[med-svn] [augustus] 04/08: Merge tag 'upstream/3.3+dfsg'
Sascha Steinbiss
satta at debian.org
Tue Jul 18 09:00:12 UTC 2017
This is an automated email from the git hooks/post-receive script.
satta pushed a commit to branch master
in repository augustus.
commit 66aa3e5e69ca44e239d27a19ea40eadf93b9d1dd
Merge: 16c4de9 fbc59e8
Author: Sascha Steinbiss <satta at debian.org>
Date: Mon Jul 17 19:19:06 2017 +0200
Merge tag 'upstream/3.3+dfsg'
Upstream version 3.3+dfsg
HISTORY.TXT | 12 +
Makefile | 4 +-
README-cgp.txt | 268 +-
README.TXT | 16 +-
auxprogs/aln2wig/aln2wig.c | 4 +-
auxprogs/filterBam/src/functions/MatePairs.cc | 0
.../filterBam/src/functions/PairednessCoverage.cc | 0
.../filterBam/src/functions/SingleAlignment.cc | 0
.../filterBam/src/functions/getReferenceLength.cc | 0
.../filterBam/src/functions/getReferenceName.cc | 0
auxprogs/filterBam/src/functions/initOptions.cc | 0
.../src/functions/printCigarOperations.cc | 0
.../filterBam/src/functions/printElapsedTime.cc | 0
.../filterBam/src/functions/sumDandIOperations.cc | 0
.../filterBam/src/functions/sumMandIOperations.cc | 0
auxprogs/filterBam/src/headers/filterBam.h | 0
auxprogs/homGeneMapping/examples/aln.hal | Bin
auxprogs/homGeneMapping/examples/gtffilenames.tbl | 0
auxprogs/homGeneMapping/examples/gtfs/chicken.gtf | 0
auxprogs/homGeneMapping/examples/gtfs/cow.gtf | 0
auxprogs/homGeneMapping/examples/gtfs/human.gtf | 0
.../homGeneMapping/examples/gtfs/human.hints.gff | 0
auxprogs/homGeneMapping/examples/gtfs/mouse.gtf | 0
.../homGeneMapping/examples/gtfs/mouse.hints.gff | 0
auxprogs/homGeneMapping/examples/make.doc | 0
auxprogs/joingenes/jg_transcript.cpp | 10 +-
common.mk | 8 +-
config/cgp/log_reg_parameters.cfg | 37 -
config/profile/blosum55.qij | 0
config/profile/blosum62.qij | 0
config/species/ancylostoma_ceylanicum/README.TXT | 0
.../bombus_impatiens1_exon_probs.pbl.withoutCRF | 0
.../bombus_impatiens1_igenic_probs.pbl.withoutCRF | 0
.../bombus_impatiens1_intron_probs.pbl.withoutCRF | 0
.../bombus_impatiens1_parameters.cfg.orig1 | 0
.../bombus_impatiens1_parameters.cfg.orig2 | 0
.../bombus_impatiens1_parameters.cfg.orig3 | 0
.../bombus_impatiens1_parameters.cfg.orig4 | 0
.../bombus_impatiens1_parameters.cfg.orig5 | 0
.../bombus_terrestris2_exon_probs.pbl.withoutCRF | 0
.../bombus_terrestris2_igenic_probs.pbl.withoutCRF | 0
.../bombus_terrestris2_intron_probs.pbl.withoutCRF | 0
.../bombus_terrestris2_parameters.cfg.orig1 | 0
.../bombus_terrestris2_parameters.cfg.orig2 | 0
.../bombus_terrestris2_parameters.cfg.orig3 | 0
.../bombus_terrestris2_parameters.cfg.orig4 | 0
config/species/brugia/brugia_splicefile | 0
.../c_elegans_trsk_exon_probs.pbl.withoutCRF | 0
.../c_elegans_trsk_igenic_probs.pbl.withoutCRF | 0
.../c_elegans_trsk_intron_probs.pbl.withoutCRF | 0
config/species/camponotus_floridanus/README.TXT | 0
config/species/chicken/README.TXT | 0
config/species/ciona/README.TXT | 13 +
config/species/ciona/ciona_exon_probs.pbl | 6597 ++++++
config/species/ciona/ciona_igenic_probs.pbl | 2420 +++
config/species/ciona/ciona_intron_probs.pbl | 4174 ++++
config/species/ciona/ciona_metapars.cfg | 48 +
config/species/ciona/ciona_metapars.cgp.cfg | 22 +
config/species/ciona/ciona_metapars.utr.cfg | 30 +
.../ciona_parameters.cfg} | 64 +-
.../ciona_parameters.cfg.orig1} | 32 +-
config/species/ciona/ciona_weightmatrix.txt | 23 +
config/species/culex/culex_exon_probs.pbl.wech | 0
config/species/culex/culex_igenic_probs.pbl.wech | 0
