.gitignore

.idea
cmake-build-*/
doc/html

# Ignore the build and lib dirs
build
tmp

# Ignore any executables
bin/*

# Ignore Mac specific files
.DS_Store

# Compiled Object files
*.slo
*.lo
*.o
*.obj

# Precompiled Headers
*.gch
*.pch

# Compiled Dynamic libraries
*.so
*.dylib
*.dll

# Fortran module files
*.mod
*.smod

# Compiled Static libraries
*.lai
*.la
*.a
*.lib

# Executables
*.exe
*.out
*.app

# Logs
*.log

# perf.data
*perf.data*

# for now, ignore test_cases subdirs
test/test_cases/*/*
*.vcf
*.fa
*.matrix
test/test_cases/localPRG_test*
indextext.k5.w1.idx

# and log.txt
log.txt

# and files for debugging and sending to other people
EcoliK12_pandora*

# local directory - michael
vm-build/

CMakeCache.txt
CMakeFiles
CTestTestfile.cmake
ext/gatb.tar.gz
gatb-prefix
ext/gatb-core-1.4.1
gtest
include/gatb
include/hdf5
include/json
include/BooPHF
pandora.cbp
test/cmake_install.cmake
test/estimate_parameters_test
test/pandora_test
coverage
Makefile
cmake_install.cmake
compile_commands.json
pandora


!example/msas
!example/reads
/example/pandora_discover_out/
/example/prgs/
/example/output_toy_example*
/example/updated_prgs/
/example/pandora-linux-precompiled*
/example/make_prg_*

#portable binary build dir
build_portable_executable*
pandora-linux-precompiled*

/archives/
/example/out/

example/make_prg*
/build_test/
.ipynb_checkpoints
scripts/compare_pandora_results/pandora_multisample.matrix*
!test/test_cases/sample_example/pangenome.prg.fa

/debugging/