Package htsjdk.samtools.util

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

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        int readerCount = 1;
        for (final VCFFileReader reader : readers) {
            log.info("Reading entries from input file " + readerCount);
            for (final VariantContext variantContext : reader) {
                sorter.add(variantContext);
                readProgress.record(variantContext.getChr(), variantContext.getStart());
            }
            reader.close();
            readerCount++;
        }
        return sorter;
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                setOptions(options).
                setOutputFile(OUTPUT).build();
        out.writeHeader(outputHeader);
        for (final VariantContext variantContext : sortedOutput) {
            out.add(variantContext);
            writeProgress.record(variantContext.getChr(), variantContext.getStart());
        }
        out.close();
    }
}
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    final MergingIterator<VariantContext> mergingIterator = new MergingIterator<VariantContext>(variantContextComparator, iteratorCollection);
    while (mergingIterator.hasNext()) {
      final VariantContext context = mergingIterator.next();
      writer.add(context);
      progress.record(context.getChr(), context.getStart());
    }

    CloserUtil.close(mergingIterator);
    writer.close();
    return 0;
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        );

        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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      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 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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          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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        // 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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