config/species/culex/culex_intron_probs.pbl.wech | 0
config/species/galdieria/galdieria_splicefile | 0
.../honeybee1/honeybee1_exon_probs.pbl.withoutCRF | 0
.../honeybee1_igenic_probs.pbl.withoutCRF | 0
.../honeybee1_intron_probs.pbl.withoutCRF | 0
.../honeybee1/honeybee1_parameters.cfg.orig1 | 0
config/species/human/README.TXT | 0
.../japaneselamprey/japaneselamprey_parameters.cfg | 2 +-
.../japaneselamprey3_exon_probs.pbl | 20253 +++++++++++++++++++
.../japaneselamprey3_exon_probs.pbl.withoutCRF | 20253 +++++++++++++++++++
.../japaneselamprey3_igenic_probs.pbl | 9680 +++++++++
.../japaneselamprey3_igenic_probs.pbl.withoutCRF | 9680 +++++++++
.../japaneselamprey3_intron_probs.pbl | 13746 +++++++++++++
.../japaneselamprey3_intron_probs.pbl.withoutCRF | 13746 +++++++++++++
.../japaneselamprey3/japaneselamprey3_metapars.cfg | 48 +
.../japaneselamprey3_metapars.utr.cfg | 30 +
.../japaneselamprey3_parameters.cfg} | 22 +-
.../japaneselamprey3_weightmatrix.txt | 23 +
config/species/maize/maize_splicefile.txt.gz | Bin
config/species/mnemiopsis_leidyi/README.TXT | 13 +
.../mnemiopsis_leidyi_exon_probs.pbl | 6599 ++++++
.../mnemiopsis_leidyi_igenic_probs.pbl | 2420 +++
.../mnemiopsis_leidyi_intron_probs.pbl | 19476 ++++++++++++++++++
.../mnemiopsis_leidyi_metapars.cfg | 48 +
.../mnemiopsis_leidyi_metapars.cgp.cfg | 40 +
.../mnemiopsis_leidyi_metapars.utr.cfg | 30 +
.../mnemiopsis_leidyi_parameters.cfg} | 34 +-
.../mnemiopsis_leidyi_parameters.cgp.cfg} | 24 +-
.../mnemiopsis_leidyi_utr_probs.pbl | 4046 ++++
.../mnemiopsis_leidyi_weightmatrix.txt | 23 +
config/species/nematostella_vectensis/README.TXT | 37 +
.../nematostella_vectensis_exon_probs.pbl | 6599 ++++++
.../nematostella_vectensis_igenic_probs.pbl | 2420 +++
.../nematostella_vectensis_intron_probs.pbl | 18632 +++++++++++++++++
.../nematostella_vectensis_parameters.cfg} | 34 +-
.../nematostella_vectensis_weightmatrix.txt | 23 +
config/species/pneumocystis/README.TXT | 0
config/species/rice/README.TXT | 0
config/species/s_aureus/README.TXT | 0
.../schistosoma/schistosoma_parameters.cfg.opt | 0
config/species/seahare/seahare_exon_probs.pbl | 6597 ++++++
.../seahare/seahare_exon_probs.pbl.withoutCRF | 6597 ++++++
config/species/seahare/seahare_igenic_probs.pbl | 2420 +++
.../seahare/seahare_igenic_probs.pbl.withoutCRF | 2420 +++
config/species/seahare/seahare_intron_probs.pbl | 6465 ++++++
.../seahare/seahare_intron_probs.pbl.withoutCRF | 6465 ++++++
config/species/seahare/seahare_metapars.cfg | 48 +
config/species/seahare/seahare_metapars.utr.cfg | 30 +
.../seahare_parameters.cfg} | 54 +-
config/species/seahare/seahare_weightmatrix.txt | 23 +
.../strongylocentrotus_purpuratus/README.TXT | 27 +
.../strongylocentrotus_purpuratus_exon_probs.pbl | 6599 ++++++
.../strongylocentrotus_purpuratus_igenic_probs.pbl | 2420 +++
.../strongylocentrotus_purpuratus_intron_probs.pbl | 19464 ++++++++++++++++++
.../strongylocentrotus_purpuratus_metapars.cfg | 48 +
.../strongylocentrotus_purpuratus_metapars.cgp.cfg | 40 +
.../strongylocentrotus_purpuratus_metapars.utr.cfg | 30 +
.../strongylocentrotus_purpuratus_parameters.cfg} | 34 +-
...rongylocentrotus_purpuratus_parameters.cgp.cfg} | 24 +-
.../strongylocentrotus_purpuratus_utr_probs.pbl | 4046 ++++
.../strongylocentrotus_purpuratus_weightmatrix.txt | 23 +
.../tribolium2012/tribolium2012_exon_probs.pbl.HMM | 0
.../tribolium2012/tribolium2012_exon_probs.pbl1 | 0
.../tribolium2012/tribolium2012_exon_probs.pbl2 | 0
