Changes in .gitignore

Former-commit-id: 7e9fcd4ed6487e52562b274d87345e0e46f1458d
Former-commit-id: bf7a58dcf96db9f8c132977aa7d3f6af97cce0f5

.gitignore

@@ -1 +1,6 @@
 /test/
+/.DS_Store
+/samples/
+/toto.embl
+/toto.fasta
+/toto.log

data/.gitignore

@@ -0,0 +1,2 @@
+/its/
+/.DS_Store

data/cds/.gitignore

@@ -0,0 +1 @@
+/.DS_Store

data/cds/chlorodb/.gitignore

@@ -0,0 +1 @@
+/.DS_Store

data/cds/chlorodb/core/.gitignore

@@ -79,3 +79,4 @@
 /ycf2/
 /ycf3/
 /ycf4/
+/.DS_Store

data/cds/chlorodb/download/.gitignore

@@ -0,0 +1 @@
+/.DS_Store

data/nucrrna/plants/.gitignore

@@ -0,0 +1,6 @@
+/nuc_RRNA_18S_RC.fst
+/nuc_RRNA_18S_RC.hmm
+/nuc_RRNA_18S.hmm
+/nuc_RRNA_28S_RC.fst
+/nuc_RRNA_28S_RC.hmm
+/nuc_RRNA_28S.hmm

data/rrna/.gitignore

@@ -0,0 +1,13 @@
+/16S.goodali.rc.fst
+/23S.goodali.rc.fst
+/4.5S.goodali.rc.fst
+/5S.goodali.rc.fst
+/plast_RRNA_16S_RC.hmm
+/plast_RRNA_16S.hmm
+/plast_RRNA_23S_RC.hmm
+/plast_RRNA_23S.hmm
+/plast_RRNA_4.5S_RC.hmm
+/plast_RRNA_4.5S.hmm
+/plast_RRNA_5S_RC.hmm
+/plast_RRNA_5S.hmm
+/.DS_Store

detectors/.gitignore

@@ -0,0 +1 @@
+/.DS_Store

detectors/normalize/bin/.gitignore

@@ -0,0 +1 @@
+/draft

detectors/nucrrna/bin/.gitignore

@@ -0,0 +1 @@
+/draft

detectors/rrna/tools/.gitignore

@@ -0,0 +1 @@
+/draft

detectors/trna/tools/.gitignore

@@ -0,0 +1 @@
+/draft

src/.gitignore

@@ -0,0 +1,3 @@
+/.DS_Store
+/trnascan-se/
+/gnuplot/

src/ITSx/.gitignore

@@ -0,0 +1 @@
+/build.i386-darwin/

src/_unix_tools_/.gitignore

@@ -0,0 +1 @@
+/.DS_Store

src/clustalo/.gitignore

@@ -0,0 +1 @@
+/.DS_Store

src/exonerate/glib2/.gitignore

@@ -1 +1,2 @@
 /build.i386-darwin/
+/.DS_Store

src/exonerate/pkg-config/.gitignore

@@ -1 +1,2 @@
 /build.i386-darwin/
+/.DS_Store

src/gawk/.gitignore

@@ -1,2 +1,3 @@
 /build.i386-darwin/
 /gawk-4/
+/.DS_Store

src/getopt/.gitignore

@@ -1 +1,2 @@
 /build.i386-darwin/
+/.DS_Store

src/hmmer3/.gitignore

@@ -1 +1,2 @@
 /build.i386-darwin/
+/.DS_Store

src/kimono/lxpack/src/.gitignore

@@ -0,0 +1,13 @@
+/fasta_io.o
+/kim_alphabet.o
+/kim_codonskew.o
+/kim_counter.o
+/kim_distance.o
+/kim_genetic.o
+/kim_indexer.o
+/kim_mixer.o
+/kim_sequence.o
+/kim_util.o
+/kim_zone.o
+/kimfit
+/kimono

