[mira_talk] Re: Parsing SSAHA output with Mira 2.9.35x1

Hi Bastien:

The reason why I discovered the bug is because I'm generating many megahubs
that don't go away when I apply the ssaha clips. Is another way to check to
see if the ssaha clips are actually getting into mira?

I'm thinking about your PS and grabbed the following out of the
traceinfo.xml for the seqence/file FF3M6TC02IZ9WF

 <trace>
        <trace_name>FF3M6TC02IZ9WF</trace_name>
        <clip_vector_right>224</clip_vector_right>
        <clip_vector_left>5</clip_vector_left>
 </trace>

In this this case the ssaha 12 base clip on the 5' end should get into mira.
If the ssaha clip was 3, I would still like to see it logged, maybe with an
asterisk  at the end of the line to denote mira didn't use it.

Thanks,
Greg

Gregory P. Harhay, PhD
Computational Biologist
Animal Health Research Unit
USDA-ARS-Roman L. Hruska  U.S. Meat Animal Research Center
Clay Center, NE 68933
v - 402.762.4250




> From: Bastien Chevreux <bach@xxxxxxxxxxxx>
> Organization: Speaking for myself, really!
> Reply-To: <mira_talk@xxxxxxxxxxxxx>
> Date: Fri, 5 Dec 2008 21:10:10 +0100
> To: <mira_talk@xxxxxxxxxxxxx>
> Subject: [mira_talk] Re: Parsing SSAHA output with Mira 2.9.35x1
> 
> On Friday 05 December 2008 18:23, Gregory Harhay wrote:
>> [...]
>> But if I look in the sal_LB_d_log/sal_LB_int_clippings.0.txt file I get
>> 
>> ======
>> load:  SSAHA clip left FF3M6TC02IZ9WF to: 0
>> load:  SSAHA clip left FF3M6TC02H6KM0 to: 0
>> load:  SSAHA clip left FF3M6TC02IWHHB to: 0
>> =======
>> I conclude from the above that the clipping info in
>> sal_BM_ssahavectorscreen_in.txt  isn't getting into mira.
>> 
>> Am I missing something? Do you have any suggestions?
> 
> Hi Greg,
> 
> I just checked: you found a bug in the logging mechanisms of the SSAHA clips.
> Your clips are getting into MIRA but a wrong variable is written into the
> logs, the assembly is unaffected and uses the SSAHA clip.
> 
> The fix for the log file will be rolled out with the next version of MIRA.
> 
> Regards,
>   Bastien
> 
> PS: as a side note: there is currently no logging of clips when they do not
> extend the clips in a meaningful way. E.g.: if the left clip of a read is
> already 20 and the SSAHA clip read via file is 12, then no log message is
> written (and the clip stays at 20). Any opinion on whether a message should
> be given in those cases?
> 
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