Fixed Indexing

Simplified Indexing and added ref_fasta option for fillout

Split reads now outputs 100% more gzipped files

Fixed issue where split reads was not outputting in gzipped format

Better split reads

Better fillout and portability

Better fillout and igv plotter

1.9.10

Deduplicate BAMs with the same sample IDs

Even more better than the older one that was already better

1.9.9

Update _version.py

Modifications for picard 2.9.0

abra 2.12 prep

Deli