src/muscle/.gitignore

@@ -0,0 +1 @@
+/.DS_Store

src/muscle/muscle3.8.31/.gitignore

@@ -0,0 +1,148 @@
+/aligngivenpath.o
+/aligngivenpathsw.o
+/aligntwomsas.o
+/aligntwoprofs.o
+/aln.o
+/alpha.o
+/anchors.o
+/bittraceback.o
+/blosum62.o
+/blosumla.o
+/clust.o
+/cluster.o
+/clwwt.o
+/color.o
+/cons.o
+/diaglist.o
+/diffobjscore.o
+/diffpaths.o
+/difftrees.o
+/difftreese.o
+/distcalc.o
+/distfunc.o
+/distpwkimura.o
+/domuscle.o
+/dosp.o
+/dpreglist.o
+/drawtree.o
+/edgelist.o
+/enumopts.o
+/enumtostr.o
+/estring.o
+/fasta.o
+/fasta2.o
+/fastclust.o
+/fastdist.o
+/fastdistjones.o
+/fastdistkbit.o
+/fastdistkmer.o
+/fastdistmafft.o
+/fastdistnuc.o
+/fastscorepath2.o
+/finddiags.o
+/finddiagsn.o
+/glbalign.o
+/glbalign352.o
+/glbaligndiag.o
+/glbalignle.o
+/glbalignsimple.o
+/glbalignsp.o
+/glbalignspn.o
+/glbalignss.o
+/glbalndimer.o
+/globals.o
+/globalslinux.o
+/globalsosx.o
+/globalsother.o
+/globalswin32.o
+/gonnet.o
+/henikoffweight.o
+/henikoffweightpb.o
+/html.o
+/hydro.o
+/intmath.o
+/local.o
+/main.o
+/makerootmsa.o
+/makerootmsab.o
+/maketree.o
+/mhack.o
+/mpam200.o
+/msa.o
+/msa2.o
+/msadistkimura.o
+/msf.o
+/muscle
+/muscle.o
+/muscleout.o
+/nucmx.o
+/nwdasimple.o
+/nwdasimple2.o
+/nwdasmall.o
+/nwrec.o
+/nwsmall.o
+/objscore.o
+/objscore2.o
+/objscoreda.o
+/onexception.o
+/options.o
+/outweights.o
+/pam200mafft.o
+/params.o
+/phy.o
+/phy2.o
+/phy3.o
+/phy4.o
+/phyfromclust.o
+/phyfromfile.o
+/physeq.o
+/phytofile.o
+/posgap.o
+/ppscore.o
+/profdb.o
+/profile.o
+/profilefrommsa.o
+/progalign.o
+/progress.o
+/progressivealign.o
+/pwpath.o
+/readmx.o
+/realigndiffs.o
+/realigndiffse.o
+/refine.o
+/refinehoriz.o
+/refinesubfams.o
+/refinetree.o
+/refinetreee.o
+/refinevert.o
+/refinew.o
+/savebest.o
+/scoredist.o
+/scoregaps.o
+/scorehistory.o
+/scorepp.o
+/seq.o
+/seqvect.o
+/setblosumweights.o
+/setgscweights.o
+/setnewhandler.o
+/spfast.o
+/sptest.o
+/stabilize.o
+/subfam.o
+/subfams.o
+/sw.o
+/termgaps.o
+/textfile.o
+/threewaywt.o
+/tomhydro.o
+/traceback.o
+/tracebackopt.o
+/tracebacksw.o
+/treefrommsa.o
+/typetostr.o
+/upgma2.o
+/usage.o
+/validateids.o
+/vtml2.o
+/writescorefile.o

