fixed fa regex to include fasta
Merge branch 'live', remote branch 'origin' into live
fixed ref_TE name bug
changed bowtie params
changed bowtie opts
added or die for file open
added non-ref TE strand info
can now use bowtie1 or bowtie2 -b2 0 or 1
now bowtie2 really works
updated readme
deleted a comment
added more filters for bowtie2
TE insert loc:was 1bp:now TSDlen
TE insert loc:was 1bp:now TSDlen
table of common TSD lens
added SAM file parsing and bowtie2
add sample data
added version to readme
updated sample_readme.txt
commented out a print test statement