Package htsjdk.samtools

Examples of htsjdk.samtools.MergingSamRecordIterator

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                iterator = new IntervalOverlapFilteringIterator(iterator,shard.getGenomeLocs());

            iteratorMap.put(readers.getReader(id), iterator);
        }

        MergingSamRecordIterator mergingIterator = readers.createMergingIterator(iteratorMap);

        // The readMetrics object being passed in should be that of this dataSource and NOT the shard: the dataSource's
        // metrics is intended to keep track of the reads seen (and hence passed to the CountingFilteringIterator when
        // we apply the decorators), whereas the shard's metrics is used to keep track the "records" seen.
        return applyDecoratingIterators(readMetrics,
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         * Creates a new merging iterator from the given map, with the given header.
         * @param iteratorMap A map of readers to iterators.
         * @return An iterator which will merge those individual iterators.
         */
        public MergingSamRecordIterator createMergingIterator(final Map<SAMFileReader,CloseableIterator<SAMRecord>> iteratorMap) {
            return new MergingSamRecordIterator(headerMerger,iteratorMap,true);
        }
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            perSampleSAMReaders.add(reader);
            headers.add(reader.getFileHeader());
        }

        SamFileHeaderMerger headerMerger = new SamFileHeaderMerger(SAMFileHeader.SortOrder.coordinate, headers, true);
        mergingIterator = new MergingSamRecordIterator(headerMerger, perSampleSAMReaders, true);
    }
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                readers.add(r);
            }

            final SamFileHeaderMerger headerMerger = new SamFileHeaderMerger(SortOrder.queryname, headers, false);

            mergingIterator = new MergingSamRecordIterator(headerMerger, readers, true);
            header = headerMerger.getMergedHeader();

        }
        // When the ends are aligned separately and don't have firstOfPair information correctly
        // set we use this branch.
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                read2.add(r);
            }

            final SamFileHeaderMerger headerMerger = new SamFileHeaderMerger(SAMFileHeader.SortOrder.coordinate, headers, false);
            read1Iterator = new PeekableIterator<SAMRecord>(
                    new SuffixTrimingSamRecordIterator(new MergingSamRecordIterator(headerMerger, read1, true), "/1"));
            read2Iterator = new PeekableIterator<SAMRecord>(
                    new SuffixTrimingSamRecordIterator(new MergingSamRecordIterator(headerMerger, read2, true), "/2"));

            header = headerMerger.getMergedHeader();
        }
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        if (headers.size() == 1) {
            return new SamHeaderAndIterator(headers.get(0), readers.get(0).iterator());
        } else {
            final SamFileHeaderMerger headerMerger = new SamFileHeaderMerger(SAMFileHeader.SortOrder.coordinate, headers, false);
            final MergingSamRecordIterator iterator = new MergingSamRecordIterator(headerMerger, readers, ASSUME_SORTED);
            return new SamHeaderAndIterator(headerMerger.getMergedHeader(), iterator);
        }
    }
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                for (final SAMFileReader reader : readers) {
                    headers.add(reader.getFileHeader());
                }
                final SortOrder sortOrder = (allQueryNameSorted? SortOrder.queryname: SortOrder.unsorted);
                final SamFileHeaderMerger merger = new SamFileHeaderMerger(sortOrder, headers, false);
                tmp = new MergingSamRecordIterator(merger, readers, false);
                header = merger.getMergedHeader();
            }
            else {
                tmp = readers.get(0).iterator();
                header = readers.get(0).getFileHeader();
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            headerMergerSortOrder = SAMFileHeader.SortOrder.unsorted;
            mergingSamRecordIteratorAssumeSorted = false;
            presorted = false;
        }
        final SamFileHeaderMerger headerMerger = new SamFileHeaderMerger(headerMergerSortOrder, headers, MERGE_SEQUENCE_DICTIONARIES);
        final MergingSamRecordIterator iterator = new MergingSamRecordIterator(headerMerger, readers, mergingSamRecordIteratorAssumeSorted);
        final SAMFileHeader header = headerMerger.getMergedHeader();
        for (final String comment : COMMENT) {
            header.addComment(comment);
        }
        header.setSortOrder(SORT_ORDER);
        final SAMFileWriterFactory samFileWriterFactory = new SAMFileWriterFactory();
        if (USE_THREADING) {
            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.");
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Related Classes of htsjdk.samtools.MergingSamRecordIterator

  • org.broadinstitute.gatk.engine.datasources.reads.SAMDataSource
  • org.broadinstitute.gatk.engine.datasources.reads.SAMDataSource$SAMReaders
  • org.broadinstitute.gatk.utils.sam.ArtificialMultiSampleReadStream
  • picard.sam.FixMateInformation
  • picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
  • picard.sam.MergeSamFiles
  • picard.sam.SamAlignmentMerger
  • picard.sam.SamAlignmentMerger$SeparateEndAlignmentIterator
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