06.01.2009  Fixed CDS warning bug in sim4.init.c when A=0 (FWD, EST_GEN),
            A=1-3 (BWD, GEN_EST).
06.01.2009  Inlined mask_shift (~11% faster) in sim4b1.c. 
07.01.2009  Replaced ad-hoc GFF output format (option A=6) with GFF3
            (patch by Geo Pertea).
07.16.2009  Fixed memory leaks of chashtab and MSS.{masks,shifts}.
01.05.2010  Replaced match_ori (relative orientation of sequences) with
            ori (strand) in gff3 output (A=6). The strand is given by the majority
            of fwd/rev signals, and is unasigned if fwd=rev or single exon 
            (see check_consistency_ori()).
06.24.2010  Fixed read from uninitialized in rsnake().
11.08.2010  Sent align.c error messages on distance limit exceeded to stderr.
11.22.2010  Freed allocated space in greedy() when exiting via "narrow gap".
