Now processes INDELs
Adds map_mismatch entry to GFF3 Note field if the sequence found does not match the orig sequence in the personal genome
Add --end parameter, to allow for only a single continuous block of input to be processed
Bugfix: The features are not processed in the order as they appear in --gff2, sorted a hash now as appropriate for numbers, formerly it sorted by default - string comparison.
Bugfix: There can be now a negative strand, formerly all are positive strands.
Results from other chromosomes are now expelled from further processing ( saves time ) ( There could be a bug for this - chromosome name on genome being mapped to should be lesser in length )