initial cleanup
remove unused subroutines
remove unused variables
cleanup parse_cigar
fix double counting bug for INDELs; other general cleanup
fix bug causing retrieval of wrong base at current position
skip to next position or read ASAP under certain conditions (cuts runtime by ~half)
more cleanup
shorten variable names; replace 'defined' with 'exists'; general cleanup
and more cleanup
convert snp_caller into a proper subroutine
remove artifacts from Pepe's quantile filtering approach
Merge branch 'feature/refactor-SNP-caller' into develop