New module for tandem repeat project
added new command line option for -blast_identity
added new command line details to usage statement
Small change to include percent identity in output blast directory name
Added fudge to deal with non-trace archive data which doesn't have ti indices in fasta header
Added extra check to die if no unique id is found in header
bug fix
bug fix...trace index identifier code has to be in two places
Okay, ti is needed in 3 places, so now put the code in a subroutine
And I missed another place where we were extracting header IDs. This should now work. Needs to handle trf and fasta file formats separately
typo in subroutine name
New script, better version of HOS_finder.pl
Fixed to have better defaults and deal with cases where first repeat in a pair is longer not shorter
Rewritten - almost completely - with more intelligent code that now finds much more HOS
Added a much needed period
Merge branch 'master' of github.com:KorfLab/Centromere_repeat_paper