First commit on 0204/2013 (debug to repro gang)
read counts need correction
datasets added
Gang's issue reproduced in bed
Tried to add opposite strand
GroupSnpInfo bug without intron SNV eg 96108701 corrected
Update areNotInSameExon cases
Gang's results reproduced done
Gang results reproduced and formatted
Minor commit with genome path removed (not needed)
User config and param files added; bug on SNV strand elminated
Minor supression on SNV -1 -1 est ERROR
gene const exons without annotation events added
Minor suppression of gene without cnost ratio
Major: can go through the whole SNV list
Major commit SNV not in same exon corrected
Major: bugs in AreNotInSameExon and find est junctions corrected
Minor: intermediate output off; est events without flanking regions removed
Stable Version: use gene const set for est, geneName upper-cased, non-flanking est events used
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