Re: [Bio-bwa-help] bwasw: I immediately after S in CIGAR

[Heng Li <lh...@sa...>]

This is a rare bug and I have also seen this a couple of times. Nonetheless, I think the alignment is still correct in this case, so have not spent time on fixing it.

Heng


On May 18, 2011, at 6:51 PM, Shaun Jackman wrote:

> Hi,
> 
> In the following alignment generated by BWA 0.5.9-r16, the CIGAR string
> is 501S38I634M1D49M29S. Note that there's an insertion immediately after
> the soft-clip without any intervening match. This doesn't seem right to
> me. I can provide the reference sequence if it helps.
> 
> Cheers,
> Shaun
> 
> BPLBP1_8855A	145	4028	1	130	501S38I634M1D49M29S	*	0	0	GTGGGAGGCTTTCAATTTGGGGCCGGGGGGAAATTTGGGTTATGTATTCCGGGGTTCCCCCTGGAAAGGGCCCTTCTTCAACGGATAAAAGCTTCCTGGGGGAAACCGGGTTTTCTCCCCCAAGGGTTCCATTTGGGGGGGAAGTTTGGGCCCTTGATTTGGGTTCTTGCCTTCCTGGGGTTAAAATAAGTTCCCAAAGGTTGGGCTTTTTCGCCCATTAAAGGGTTACCCGAGCTGGGTTTAGAACGTCGTGAGACATTTCGGTCCCTATCTGTCGTGGGCGCAAGAAATTTGGAAGAAGCTGTCCTTAGTACGAGAGGACCGGGATTGACGTACCGCTGGTGTACCAGTTGTTCCGCCAGGAGCACAGCTGGGTAGCTATGTACGGAAGGGATAAGCGCTGAAAGCATCTAAGCGTGAAGCCCGCCTCAAGATGAGATTTCNCAAGTAGTAAGACCCCTTGAAGACGACGAGGTAGATAGGTTGGGGGTGGAAGCGCAGCAATGCGTGGAGCTGACCAATACTAATCGGTCGAGGGCTTATCCTAAAGAAACAACTGTTCTAAGTACACTTTGCTTCGCTGCTAGTTTTCAGGGTGCAAGAGGCTGGTTCAAGCTGCATGCCTTTTCTAAGGCAGGATATTTTCTCGCAGCCTGATCGAAGCAGTAACGCTTCGAAAAATCCGGTTTGGTGACGATAGCGGAAGGGAACCACGCGTACCCATCCCGAACACGGCCGTTAAGCCTTCCAGCGCCGATGGTACTTGGACCGAAGGGTCCTGGGAGAGTAGGACGTTGCCAAGCAATAAGAAAACCTTTTTGGAACTAATCCAAAAAGGTTTTTTTGTTTTAATGATTTTTCACCATTAAGACTCGAGACGCGTATACTTTCTTTATATTTTCTGAGTGAAGGGGAGAGTGAGGCTAGGGATTTAGTTGGACACTTTGGATGCAAAAGTAAGATAACCAAAAGGTGGTATCAACTTCCCTAGCGTAAGTTATAACAGGAGACTATTGACGGTAGCAAGATAGTGTCCACCGGGTTATGAGCACCCATGAAACTTCAGAGAGCTGTTTGCAGCGCATCAGAAAGAAAAACCGCGGTAACAGAATCCAGAGGTGGAAAAAGAACAGATTTACGGGCACTAGTACAGGCAGCCAAACAAAAAAAGCTTTAAAAGCAATCCTCCTATGGCAAATACGTGCAAGTGCAGTTTCATCATGTAGTGATGACTACTACTGTGCCNNNNNN	*	AS:i:801	XS:i:421	XF:i:0	XE:i:11	XN:i:0
> 
> 
> 
> ------------------------------------------------------------------------------
> What Every C/C++ and Fortran developer Should Know!
> Read this article and learn how Intel has extended the reach of its 
> next-generation tools to help Windows* and Linux* C/C++ and Fortran 
> developers boost performance applications - including clusters. 
> http://p.sf.net/sfu/intel-dev2devmay
> _______________________________________________
> Bio-bwa-help mailing list
> Bio...@li...
> https://lists.sourceforge.net/lists/listinfo/bio-bwa-help



-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE.