.gitignore

auxprogs/utrrnaseq/build
auxprogs/utrrnaseq/utrrnaseq
auxprogs/utrrnaseq/*.gff
src/*.o
src/googletest/*.o
auxprogs/aln2wig/aln2wig
auxprogs/aln2wig/aln2wig.o
auxprogs/bam2hints/bam2hints
auxprogs/bam2hints/bam2hints.o
auxprogs/bam2wig/bam2wig
auxprogs/bam2wig/bam2wig.o
auxprogs/compileSpliceCands/compileSpliceCands
auxprogs/compileSpliceCands/compileSpliceCands.o
auxprogs/compileSpliceCands/list.o
auxprogs/filterBam/src/*.o
auxprogs/filterBam/src/filterBam
auxprogs/homGeneMapping/src/gene.o
auxprogs/homGeneMapping/src/genome.o
auxprogs/homGeneMapping/src/sqliteDB.o
auxprogs/homGeneMapping/src/homGeneMapping
auxprogs/homGeneMapping/test/
auxprogs/joingenes/jg_ios.o
auxprogs/joingenes/jg_transcript.o
auxprogs/joingenes/joingenes
auxprogs/joingenes/joingenes.o
bin/
examples/cgp/out/
include/ann.hh~
src/ann.cc~
src/augustus
src/cxxflags
src/espoca
src/etraining
src/fastBlockSearch
src/getSeq
src/load2db
src/load2sqlitedb
src/parser/parse.o
src/pp_simScore
src/prepareAlign
src/scanner/lex.o
src/unittests/fasta_unittest.o
src/unittests/lldouble_unittest.o
src/unittests/alignment_unittest.o
src/unittests/codonevo_unittest.o
src/unittests/evo_unittest.o
src/unittests/unittests

# ignore VS Code configuration files
.vscode

# ignore generated test output
tests/short/examples/results/
tests/short/output_html/

# ignore tmp test case data
tests/short/examples/data/tmp/
tests/short/auxprogs/*/tmp/
tests/short/auxprogs/*/result_files/

# ignore longrunning test data and output files
tests/longrunning/single_genome/data/
tests/longrunning/single_genome/output/
tests/longrunning/single_genome/tmp.*/
tests/longrunning/cgp/data/cgp12way/
tests/longrunning/cgp/data/cgp12way.tar.gz

# ignore test species
config/species/test_aug_dev_species/
config/species/human_longrunningtest_crf/
config/species/human_longrunningtest_hmm/

# ignore python bytecode
__pycache__
*.pyc

# documentation
doxygen/

# mac
*.DS_Store
*.dSYM