Package htsjdk.samtools

Examples of htsjdk.samtools.SamFileHeaderMerger

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                headersList.add(curHeader);
                sortOrder = curHeader.getSortOrder();
            }
        }
        if(sortOrder != null){
            SamFileHeaderMerger headerMerger = new SamFileHeaderMerger(sortOrder, headersList, true);
            return headerMerger.getMergedHeader();
        }

        return null;
    }
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                }

                headers.add(header);
            }

            headerMerger = new SamFileHeaderMerger(SAMFileHeader.SortOrder.coordinate,headers,true);

            // update all read groups to GATKSAMRecordReadGroups
            final List<SAMReadGroupRecord> gatkReadGroups = new LinkedList<SAMReadGroupRecord>();
            for ( final SAMReadGroupRecord rg : headerMerger.getMergedHeader().getReadGroups() ) {
                gatkReadGroups.add(new GATKSAMReadGroupRecord(rg));
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                                                               thisStreamReads.toArray(new SAMRecord[thisStreamReads.size()]));
            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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                final SAMFileReader r = new SAMFileReader(f);
                headers.add(r.getFileHeader());
                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.
        else {
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                final SAMFileReader r = new SAMFileReader(f);
                headers.add(r.getFileHeader());
                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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                final List<SAMFileHeader> headers = new ArrayList<SAMFileHeader>(readers.size());
                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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            log.info("Sorting input files using temp directory " + TMP_DIR);
            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();
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Related Classes of htsjdk.samtools.SamFileHeaderMerger

  • org.broad.igv.sam.reader.MergedAlignmentReader
  • 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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