Allow genome names longer than 7 characters to be output in matrix files
Made extend anchors more robust, allowed fewer CGNs for ends of contigs, reduced window sizes, and some other minor stuff
Modified selection of seeds to be less restrictive on possibly poorly trimmed alleles. Changed best hits to prefer full length matches over bitscore. Modified hash reference to avoid warning message. Added two overalp cases for allele check which shouldn't actually change behavior but is more correct.
fixing last fix continue/next
change zero length Blast results from ERROR to ...
check that hash is defined before calling keys
fix hardcoding of max_mismatch in pull_seqs
Fix create seed for no redundant allele case