[med-svn] [augustus] branch master updated (fe5c809 -> c684d5c)
Sascha Steinbiss
satta at debian.org
Tue Jul 18 09:00:08 UTC 2017
This is an automated email from the git hooks/post-receive script.
satta pushed a change to branch master
in repository augustus.
from fe5c809 Added RRID (SCR_008417) for Augustus
new 1ddc94a adjust binaries to remove
new 16c4de9 new upstream release
new fbc59e8 New upstream version 3.3+dfsg
new 66aa3e5 Merge tag 'upstream/3.3+dfsg'
new ff1f062 bump Standards-Version
new 0b9e30f fix script permissions
new 02ffaa0 fix wildcards
new c684d5c remove unnecessary files
The 8 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
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 ++++
.../ciona_metapars.cfg} | 0
.../ciona_metapars.cgp.cfg} | 0
.../ciona_metapars.utr.cfg} | 0
.../ciona_parameters.cfg} | 62 +-
.../ciona_parameters.cfg.orig1} | 24 +-
.../ciona_weightmatrix.txt} | 0
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} | 0
.../japaneselamprey3_exon_probs.pbl.withoutCRF} | 0
.../japaneselamprey3_igenic_probs.pbl} | 0
.../japaneselamprey3_igenic_probs.pbl.withoutCRF} | 0
.../japaneselamprey3_intron_probs.pbl} | 0
.../japaneselamprey3_intron_probs.pbl.withoutCRF} | 0
.../japaneselamprey3_metapars.cfg} | 0
.../japaneselamprey3_metapars.utr.cfg} | 0
.../japaneselamprey3_parameters.cfg} | 22 +-
.../japaneselamprey3_weightmatrix.txt} | 0
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} | 0
.../mnemiopsis_leidyi_metapars.cgp.cfg} | 0
.../mnemiopsis_leidyi_metapars.utr.cfg} | 0
.../mnemiopsis_leidyi_parameters.cfg} | 22 +-
.../mnemiopsis_leidyi_parameters.cgp.cfg} | 24 +-
.../mnemiopsis_leidyi_utr_probs.pbl | 4046 ++++
.../mnemiopsis_leidyi_weightmatrix.txt} | 0
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} | 24 +-
.../nematostella_vectensis_weightmatrix.txt} | 0
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 ++++++
.../seahare_metapars.cfg} | 0
.../seahare_metapars.utr.cfg} | 0
.../seahare_parameters.cfg} | 50 +-
.../seahare_weightmatrix.txt} | 0
.../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} | 0
...strongylocentrotus_purpuratus_metapars.cgp.cfg} | 0
...strongylocentrotus_purpuratus_metapars.utr.cfg} | 0
.../strongylocentrotus_purpuratus_parameters.cfg} | 24 +-
...rongylocentrotus_purpuratus_parameters.cgp.cfg} | 24 +-
.../strongylocentrotus_purpuratus_utr_probs.pbl | 4046 ++++
...strongylocentrotus_purpuratus_weightmatrix.txt} | 0
.../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
debian/changelog | 10 +-
debian/control | 2 +-
debian/copyright | 10 +-
debian/rules | 4 +-
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 +-
230 files changed, 139282 insertions(+), 2110 deletions(-)
mode change 100755 => 100644 auxprogs/filterBam/src/functions/MatePairs.cc
mode change 100755 => 100644 auxprogs/filterBam/src/functions/PairednessCoverage.cc
mode change 100755 => 100644 auxprogs/filterBam/src/functions/SingleAlignment.cc
mode change 100755 => 100644 auxprogs/filterBam/src/functions/getReferenceLength.cc
mode change 100755 => 100644 auxprogs/filterBam/src/functions/getReferenceName.cc
mode change 100755 => 100644 auxprogs/filterBam/src/functions/initOptions.cc
mode change 100755 => 100644 auxprogs/filterBam/src/functions/printCigarOperations.cc
mode change 100755 => 100644 auxprogs/filterBam/src/functions/printElapsedTime.cc
mode change 100755 => 100644 auxprogs/filterBam/src/functions/sumDandIOperations.cc
mode change 100755 => 100644 auxprogs/filterBam/src/functions/sumMandIOperations.cc
mode change 100755 => 100644 auxprogs/filterBam/src/headers/filterBam.h
mode change 100755 => 100644 auxprogs/homGeneMapping/examples/aln.hal
mode change 100755 => 100644 auxprogs/homGeneMapping/examples/gtffilenames.tbl
mode change 100755 => 100644 auxprogs/homGeneMapping/examples/gtfs/chicken.gtf
mode change 100755 => 100644 auxprogs/homGeneMapping/examples/gtfs/cow.gtf
mode change 100755 => 100644 auxprogs/homGeneMapping/examples/gtfs/human.gtf
mode change 100755 => 100644 auxprogs/homGeneMapping/examples/gtfs/human.hints.gff
