There are a couple of things here. Firstly,fixmateshould not be removing the paired flag (0x1). That flag is an indication about the sequencing technology rather than the alignments themselves. We will have to look at fixing that. Secondly, a flags value of 72, that is MUNMAP (0x8) an...
5 //以:作为分隔 列出第3列和第5列的数据 //刚才的cut是做切割,
* Is the given read one for which we can fix its mate? * * @param read the read * @return true if we could fix its mate, false otherwise */ protectedbooleanisMateFixableRead(finalSAMRecordread){ returnread.getReadPairedFlag()&&!read.isSecondaryOrSupplementary(); } 代码示例来源:origin:...
return record.getReadPairedFlag() && !record.getReadUnmappedFlag() && !record.getMateUnmappedFlag(); } 代码示例来源:origin: broadinstitute/picard private void fixRecord(SAMRecord record, ReferenceSequenceFileWalker refSeqWalker){ if (!record.getReadUnmappedFlag()) { if (SET_ONLY_UQ) { Abstract...