Need to check cigar

[lufuhao]

Is it possible to add one function to check cigar length == sequence length before samtools calmd, or sometimes it report error

It seems come from this situation: _N_N*
so it will divide into 3 parts. the read sequence of the second part will include the sequence of third part. Need to trim off.

[mjafin]

Hi @lufuhao,
Thanks for opening the issue. Could you send me a read that presents this problem and I can try modifying the code? I presume this is a bug in splitNreads.py that you've identified?

If you are able to help in fixing the bug, I'm more than happy to accept pull requests.

Using splitNreads.py is far from optimal - ideally the variant caller should be able to handle spliced alignments (I think FreeBayes is heading in that direction).

[lufuhao]

yes, i will send that to you tomorrow.

Cheers

Sent from my iPhone

On 30 Mar 2015, at 18:17, Miika Ahdesmaki notifications@github.com wrote:

Hi @lufuhao,
Thanks for opening the issue. Could you send me a read that presents this problem and I can try modifying the code? I presume this is a bug in splitNreads.py that you've identified?

If you are able to help in fixing the bug, I'm more than happy to accept pull requests.

Using splitNreads.py is far from optimal - ideally the variant caller should be able to handle spliced alignments (I think FreeBayes is heading in that direction).

—
Reply to this email directly or view it on GitHub.

[lufuhao]

Be sure to check the the sequence of the middle part if the alignments have
2N in CIGAR.
Besides, how do you recalculate the tlen ( insert size) for the new
splitted alignments?

Thanks.

Fu-Hao

---

Dr. Fu-Hao Lu (Post-Doc)

Room 230, JIC Biffen Building,
Cell and Developmental Biology,
John Innes Center,
Norwich NR4 7UH, UK

2015-03-30 18:55 GMT+01:00 Fu-Hao Lu lufuhao@gmail.com:

yes, i will send that to you tomorrow.

Cheers

Sent from my iPhone

On 30 Mar 2015, at 18:17, Miika Ahdesmaki notifications@github.com
wrote:

Hi @lufuhao https://github.com/lufuhao,
Thanks for opening the issue. Could you send me a read that presents this
problem and I can try modifying the code? I presume this is a bug in
splitNreads.py that you've identified?

If you are able to help in fixing the bug, I'm more than happy to accept
pull requests.

Using splitNreads.py is far from optimal - ideally the variant caller
should be able to handle spliced alignments (I think FreeBayes is heading
in that direction).

—
Reply to this email directly or view it on GitHub
#1 (comment).