add tests and a few other fixes to account for cut matches at beginning
tree1521ff3bb213797f12fc60c01fe6e5648531bcf9
-rw-r--r-- 176 .gitignore
-rw-r--r-- 6407 AUTHORS
-rw-r--r-- 5446 BUGS
drwxr-xr-x - Bio
-rw-r--r-- 9168 BioPerl.pm
-rwxr-xr-x 18518 Build.PL
-rw-r--r-- 59229 Changes
-rw-r--r-- 45919 DEPENDENCIES
-rw-r--r-- 3154 DEPRECATED
-rw-r--r-- 18181 INSTALL
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-rw-r--r-- 41656 LICENSE
-rw-r--r-- 56201 MANIFEST
-rw-r--r-- 1182 MANIFEST.SKIP
-rw-r--r-- 12186 README
drwxr-xr-x - doc
drwxr-xr-x - examples
drwxr-xr-x - ide
drwxr-xr-x - maintenance
drwxr-xr-x - models
drwxr-xr-x - scripts
drwxr-xr-x - t