Doesn't quite align to end and circ fails

[tseemann]

tig00000001     dna     4736005

 Score = 55308 bits (29950),  Expect = 0.0
 Identities = 29995/30013 (99%), Gaps = 17/30013 (0%)
 Strand=Plus/Plus

Query  1        CGCTGTCGGCAAGAATATAGCGGCTTGATGCCAAAG-CGCCT-GGTCATTTCGACAAAAA  58
                |||||||||||||||||||||||||||||||||||| ||||| |||||||||||||||||
Sbjct  4704147  CGCTGTCGGCAAGAATATAGCGGCTTGATGCCAAAGGCGCCTGGGTCATTTCGACAAAAA  4704206

<snip>

Query  29988    ACGGTTTTTCAGT  30000
                |||||||||||||
Sbjct  4734143  ACGGTTTTTCAGT  4734155

[tseemann]

I think this is just because the default --readlen if 30,000 is shorter than the overhang!

[tseemann]

Still can happen:

tig00000001     dna     4736706

Query  31657    CAATGAAACCGCAGCTGCATTAAATAAAAATACCAACTCATCCTTTCTTTCCGTAATCAA  31716
                ||||||||||||||| ||||||||||||||||||||||||||| |||||| |||||||||
Sbjct  4736624  CAATGAAACCGCAGC-GCATTAAATAAAAATACCAACTCATCC-TTCTTTTCGTAATCAA  4736681

Query  31717    AAATCCAGTTTT-GCTTCAGCTTT  31739
                |||||||||||| ||||||| |||
Sbjct  4736682  AAATCCAGTTTTTGCTTCAGATTT  4736705

This one was only 1 bp short of the end. Need to apply the same rule to the "1" starting position as we do to the end position.

[tseemann]

Added new --fuzz parameter.