mode change 100755 => 100644 auxprogs/homGeneMapping/examples/gtfs/mouse.gtf
mode change 100755 => 100644 auxprogs/homGeneMapping/examples/gtfs/mouse.hints.gff
mode change 100755 => 100644 auxprogs/homGeneMapping/examples/make.doc
delete mode 100644 config/cgp/log_reg_parameters.cfg
mode change 100755 => 100644 config/profile/blosum55.qij
mode change 100755 => 100644 config/profile/blosum62.qij
mode change 100755 => 100644 config/species/ancylostoma_ceylanicum/README.TXT
mode change 100755 => 100644 config/species/bombus_impatiens1/bombus_impatiens1_exon_probs.pbl.withoutCRF
mode change 100755 => 100644 config/species/bombus_impatiens1/bombus_impatiens1_igenic_probs.pbl.withoutCRF
mode change 100755 => 100644 config/species/bombus_impatiens1/bombus_impatiens1_intron_probs.pbl.withoutCRF
mode change 100755 => 100644 config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig1
mode change 100755 => 100644 config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig2
mode change 100755 => 100644 config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig3
mode change 100755 => 100644 config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig4
mode change 100755 => 100644 config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig5
mode change 100755 => 100644 config/species/bombus_terrestris2/bombus_terrestris2_exon_probs.pbl.withoutCRF
mode change 100755 => 100644 config/species/bombus_terrestris2/bombus_terrestris2_igenic_probs.pbl.withoutCRF
mode change 100755 => 100644 config/species/bombus_terrestris2/bombus_terrestris2_intron_probs.pbl.withoutCRF
mode change 100755 => 100644 config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig1
mode change 100755 => 100644 config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig2
mode change 100755 => 100644 config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig3
mode change 100755 => 100644 config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig4
mode change 100755 => 100644 config/species/brugia/brugia_splicefile
mode change 100755 => 100644 config/species/c_elegans_trsk/c_elegans_trsk_exon_probs.pbl.withoutCRF
mode change 100755 => 100644 config/species/c_elegans_trsk/c_elegans_trsk_igenic_probs.pbl.withoutCRF
mode change 100755 => 100644 config/species/c_elegans_trsk/c_elegans_trsk_intron_probs.pbl.withoutCRF
mode change 100755 => 100644 config/species/camponotus_floridanus/README.TXT
mode change 100755 => 100644 config/species/chicken/README.TXT
create mode 100644 config/species/ciona/README.TXT
create mode 100644 config/species/ciona/ciona_exon_probs.pbl
create mode 100644 config/species/ciona/ciona_igenic_probs.pbl
create mode 100644 config/species/ciona/ciona_intron_probs.pbl
copy config/species/{Conidiobolus_coronatus/Conidiobolus_coronatus_metapars.cfg => ciona/ciona_metapars.cfg} (100%)
copy config/species/{generic/generic_metapars.cgp.cfg => ciona/ciona_metapars.cgp.cfg} (100%)
copy config/species/{generic/generic_metapars.utr.cfg => ciona/ciona_metapars.utr.cfg} (100%)
copy config/species/{generic/generic_parameters.cfg => ciona/ciona_parameters.cfg} (76%)
copy config/species/{generic/generic_parameters.cfg => ciona/ciona_parameters.cfg.orig1} (86%)
copy config/species/{Conidiobolus_coronatus/Conidiobolus_coronatus_weightmatrix.txt => ciona/ciona_weightmatrix.txt} (100%)
mode change 100755 => 100644 config/species/culex/culex_exon_probs.pbl.wech
mode change 100755 => 100644 config/species/culex/culex_igenic_probs.pbl.wech
mode change 100755 => 100644 config/species/culex/culex_intron_probs.pbl.wech
mode change 100755 => 100644 config/species/galdieria/galdieria_splicefile
mode change 100755 => 100644 config/species/honeybee1/honeybee1_exon_probs.pbl.withoutCRF
mode change 100755 => 100644 config/species/honeybee1/honeybee1_igenic_probs.pbl.withoutCRF
mode change 100755 => 100644 config/species/honeybee1/honeybee1_intron_probs.pbl.withoutCRF
mode change 100755 => 100644 config/species/honeybee1/honeybee1_parameters.cfg.orig1
