diff --git a/.gitignore b/.gitignore index a007bb0..eacb03f 100644 --- a/.gitignore +++ b/.gitignore @@ -1,135 +1,25 @@ -cpu.pprof -cpu.trace -test -bin -vendor -*.fastq -*.fasta -*.fastq.gz -*.fasta.gz -.DS_Store -*.gml -*.log -/argaly +**/cpu.pprof +**/cpu.trace +**/test +**/bin +**/vendor +**/*.fastq +**/*.fasta +**/*.fastq.gz +**/*.fasta.gz +**/.DS_Store +**/*.gml +**/*.log +**/xxx* +**/*.sav +**/*.old +**/*.tgz -/obiconvert -/obicount -/obimultiplex -/obipairing -/obipcr -/obifind -/obidistribute -/obiuniq +.rhistory +/.vscode /build -/Makefile.old -.Rproj.user -obitools.Rproj -Stat_error.knit.md -.Rhistory -Stat_error.nb.html -Stat_error.Rmd -/.luarc.json -/doc/TAXO/ -/doc/results/ -/doc/_main.log -/doc/_book/_main.tex -/doc/_freeze/ -/doc/tutorial_files/ -/doc/wolf_data/ -/taxdump/ -/.vscode/ +/ncbitaxo -/Algo-Alignement.numbers -/Estimate_proba_true_seq.html -/Estimate_proba_true_seq.nb.html -/Estimate_proba_true_seq.Rmd -/modele_error_euka.qmd -/obitools.code-workspace -.DS_Store -.RData -x -xxx -y -/doc/wolf_diet.tgz -/doc/man/depends -/sample/wolf_R1.fasta.gz -/sample/wolf_R2.fasta.gz -/sample/euka03.ecotag.fasta.gz -/sample/ratio.csv -/sample/STD_PLN_1.dat -/sample/STD_PLN_2.dat -/sample/subset_Pasvik_R1.fastq.gz -/sample/subset_Pasvik_R2.fastq.gz -/sample/test_gobitools.fasta.bz2 -euka03.csv* -gbbct793.seq.gz -gbinv1003.seq.gz -gbpln210.seq -/doc/book/OBITools-V4.aux -/doc/book/OBITools-V4.fdb_latexmk -/doc/book/OBITools-V4.fls -/doc/book/OBITools-V4.log -/doc/book/OBITools-V4.pdf -/doc/book/OBITools-V4.synctex.gz -/doc/book/OBITools-V4.tex -/doc/book/OBITools-V4.toc -getoptions.adoc -Archive.zip -.DS_Store -sample/.DS_Store -sample/consensus_graphs/specimen_hac_plants_Vern_disicolor_.gml -93954 -Bact03.e5.gb_R254.obipcr.idx.fasta.save -sample/test.obipcr.log -Bact02.e3.gb_R254.obipcr.fasta.gz -Example_Arth03.ngsfilter -SPER01.csv -SPER03.csv -wolf_diet_ngsfilter.txt -xx -xxx.gb -yyy_geom.csv -yyy_LCS.csv -yyy.json -bug_obimultiplex/toto -bug_obimultiplex/toto_mapping -bug_obimultiplex/tutu -bug_obimultiplex/tutu_mapping -bug_obipairing/GIT1_GH_ngsfilter.txt -doc/book/TAXO/citations.dmp -doc/book/TAXO/delnodes.dmp -doc/book/TAXO/division.dmp -doc/book/TAXO/gc.prt -doc/book/TAXO/gencode.dmp -doc/book/TAXO/merged.dmp -doc/book/TAXO/names.dmp -doc/book/TAXO/nodes.dmp -doc/book/TAXO/readme.txt -doc/book/wolf_data/Release-253/ncbitaxo/citations.dmp -doc/book/wolf_data/Release-253/ncbitaxo/delnodes.dmp -doc/book/wolf_data/Release-253/ncbitaxo/division.dmp -doc/book/wolf_data/Release-253/ncbitaxo/gc.prt -doc/book/wolf_data/Release-253/ncbitaxo/gencode.dmp -doc/book/wolf_data/Release-253/ncbitaxo/merged.dmp -doc/book/wolf_data/Release-253/ncbitaxo/names.dmp -doc/book/wolf_data/Release-253/ncbitaxo/nodes.dmp -doc/book/wolf_data/Release-253/ncbitaxo/readme.txt -doc/book/results/toto.tasta -sample/.DS_Store -GO -ncbitaxo/citations.dmp -ncbitaxo/delnodes.dmp -ncbitaxo/division.dmp -ncbitaxo/gc.prt -ncbitaxo/gencode.dmp -ncbitaxo/merged.dmp -ncbitaxo/names.dmp -ncbitaxo/nodes.dmp -ncbitaxo/readme.txt -template.16S -xxx.gz -*.sav -*.old -ncbitaxo.tgz -*.csv +!/obitests/** +!/sample/** \ No newline at end of file diff --git a/obitests/obitools/obicount/test.sh b/obitests/obitools/obicount/test.sh index d0ef2a8..be24a31 100755 --- a/obitests/obitools/obicount/test.sh +++ b/obitests/obitools/obicount/test.sh @@ -50,7 +50,7 @@ log "Testing $TEST_NAME..." log "Test directory is $TEST_DIR" log "obitools directory is $OBITOOLS_DIR" log "Temporary directory is $TMPDIR" -log "files: "$(find $TEST_DIR | awk -F'/' '{print $NF}') +log "files: "$(find $TEST_DIR | awk -F'/' '{print $NF}' | tail -n +2) ###################################################################### #### diff --git a/obitests/obitools/obicount/wolf_F.fasta.gz b/obitests/obitools/obicount/wolf_F.fasta.gz new file mode 100644 index 0000000..e5f2a49 Binary files /dev/null and b/obitests/obitools/obicount/wolf_F.fasta.gz differ diff --git a/obitests/obitools/obicount/wolf_F.fastq.gz b/obitests/obitools/obicount/wolf_F.fastq.gz new file mode 100644 index 0000000..fed63e9 Binary files /dev/null and b/obitests/obitools/obicount/wolf_F.fastq.gz differ