# Ignore Eclipse config files
.cproject
.project
.settings/*

# Ignore Netbeans config files
nbproject
tests


# Ignore the compiled object files
*.o
*.gcno
*.d
*.lo
# Ignore compiled static library
*.a
*.gcda
*.la
# Ignore temporary files
*.cpp~
*.sh~
#Ignore generated Makefiles
Makefile

#Ignore python generated files
*.pyc
*.py~

# Ignore autoconf stuff
**/.deps
**/.libs
**/aclocal.m4
**/config.h.in
**/config.log
**/config.stamp
**/config.status
**/ltmain.sh
**/Makefile.in
autom4te.cache
compile
config.guess
config.sub
configure
depcomp
install-sh
libtool
m4
missing
config.h

# Ignore jemalloc generated material
libs/jemalloc/VERSION
libs/jemalloc/bin
libs/jemalloc/doc/
libs/jemalloc/include/
libs/jemalloc/jemalloc.pc
libs/jemalloc/test/

# Ignore GSL generated material
libs/gsl_sub/config.h
libs/gsl_sub/gsl.spec
libs/gsl_sub/stamp-h1
igor_src/igor
libs/gsl_sub/gsl-config
libs/gsl_sub/gsl-histogram
libs/gsl_sub/gsl.pc
libs/gsl_sub/gsl/*.h
libs/jemalloc/lib
libs/jemalloc/src/*.sym

#Ignore documentation generated files
README.html
docs/html/
docs/latex/
docs/IGoR_CPP_manual.pdf
igor.1
libs/gsl_sub/config.h.in~
stamp-h1

#Ignore documentation demo generated files
demo/aligns_info.out
demo/demo_write_model_marginals.txt
demo/demo_write_model_parms.txt
demo/generated_seqs_indexed_demo.csv
demo/generated_seqs_realizations_demo.csv
demo/murugan_naive1_noncoding_demo_seqs_alignments_D.csv
demo/murugan_naive1_noncoding_demo_seqs_alignments_J.csv
demo/murugan_naive1_noncoding_demo_seqs_alignments_V.csv
demo/murugan_naive1_noncoding_demo_seqs_indexed_seq.csv
demo/run_demo/