# Binaries #
############
bin/bgzip
bin/cnvnator-multi
src/cnvnator/bin/cnvnator-multi
bin/cnvnator2VCF.pl
bin/cnvnator_wrapper.py
bin/annotate_rd.py
bin/freebayes
bin/lumpy
bin/lumpyexpress
bin/pairend_distro.py
bin/samblaster
bin/svtyper
bin/tabix
bin/vawk
bin/vcfToBedpe
bin/Bio
bin/bwa
bin/parallel
bin/sambamba
bin/variant_effect_predictor.pl
bin/annotateBed
bin/bamToBed
bin/bamToFastq
bin/bed12ToBed6
bin/bedToBam
bin/bedToIgv
bin/bedpeToBam
bin/bedtools
bin/closestBed
bin/clusterBed
bin/complementBed
bin/coverageBed
bin/expandCols
bin/fastaFromBed
bin/flankBed
bin/genomeCoverageBed
bin/getOverlap
bin/groupBy
bin/intersectBed
bin/linksBed
bin/mapBed
bin/maskFastaFromBed
bin/mergeBed
bin/multiBamCov
bin/multiIntersectBed
bin/nucBed
bin/pairToBed
bin/pairToPair
bin/randomBed
bin/shuffleBed
bin/slopBed
bin/sortBed
bin/subtractBed
bin/tagBam
bin/unionBedGraphs
bin/windowBed
bin/windowMaker
bin/mbuffer
bin/parallel
bin/bamheadrg.py
bin/bamtofastq.py
bin/bamgroupreads.py
bin/bamfilterrg.py
bin/bamcleanheader.py
bin/bamlibs.py

# Compiled source #
###################
*.com
*.class
*.dll
*.exe
*.o
*.so

# Packages #
############
# it's better to unpack these files and commit the raw source
# git has its own built in compression methods
*.7z
*.dmg
*.gz
*.iso
*.jar
*.rar
*.tar
*.zip

# Logs and databases #
######################
*.log
*.sql
*.sqlite

# OS generated files #
######################
*~
\#*\#
.DS_Store
.DS_Store?
._*
.Spotlight-V100
.Trashes
Icon?
ehthumbs.db
Thumbs.db

# mbuffer compile files #
#########################
src/mbuffer/Makefile
src/mbuffer/config.h
src/mbuffer/config.status
src/mbuffer/mbuffer
src/mbuffer/mbuffer.1