src/muscle/muscle3.8.31/src/.gitignore

@@ -0,0 +1,150 @@
+/aligngivenpath.o
+/aligngivenpathsw.o
+/aligntwomsas.o
+/aligntwoprofs.o
+/aln.o
+/alpha.o
+/anchors.o
+/bittraceback.o
+/blosum62.o
+/blosumla.o
+/clust.o
+/cluster.o
+/clwwt.o
+/color.o
+/cons.o
+/diaglist.o
+/diffobjscore.o
+/diffpaths.o
+/difftrees.o
+/difftreese.o
+/distcalc.o
+/distfunc.o
+/distpwkimura.o
+/domuscle.o
+/dosp.o
+/dpreglist.o
+/drawtree.o
+/edgelist.o
+/enumopts.o
+/enumtostr.o
+/estring.o
+/fasta.o
+/fasta2.o
+/fastclust.o
+/fastdist.o
+/fastdistjones.o
+/fastdistkbit.o
+/fastdistkmer.o
+/fastdistmafft.o
+/fastdistnuc.o
+/fastscorepath2.o
+/finddiags.o
+/finddiagsn.o
+/glbalign.o
+/glbalign352.o
+/glbaligndiag.o
+/glbalignle.o
+/glbalignsimple.o
+/glbalignsp.o
+/glbalignspn.o
+/glbalignss.o
+/glbalndimer.o
+/globals.o
+/globalslinux.o
+/globalsosx.o
+/globalsother.o
+/globalswin32.o
+/gonnet.o
+/henikoffweight.o
+/henikoffweightpb.o
+/html.o
+/hydro.o
+/intmath.o
+/local.o
+/main.o
+/makerootmsa.o
+/makerootmsab.o
+/maketree.o
+/mhack.o
+/mpam200.o
+/msa.o
+/msa2.o
+/msadistkimura.o
+/msf.o
+/muscle
+/muscle.make.stderr.txt
+/muscle.make.stdout.txt
+/muscle.o
+/muscleout.o
+/nucmx.o
+/nwdasimple.o
+/nwdasimple2.o
+/nwdasmall.o
+/nwrec.o
+/nwsmall.o
+/objscore.o
+/objscore2.o
+/objscoreda.o
+/onexception.o
+/options.o
+/outweights.o
+/pam200mafft.o
+/params.o
+/phy.o
+/phy2.o
+/phy3.o
+/phy4.o
+/phyfromclust.o
+/phyfromfile.o
+/physeq.o
+/phytofile.o
+/posgap.o
+/ppscore.o
+/profdb.o
+/profile.o
+/profilefrommsa.o
+/progalign.o
+/progress.o
+/progressivealign.o
+/pwpath.o
+/readmx.o
+/realigndiffs.o
+/realigndiffse.o
+/refine.o
+/refinehoriz.o
+/refinesubfams.o
+/refinetree.o
+/refinetreee.o
+/refinevert.o
+/refinew.o
+/savebest.o
+/scoredist.o
+/scoregaps.o
+/scorehistory.o
+/scorepp.o
+/seq.o
+/seqvect.o
+/setblosumweights.o
+/setgscweights.o
+/setnewhandler.o
+/spfast.o
+/sptest.o
+/stabilize.o
+/subfam.o
+/subfams.o
+/sw.o
+/termgaps.o
+/textfile.o
+/threewaywt.o
+/tomhydro.o
+/traceback.o
+/tracebackopt.o
+/tracebacksw.o
+/treefrommsa.o
+/typetostr.o
+/upgma2.o
+/usage.o
+/validateids.o
+/vtml2.o
+/writescorefile.o

src/ncbiblast/binaries/.gitignore

@@ -1 +1,2 @@
 /bin.i386-darwin/
+/.DS_Store

src/prokov/lxpack/src/.gitignore

@@ -0,0 +1,9 @@
+/fasta_io.o
+/libkov_io.o
+/libkov_proba.o
+/libkov_util.o
+/prokov_cds
+/prokov_curve
+/prokov_learn
+/prokov_orf
+/prokov_score

src/sumaclust/.gitignore

@@ -0,0 +1 @@
+/.DS_Store

src/sumatra/sumatra-1.0.10/sumalibs/libfasta/.gitignore

@@ -0,0 +1,6 @@
+/fasta_header_handler.o
+/fasta_header_parser.o
+/fasta_seq_writer.o
+/header_mem_handler.o
+/libfasta.a
+/sequence.o

src/sumatra/sumatra-1.0.10/sumalibs/libfile/.gitignore

@@ -0,0 +1,2 @@
+/fileHandling.o
+/libfile.a

src/sumatra/sumatra-1.0.10/sumalibs/liblcs/.gitignore

@@ -0,0 +1,3 @@
+/liblcs.a
+/sse_banded_LCS_alignment.o
+/upperband.o

src/sumatra/sumatra-1.0.10/sumalibs/libutils/.gitignore

@@ -0,0 +1,3 @@
+/debug.o
+/libutils.a
+/utilities.o

src/tcsh/.gitignore

@@ -0,0 +1,2 @@
+/build.i386-darwin/
+/.DS_Store

src/trnascan-se/.gitignore

@@ -0,0 +1 @@
+/.DS_Store