Initial commit. Taken from https://github.com/andreaswilm/compbio-utils
Made dbsnp arg mandatory in ngs_pipeline.py (needed for base recal anyway)
samflag.py: Now printing help if no arg was given instead of wrongly assuming flag 0
- Initial commit of FIXME
- merged changes for backup files in .gitignore
Added description of programs to README
Fixed markdown list syntax in README
initial commit based on https://github.com/andreaswilm/compbio-utils
Merge branch 'master' of github.com:CSB5/misc-scripts
Merge branch 'master' of https://github.com/lch14forever/misc-scripts into lch14forever-master
Also removed dangling else in run_baserecalibrator_table cleaned up up whitespaces

Conflicts:
	ngs_pipeline.py
Merge branch 'lch14forever-master'