Started code for Spoligo/MIRU information retrieval for isolates with certain mutations
Replaced gzip, added pysam, updated args Using pysam instead of gzip Fixed args to take in a mutation file from vep-count.py Started code that will try to find isolates with the given mutation(s)
Checked out vep-count.py version from master
Added stdin and stdout functionality
Separate pattern dicts, output
Created separate spoligo and miru dictionaries for separate analyses Checked for minimal output flag for output: if flagged, prints number of patterns; otherwise, it prints unique patterns with corresponding isolates
Removed requirement of input file
Renamed GWA_analyze to gwa-check-clonality