search

duncanca / mosaik-aligner

Automatically exported from code.google.com/p/mosaik-aligner
0 stars 0 forks source link

MosaikText does not generate MD tag in SAM output #74

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1. MosaikText -sam
2. Use "samtools view"

What is the expected output? What do you see instead?
The file is missing a SAM tag. The MD tag describes the location of any 
mismatches or indels to the reference sequence. In particular it's used by 
tools for SNP calling.

See page 7 http://samtools.sourceforge.net/SAM1.pdf

What version of the product are you using? On what operating system?
1.1.0017

Please provide any additional information below.

Original issue reported on code.google.com by maur...@gmail.com on 4 Nov 2010 at 6:53

GoogleCodeExporter commented 9 years ago 
Hi there,

I just put the latest MOSAIK, 1.1.0020, which supports MD tags for SAM.

Original comment by WanPing....@gmail.com on 4 Nov 2010 at 8:30

GoogleCodeExporter commented 9 years ago 
Wow, that's fast service :) thanks much!

Note that this patch does not fix the issue for .bam output. A workaround is to 
generate sam output and convert to bam afterwards.

Original comment by maur...@gmail.com on 5 Nov 2010 at 10:26

GoogleCodeExporter commented 9 years ago 
I forget to patch MD tags for BAM. Will do that soon.  :D

Original comment by WanPing....@gmail.com on 8 Nov 2010 at 3:21

GoogleCodeExporter commented 9 years ago 
Fantastic!

In the meantime, I think this patch caused a regression: Running MosaikText 
-sam (v1.1.0020) on an alignment of 34M reads now uses up effectively all of 
the 16GB of ram on a cluster node and crashes. Smaller datasets finish, but 
with higher memory usage. MosaikText -sam v1.1.0018 uses negligible ram. Doing 
BAM output in v1.1.0020 also uses negligible memory.

Original comment by maur...@gmail.com on 10 Nov 2010 at 9:13

GoogleCodeExporter commented 9 years ago 
It's my bad. I created a huge memory leakage in 1.1.0020/MosaikText.
I fix it in 1.1.0021.

Please try it and let me know if still problems.

Original comment by WanPing....@gmail.com on 10 Nov 2010 at 11:37

GoogleCodeExporter commented 9 years ago 
Yup, that fixed it. Thanks!

Original comment by maur...@gmail.com on 12 Nov 2010 at 9:01

GoogleCodeExporter commented 9 years ago

Original comment by WanPing....@gmail.com on 12 Nov 2010 at 9:10