Package htsjdk.samtools

Examples of htsjdk.samtools.SAMFileHeader.addComment()

51
52
53
54
55
56
57
58
59
60
61
        final SAMFileHeader samFileHeader = new SAMFileReader(INPUT).getFileHeader();
        for (final String comment : COMMENT) {
            if (comment.contains("\n")) {
                throw new PicardException("Comments can not contain a new line");
            }
            samFileHeader.addComment(comment);
        }

        BamFileIoUtils.reheaderBamFile(samFileHeader, INPUT, OUTPUT, CREATE_MD5_FILE, CREATE_INDEX);

        return 0;
View Full Code Here
260
261
262
263
264
265
266
267
268
269
270
        final SAMFileHeader header = new SAMFileHeader();
        header.addReadGroup(rgroup);

        for (final String comment : COMMENT) {
            header.addComment(comment);
        }

        header.setSortOrder(this.SORT_ORDER);
        return header ;
    }
View Full Code Here
223
224
225
226
227
228
229
230
231
232
233
        }

        // Add any comments
        if (COMMENT != null) {
            for (final String comment : COMMENT) {
                header.addComment(comment);
            }
        }

        final IntervalList output = new IntervalList(header);
        for (final Interval i : finalIntervals) {
View Full Code Here
140
141
142
143
144
145
146
147
148
149
150
        }
        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);
View Full Code Here
TOP
Copyright © 2018 www.massapi.com. All rights reserved.
All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.