
Input files, with alignments check into to avoid dependency on spidey being
installed to run the tests.

Sequences:
  - close.mrna.fa - two mRNAs that very closely align to the DNA.
  - close.dna.fa
  - close.mrnaRC.fa - reverse-complement of close.mrna.fa
  - close.dnaRC.fa - reverse-complement of close.dna.fa
  - overlap.*.fa - case where spidey produced exons
    that overlapped.  Second, partial version of mRNA to make sure
    that subsequent alignments are processed.
  - zeroBlk.*.fa -
 
Alignments:
  - alignments are named after the test that uses them, some of them
    are generated by various different combinations of RC files.
    See makefile for command to create alignments

  - input/close.aln
    spidey -m input/close.mrna.fa -i input/close.dna.fa -o input/close.aln

  - input/closeMrnaRC.aln
    spidey -m input/close.mrnaRC.fa -i input/close.dna.fa -o input/closeMrnaRC.aln

  - input/closeDnaRC.aln
    spidey -m input/close.mrna.fa -i input/close.dnaRC.fa -o input/closeDnaRC.aln

  - input/closeMrnaDnaRC.aln
    spidey -m input/close.mrnaRC.fa -i input/close.dnaRC.fa -o input/closeMrnaDnaRC.aln

  - input/overlap.aln
    spidey -m input/overlap.mrna.fa -i input/overlap.dna.fa -o input/overlap.aln

  - input/zeroBlk.aln
    spidey -m input/zeroBlk.mrna.fa -i input/zeroBlk.dna.fa -o input/zeroBlk.aln
