suggestion for change to interactive clipping in pregap

Andy Law Andy.Law at bbsrc.ac.uk
Thu Dec 12 05:23:38 EST 1996

Having kicked the software around for about a week now, I've come to the
conclusion that the following would be useful to my group. I'll pitch it
into this forum to gauge other folks feelings on it.

When clipping poor sequence and vector, the software gets it right about
90% of the time with our sequences. Given that I already know roughly where
the vector will end, I don't really want to interactively edit each and
every sequence, only the ones that haven't been spotted. Likewise, 
occasionally a sequence will be entirely discarded on quality grounds and I
want to reset the left and right clip points before it gets passed to
sequence vector clipping.

So, my suggestion is....

If interactive clipping is required...

Add a QL_expected_max and QR_expected_min value to the .pregaprc file and
have the interactive editor pop up with any sequence that has a QL or QR
value greater or less than (respectively) these values BEFORE the vepe
option 1 (sequence vector clipping) stage if they are defined.

Likewise add a SL_expected_min value and pop up the editor if a sequence is
recorded as having an SL value less than this.

I know I can recheck the sequences that have failed after the event, but I
figure I can do it much more efficiently if it is done on-the-fly. Also, I
don't want/need to go through all the sequences that are correctly clipped.

It would also be nice to be able to specify sequence ends in trev, but
that's just me being greedy :o}

Andy Law
( Andy.Law at bbsrc.ac.uk )
( Big Nose in Edinburgh )

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