setting up indexer to use one reference
redoing indexing script to make only one index
cleaning up index script
single ends new alignment working
paired end working
Merge branch 'master' of https://github.com/mgymrek/lobstr-code into epic-alignment-changes
removing code for next best period checking
removing align debug info
updating tests. NOTE: still need to change allelotyper (and tests) to use new index
adding missing files
making allelotype deal with new index
moving alignment utils to a separate module
speeding up alignment by not allow gaps in flanks
merging in alignment speedups. traumatizing git merge
fixing stitching problems
fixing stithcing substr bug
fixing thresholds to fix alignment problems with new reference
changing stitching threshold so tests still pass
resolving merge conflict in main_allelotype
deleted inproperly merged code in GetSharedAlns