Avoid processing out-of-target reads
Avoid processing out-of-target reads

Now that we only store sequence corresponding to our current targets, we
must make sure not to process portions of reads that stretch outside of
the target, as this causes substr errors.

godotgildor/freebayes,ekg/freebayes,nh13/freebayes,ekg/freebayes,nh13/freebayes,godotgildor/freebayes,godotgildor/freebayes,gkno/freebayes,ekg/freebayes,gkno/freebayes,gkno/freebayes,ekg/freebayes,gkno/freebayes,ekg/freebayes,godotgildor/freebayes,nh13/freebayes,nh13/freebayes,nh13/freebayes,gkno/freebayes,godotgildor/freebayes