mode change 100755 => 100644 config/species/human/README.TXT
copy config/species/{japaneselamprey/japaneselamprey_exon_probs.pbl => japaneselamprey3/japaneselamprey3_exon_probs.pbl} (100%)
copy config/species/{japaneselamprey/japaneselamprey_exon_probs.pbl => japaneselamprey3/japaneselamprey3_exon_probs.pbl.withoutCRF} (100%)
copy config/species/{japaneselamprey/japaneselamprey_igenic_probs.pbl => japaneselamprey3/japaneselamprey3_igenic_probs.pbl} (100%)
copy config/species/{japaneselamprey/japaneselamprey_igenic_probs.pbl => japaneselamprey3/japaneselamprey3_igenic_probs.pbl.withoutCRF} (100%)
copy config/species/{japaneselamprey/japaneselamprey_intron_probs.pbl => japaneselamprey3/japaneselamprey3_intron_probs.pbl} (100%)
copy config/species/{japaneselamprey/japaneselamprey_intron_probs.pbl => japaneselamprey3/japaneselamprey3_intron_probs.pbl.withoutCRF} (100%)
copy config/species/{Conidiobolus_coronatus/Conidiobolus_coronatus_metapars.cfg => japaneselamprey3/japaneselamprey3_metapars.cfg} (100%)
copy config/species/{generic/generic_metapars.utr.cfg => japaneselamprey3/japaneselamprey3_metapars.utr.cfg} (100%)
copy config/species/{japaneselamprey/japaneselamprey_parameters.cfg => japaneselamprey3/japaneselamprey3_parameters.cfg} (87%)
copy config/species/{Conidiobolus_coronatus/Conidiobolus_coronatus_weightmatrix.txt => japaneselamprey3/japaneselamprey3_weightmatrix.txt} (100%)
mode change 100755 => 100644 config/species/maize/maize_splicefile.txt.gz
create mode 100644 config/species/mnemiopsis_leidyi/README.TXT
create mode 100644 config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_exon_probs.pbl
create mode 100644 config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_igenic_probs.pbl
create mode 100644 config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_intron_probs.pbl
copy config/species/{Conidiobolus_coronatus/Conidiobolus_coronatus_metapars.cfg => mnemiopsis_leidyi/mnemiopsis_leidyi_metapars.cfg} (100%)
copy config/species/{schistosoma2/schistosoma2_metapars.cgp.cfg => mnemiopsis_leidyi/mnemiopsis_leidyi_metapars.cgp.cfg} (100%)
copy config/species/{generic/generic_metapars.utr.cfg => mnemiopsis_leidyi/mnemiopsis_leidyi_metapars.utr.cfg} (100%)
copy config/species/{generic/generic_parameters.cfg => mnemiopsis_leidyi/mnemiopsis_leidyi_parameters.cfg} (89%)
copy config/species/{fly/fly_parameters.cgp.cfg => mnemiopsis_leidyi/mnemiopsis_leidyi_parameters.cgp.cfg} (50%)
create mode 100644 config/species/mnemiopsis_leidyi/mnemiopsis_leidyi_utr_probs.pbl
copy config/species/{Conidiobolus_coronatus/Conidiobolus_coronatus_weightmatrix.txt => mnemiopsis_leidyi/mnemiopsis_leidyi_weightmatrix.txt} (100%)
create mode 100644 config/species/nematostella_vectensis/README.TXT
create mode 100644 config/species/nematostella_vectensis/nematostella_vectensis_exon_probs.pbl
create mode 100644 config/species/nematostella_vectensis/nematostella_vectensis_igenic_probs.pbl
create mode 100644 config/species/nematostella_vectensis/nematostella_vectensis_intron_probs.pbl
copy config/species/{generic/generic_parameters.cfg => nematostella_vectensis/nematostella_vectensis_parameters.cfg} (86%)
copy config/species/{Conidiobolus_coronatus/Conidiobolus_coronatus_weightmatrix.txt => nematostella_vectensis/nematostella_vectensis_weightmatrix.txt} (100%)
mode change 100755 => 100644 config/species/pneumocystis/README.TXT
mode change 100755 => 100644 config/species/rice/README.TXT
mode change 100755 => 100644 config/species/s_aureus/README.TXT
mode change 100755 => 100644 config/species/schistosoma/schistosoma_parameters.cfg.opt
create mode 100644 config/species/seahare/seahare_exon_probs.pbl
create mode 100644 config/species/seahare/seahare_exon_probs.pbl.withoutCRF
create mode 100644 config/species/seahare/seahare_igenic_probs.pbl
create mode 100644 config/species/seahare/seahare_igenic_probs.pbl.withoutCRF
create mode 100644 config/species/seahare/seahare_intron_probs.pbl
create mode 100644 config/species/seahare/seahare_intron_probs.pbl.withoutCRF
