Add QC module
add find_incorrect_ref_bases; remove magic numbers; extract common code from iva and iva_qc scripts
Addd option for gage analysis
pass gage option to qc object
Add option to run RATT
Clean up unsorted bam
Clean up temporary reads files
Add option to run REAPR
added subsample_bam
remove option to supply bam files. Always require reads, to keep control of mapping
Take out subsetting before reapr. It will break reapr
Only take reads as input, not BAM; various little fixes to running ratt,gage,reapr
Update to reflect module changes, i.e. need reference embl files
Find ref using kraken; add wrapper for making kraken database