Clean up intermediate bam files unless specified otherwise
Bugfix Fastqc summary generation
Bugfix: filename of bam annotate plot truncated
Bugfix: rerun tests without make clean first
Enhancement: increased use tmp directory / scratch space
bamannotate plot name extended to use 60 character prefix
Patch 0.4.0.3
Bugfix summary generation on mac osx
Bugfix NGSANE version detection on mac osx
gitignore added
Bugfix custom output folder name
Bugfix parser for est. frament length
Bugfix: recovery staging, checkpoints adjusted
Merge branch 'master' of github.com:clark-lab/ngsane
file handling refactored
Bugfix fragment size calculation
Keep duplicates in bw if requested
Bugfix Keep duplicates
Merge branch 'master' into masai_fseq

Conflicts:
	mods/hiclibCorrelate.sh
Merge branch 'masai_fseq' of github.com:clark-lab/ngsane into masai_fseq