Hi Tony,

Ok, no problem. Thanks a lot!


Cheers,
Condomitti.

Em terça-feira, 3 de junho de 2014 14h52min33s UTC-3, tray...@bcgsc.ca escreveu:

Hi Condomitti,

I sent out that patch a little hastily. There seems to be some issues that I didn't deal with downstream of abyss-fixmate. I'll send you another patch shortly.

Tony

 

On 2014-06-02, at 4:17 PM, George Willian Condomitti wrote:

Tony, thanks a lot mate! I really appreciate your help!


I'm gonna ask the administrator to apply the patch and recompile or give me privileges to do so.
I'll get back to you soon with the new results.

Thanks again mate!

Cheers,
Condomitti.




On Monday, June 2, 2014 8:05:53 PM UTC-3, tray...@bcgsc.ca wrote:

Hi Condomitti,

It was bugging me that there wasn't a way to make abyss-pe behave like you wanted. So I've made a change to abyss-fixmate that will let you do what you were expecting abyss-pe to do.

If you felt adventurous, I've attached the patch that you could apply to the abyss source and then recompile. It adds an option to abyss-fixmate (--all) to print all of the alignments to the SAM files. To apply the patch run the following in the source root directory:

patch -p1 <all_opt.patch

Then to assemble, getting all of the alignments, you'd specify all the same options, but add `FIXMATE_OPTIONS=--all`. 

Cheers,

Tony

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