.gitignore

.DS_Store
.cproject
.project
.dirstamp
*.o
*.a
*.gz
*.tar
*.tgz
*.tab
*.txt
*.out
*.html
*.tab
*.swp
*.tmproj
*.idea
*.pyc

## These are for autoconf/automake/libtool
*.deps
*stamp-h1
*.la
*.lai
*.lo
*.orig
*.libs
aux_build
autom4te.cache
config.log
config.status
libtool
aclocal.m4
Makefile.in
configure

autoscan.log
configure.scan

## These are for Perl modules in general
_build
blib
MYMETA.yml
MYMETA.json
MANIFEST.SKIP
#Makefile.PL

## This is user/architecture specific
tags

Makefile
INSTALL

breseq-*

tests/*/output*
tests/*/0*
tests/*/data
tests/test.config
tests/lambda_mixed_pop_cl_tabulate/contingency_loci.csv

src/c/breseq/breseq/
src/c/breseq/breseq
src/c/breseq/gdtools

Rplots.pdf

package

## samtools
extern/samtools-*/samtools
extern/samtools-*/bcftools/bcftools
extern/samtools-*/razip
extern/samtools-*/misc/md5fa
extern/samtools-*/misc/md5sum-lite
extern/samtools-*/misc/seqtk
extern/samtools-*/misc/wgsim
extern/samtools-*/.dirstamp
extern/samtools-*/version.h
extern/samtools-*/htslib-*/.dirstamp
extern/samtools-*/htslib-*/version.h

## Perl GenomeDiff
src/perl/GenomeDiff/GenomeDiff-*
src/perl/GenomeDiff/Build
src/perl/GenomeDiff/GenomeDiff-
src/perl/GenomeDiff/META.yml

## For Xcode

src/c/build
xcworkspace
xcuserdata
xcshareddata
xcscheme


## For Various IDEs
nbproject/*
Debug/*
Release/*