Max_mismatch almost ready
Max_mismatch cleanup; generalize to any # of masks
Minor readability improvements
Update setup.sh for new method
Move max_mismatch to the flowcells dir

Should have put it there from the beginning!
Quick fix for bamcounts

Need to & with flag, |'ing with a constant is always true.
Merge pull request #14 from fwip/fix_counts

Quick fix for bamcounts
Standardize window/bin bucket filename reference
Merge branch 'master' of github.com:StamLab/stampipes
Necessary bit operations tweak in bamcounts.py
Merge pull request #13 from fwip/rewrite_max_mismatch

Rewrite max mismatch

Now actually works for more than the trivial case!
Fix bug where Picard reports uploaded to wrong alignment object
First step at barcode tallying

barcode_tally.bash needs to be rewritten to use processing.json
Use processing.json
Switch to bash script for barcodes; ~6x speedup
Bump version
Merge pull request #15 from StamLab/barcode_tally

Barcode tally
Add in duplicate stats of entire BAM, upload to LIMS
Bump version
A script that moves a tag from one slug to another, used in processing pipelines.