[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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