extensive changes -- removed the use of calls to process_locations for masking sequence, instead use calls to feature blocks added the ability to specify a start position within the sequence.  This fixes a big bug where a subsequence is used and the annotations were not adjusting accordingly
extensive changes -- removed the use of calls to process_locations for masking sequence, instead use calls to feature blocks
added the ability to specify a start position within the sequence.  This fixes a big bug where a subsequence is used and the annotations were not adjusting accordingly

LyonsLab/coge,LyonsLab/coge,LyonsLab/coge,asherkhb/coge,asherkhb/coge,asherkhb/coge,asherkhb/coge,LyonsLab/coge,asherkhb/coge,LyonsLab/coge,asherkhb/coge,LyonsLab/coge,asherkhb/coge,asherkhb/coge,LyonsLab/coge,asherkhb/coge,LyonsLab/coge,LyonsLab/coge