#393 revcomp problem w/sim4 features on reverse strand

[Brian O.]

code is not properly revcomping genomic/query alignemnts on
sim4 features on reverse strand. [Or is this a sim4 bug? Could BOP
compensate for it?]
3/12/2004: There still seems to be a problem with this.
If you bring up scaffold AE003602 in gadfly3, then use the third menu
after selecting a dark green DGC clone from the reverse strand, and say
"Align same type features in the region", some of the alignments seem to
get off by a base pair or more somewhere along the line. See AT12695,
LD13730, etc.