator();

      while (iterator.hasNext()) {
        final VariantContext context = iterator.next();
            writer.add(context);
            progress.record(context.getChr(), context.getStart());
        }

      CloserUtil.close(iterator);
      CloserUtil.close(reader);
        writer.close();
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        final VariantContextWriter vcfWriter = builder.setOutputFile(OUTPUT).build();
        fileHeader.setSequenceDictionary(samSequenceDictionary);
        vcfWriter.writeHeader(fileHeader);

        final ProgressLogger progress = new ProgressLogger(log, 10000);
        final CloseableIterator<VariantContext> iterator = fileReader.iterator();
        while (iterator.hasNext()) {
            final VariantContext context = iterator.next();
            vcfWriter.add(context);
            progress.record(context.getChr(), context.getStart());
        }

        CloserUtil.close(iterator);
        CloserUtil.close(fileReader);
        vcfWriter.close();
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        IOUtil.assertFileIsWritable(OUTPUT);
        final SAMFileReader reader = new SAMFileReader(IOUtil.openFileForReading(INPUT));
        reader.getFileHeader().setSortOrder(SORT_ORDER);
        final SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(reader.getFileHeader(), false, OUTPUT);
      writer.setProgressLogger(
          new ProgressLogger(log, (int) 1e7, "Wrote", "records from a sorting collection"));

        final ProgressLogger progress = new ProgressLogger(log, (int) 1e7, "Read");
        for (final SAMRecord rec: reader) {
            writer.addAlignment(rec);
            progress.record(rec);
        }

        log.info("Finished reading inputs, merging and writing to output now.");

        reader.close();
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            samFileWriterFactory.setUseAsyncIo(true);
        }
        final SAMFileWriter out = samFileWriterFactory.makeSAMOrBAMWriter(header, presorted, OUTPUT);

        // Lastly loop through and write out the records
        final ProgressLogger progress = new ProgressLogger(log, PROGRESS_INTERVAL);
        while (iterator.hasNext()) {
            final SAMRecord record = iterator.next();
            out.addAlignment(record);
            progress.record(record);
        }

        log.info("Finished reading inputs.");
        out.close();
        return 0;
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Related Classes of htsjdk.samtools.util.ProgressLogger

  • picard.analysis.CollectGcBiasMetrics
  • picard.analysis.CollectQualityYieldMetrics
  • picard.analysis.CollectRrbsMetrics
  • picard.analysis.CollectWgsMetrics
  • picard.analysis.directed.CollectTargetedMetrics
  • picard.analysis.SinglePassSamProgram
  • picard.illumina.MarkIlluminaAdapters
  • picard.sam.AbstractAlignmentMerger
  • picard.sam.AddOrReplaceReadGroups
  • picard.sam.CleanSam
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