Add initial rough code notes for snp ID w/o BioPerl
Count pre-insert bases together with non-inserts
Capture sequences of variable length inserts and remove them from $read_bases
Get insert counts by position and nucleotide
Make get_inserts and get_insert_counts subs
Output insert lines
Clean up
Filter SNPs based on min cov & ratio
Keep '*' deletion indicator, but remove '-1A'-type
Output file header
Change min threshold equations from '==' to '>='
Make get_consensus_base sub
Make count_bases sub
Clean up
Make output_snp and output_insert subs
Make clean_pileup sub
Make output_snp more readable
Add coverage filter for output_insert
Change min_ins_ratio to match old script
Identify most abundant insert