.gitignore

# objects, dependencies and libraries
*.o
*.d
*.a
*.so

# hidden files except .gitignore
.*
!.gitignore

# output files
cppOutput*
*.csv

# large fasta files
d*.fasta

# binaries
bin/

# temp files
*~

# cmake build dir
build

# external libs compiled
*/lib/*.so
*/lib/*.so.*
lib/boost_1_70_0*
lib/boost

# qtCreator files
GeometricHashingPaper.cflags
GeometricHashingPaper.config
GeometricHashingPaper.creator*
GeometricHashingPaper.files
GeometricHashingPaper.includes
GeometricHashingPaper.cxxflags
*.autosave

# backup stuff (that ends in .bak)
*.bak

# log files
*.log
*.out*

# json files
*.json

# test files
testrun/
testdata/*
!testdata/generateTestcode.pl
!testdata/*.fa
!testdata/geometricHashing/*.fasta
!testdata/metagraph
testdata/metagraph/*
!testdata/metagraph/*.py
!testdata/yass
testdata/yass/*
!testdata/yass/cds.json
!testdata/yass/command.txt
!testdata/yass/hg38.fa
!testdata/yass/mm10.fa
!testdata/yass/matches0.json
!testdata/yass/orthologPairs.json
!testdata/pGH
testdata/pGH/*
!testdata/pGH/hg38.fa
!testdata/pGH/mm10.fa
!testdata/pGH/pGhTestSeeds.json

# doxygen generated files
doc/*
!doc/Doxyfile

# data-nas link
data-*

# other files
runParallelSpeedBenchmark.sh
firstSubmission