.../tribolium2012/tribolium2012_exon_probs.pbl3 | 0
.../tribolium2012/tribolium2012_exon_probs.pbl4 | 0
.../tribolium2012_igenic_probs.pbl.HMM | 0
.../tribolium2012/tribolium2012_igenic_probs.pbl1 | 0
.../tribolium2012/tribolium2012_igenic_probs.pbl2 | 0
.../tribolium2012/tribolium2012_igenic_probs.pbl3 | 0
.../tribolium2012/tribolium2012_igenic_probs.pbl4 | 0
.../tribolium2012_intron_probs.pbl.HMM | 0
.../tribolium2012/tribolium2012_intron_probs.pbl1 | 0
.../tribolium2012/tribolium2012_intron_probs.pbl2 | 0
.../tribolium2012/tribolium2012_intron_probs.pbl3 | 0
.../tribolium2012/tribolium2012_intron_probs.pbl4 | 0
.../tribolium2012_parameters.cfg.orig1 | 0
.../tribolium2012_parameters.cfg.orig2 | 0
.../tribolium2012_parameters.cfg.orig3 | 0
.../tribolium2012_parameters.cfg.orig4 | 0
.../tribolium2012_parameters.cfg.orig5 | 0
.../tribolium2012_parameters.cfg.orig6 | 0
.../tribolium2012_parameters.cfg.orig7 | 0
.../tribolium2012/tribolium2012_utr_probs.pbl.HMM | 0
.../verticillium_longisporum1_parameters.cfg.orig1 | 0
config/species/zebrafish/README.TXT | 0
.../species/zebrafish/zebrafish_exon_probs.pbl.HMM | 0
.../zebrafish/zebrafish_igenic_probs.pbl.HMM | 0
.../zebrafish/zebrafish_intron_probs.pbl.HMM | 0
docs/tutorial/index.html | 4 +-
docs/tutorial/prediction.html | 10 +-
examples/autoAug/genome.fa.cidx | Bin 0 -> 2121 bytes
examples/autoAug/h.gff | 2 +
examples/database.db | Bin 0 -> 10240 bytes
examples/hsackI10.fa.gz | Bin 0 -> 2164 bytes
include/alignment.hh | 4 +-
include/codonMSA.hh | 3 +-
include/contTimeMC.hh | 2 +-
include/gene.hh | 2 +-
include/geneMSA.hh | 4 +-
include/orthoexon.hh | 8 +-
include/orthograph.hh | 7 +-
include/phylotree.hh | 3 +-
include/pp_profile.hh | 9 +-
include/properties.hh | 3 +-
include/train_logReg_param.hh | 59 +
include/types.hh | 22 +-
scripts/README.autoAug | 0
scripts/SplicedAlignment.pm | 0
scripts/autoAugTrain.pl | 8 +-
scripts/autoRun.pathInfo | 0
scripts/checkUTR | 0
scripts/eval_dualdecomp.pl | 334 +
scripts/filterGenesIn_mRNAname.pl | 0
scripts/filterGenesIn_mRNAname.pl.patch | 21 +
scripts/gbrowse.conf | 0
scripts/gff2gbSmallDNA.pl | 46 +-
scripts/gff2ps_mycustom | 0
scripts/gtf2gff.pl | 11 +-
scripts/{gtf2gff.pl => gtf2gff.pl.origexit} | 15 +-
scripts/helpMod.pm | 0
scripts/intron2exex.pl | 2 +-
scripts/new_species.pl | 6 +
scripts/optimize_augustus.pl | 64 +-
scripts/webserver-results.body | 0
scripts/webserver-results.head | 0
scripts/webserver-results.tail | 0
src/Makefile | 7 +-
src/alignment.cc | 2 +-
src/augustus.cc | 3 +
src/cflags | 2 +-
src/codonMSA.cc | 26 +-
src/compgenepred.cc | 107 +-
src/contTimeMC.cc | 72 +-
src/cxxflags | 2 +-
src/emptyalirow.patch | 15 +
src/espoca.cc | 13 +-
src/extrinsicinfo.cc | 3 +-
src/gene.cc | 17 +-
src/geneMSA.cc | 72 +-
src/genomicMSA.cc | 4 +-
src/graph.cc | 1 -
src/mea.cc | 4 +-
src/meaPath.cc | 3 +-
src/namgene.cc | 16 +-
src/orthoexon.cc | 28 +-
src/orthograph.cc | 53 +-
src/parser/grammar | 14 +-
src/parser/parse.cc | 250 +-
src/parser/parser.h | 1 +
src/parser/parserbase.h | 7 +-
src/phylotree.cc | 19 +-
src/properties.cc | 19 +-
src/properties.cc.backup | 709 -
src/properties.cc.orig | 711 -
src/remove_PATH_MAX.patch | 71 -
src/scanner/lex.cc | 154 +-
src/scanner/lexer | 4 +-
src/scanner/scannerbase.h | 6 +-
src/speciesgraph.cc | 52 +-
src/train_logReg_param.cc | 616 +
src/types.cc | 31 +-
226 files changed, 227272 insertions(+), 2128 deletions(-)
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