bwa_seq: sampe not supported

[GoogleCodeExporter]

I looked trough the sources in truck and figured out that bwa_seq always do 
'aln' followed by 'samse'. Do you have any plans to implement also paired end 
alignment method ('sampe'). We have Illumina paired end data and I would like 
to able to align it with 'sampe'.

Teemu

Original issue reported on code.google.com by teemu.ku...@gmail.com on 6 Jul 2012 at 6:32

[GoogleCodeExporter]

Hello Teemu,

I implement features from the different tools on the basis of "I need this". So 
far I have not had any need for BWA sampe - and thus it is not supported by 
bwa_seq. I suggest you use vanilla BWA - unless you are really keen on this - 
and I will see If I can do something about it.

Martin

Original comment by martinah...@gmail.com on 9 Jul 2012 at 7:55

• Added labels: Type-Enhancement
• Removed labels: Type-Defect

[GoogleCodeExporter]

Hi,

I really appreciate your effort and my intention was not push you in
anyway. I just wanted to ask if this feature is coming or planned. I will
use bwa directly for sampe analysis.

Thank you for your effort,

Teemu

Original comment by teemu.ku...@gmail.com on 9 Jul 2012 at 9:42