Re: [Seqan-dev] SAM issue?

["Holtgrewe, Manuel" <manuel.holtgrewe@fu-berlin.de>]

Your problem is that you use an alignment id as the read id. See my proposal for a fixed version attached that yields consistent results for me (regarding the positions, there still is the bug using alignment ids for read ids so the printed read names are wrong).

$ ./demos/SAMtest -s bug2.sam 
Loading SAM file bug2.sam
Reads cached...
n:2825 id: 1022
illumina_80bp_3kb.000000199
19625,19705

$ ./demos/SAMtest -s bug3.sam 
Loading SAM file bug3.sam
Reads cached...
n:3253 id: 1022
illumina_80bp_3kb.000000170
19625,19705

$ ./demos/SAMtest -s bug4.sam
Loading SAM file bug4.sam
Reads cached...
n:3648 id: 1022
illumina_80bp_3kb.000000148
19625,19705


Am 21.03.2011 um 12:52 schrieb Mat:

> Hi!
> 
> So if i adapt the code i still get the weired results:
> 
> test.sam:
> 
> illumina_80bp_3kb.000000571
> 2128,2048
> 
> 
> bug2.sam (70000 lines of test.sam):
> 
> illumina_80bp_3kb.000000571
> 237,157
> 
> (code attached...)
> 
> cheers
> <SAMtest.cpp><ATT00001..txt>

Attachment: SAMtest.cpp
Description: SAMtest.cpp