copy config/species/{Conidiobolus_coronatus/Conidiobolus_coronatus_metapars.cfg => seahare/seahare_metapars.cfg} (100%)
copy config/species/{generic/generic_metapars.utr.cfg => seahare/seahare_metapars.utr.cfg} (100%)
copy config/species/{generic/generic_parameters.cfg => seahare/seahare_parameters.cfg} (80%)
copy config/species/{Conidiobolus_coronatus/Conidiobolus_coronatus_weightmatrix.txt => seahare/seahare_weightmatrix.txt} (100%)
create mode 100644 config/species/strongylocentrotus_purpuratus/README.TXT
create mode 100644 config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_exon_probs.pbl
create mode 100644 config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_igenic_probs.pbl
create mode 100644 config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_intron_probs.pbl
copy config/species/{Conidiobolus_coronatus/Conidiobolus_coronatus_metapars.cfg => strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_metapars.cfg} (100%)
copy config/species/{schistosoma2/schistosoma2_metapars.cgp.cfg => strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_metapars.cgp.cfg} (100%)
copy config/species/{generic/generic_metapars.utr.cfg => strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_metapars.utr.cfg} (100%)
copy config/species/{generic/generic_parameters.cfg => strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_parameters.cfg} (85%)
rename config/species/{fly/fly_parameters.cgp.cfg => strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_parameters.cgp.cfg} (50%)
create mode 100644 config/species/strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_utr_probs.pbl
copy config/species/{Conidiobolus_coronatus/Conidiobolus_coronatus_weightmatrix.txt => strongylocentrotus_purpuratus/strongylocentrotus_purpuratus_weightmatrix.txt} (100%)
mode change 100755 => 100644 config/species/tribolium2012/tribolium2012_exon_probs.pbl.HMM
mode change 100755 => 100644 config/species/tribolium2012/tribolium2012_exon_probs.pbl1
mode change 100755 => 100644 config/species/tribolium2012/tribolium2012_exon_probs.pbl2
mode change 100755 => 100644 config/species/tribolium2012/tribolium2012_exon_probs.pbl3
mode change 100755 => 100644 config/species/tribolium2012/tribolium2012_exon_probs.pbl4
mode change 100755 => 100644 config/species/tribolium2012/tribolium2012_igenic_probs.pbl.HMM
mode change 100755 => 100644 config/species/tribolium2012/tribolium2012_igenic_probs.pbl1
mode change 100755 => 100644 config/species/tribolium2012/tribolium2012_igenic_probs.pbl2
mode change 100755 => 100644 config/species/tribolium2012/tribolium2012_igenic_probs.pbl3
mode change 100755 => 100644 config/species/tribolium2012/tribolium2012_igenic_probs.pbl4
mode change 100755 => 100644 config/species/tribolium2012/tribolium2012_intron_probs.pbl.HMM
mode change 100755 => 100644 config/species/tribolium2012/tribolium2012_intron_probs.pbl1
mode change 100755 => 100644 config/species/tribolium2012/tribolium2012_intron_probs.pbl2
mode change 100755 => 100644 config/species/tribolium2012/tribolium2012_intron_probs.pbl3
mode change 100755 => 100644 config/species/tribolium2012/tribolium2012_intron_probs.pbl4
mode change 100755 => 100644 config/species/tribolium2012/tribolium2012_parameters.cfg.orig1
mode change 100755 => 100644 config/species/tribolium2012/tribolium2012_parameters.cfg.orig2
mode change 100755 => 100644 config/species/tribolium2012/tribolium2012_parameters.cfg.orig3
mode change 100755 => 100644 config/species/tribolium2012/tribolium2012_parameters.cfg.orig4
mode change 100755 => 100644 config/species/tribolium2012/tribolium2012_parameters.cfg.orig5
mode change 100755 => 100644 config/species/tribolium2012/tribolium2012_parameters.cfg.orig6
mode change 100755 => 100644 config/species/tribolium2012/tribolium2012_parameters.cfg.orig7
mode change 100755 => 100644 config/species/tribolium2012/tribolium2012_utr_probs.pbl.HMM
mode change 100755 => 100644 config/species/verticillium_longisporum1/verticillium_longisporum1_parameters.cfg.orig1
mode change 100755 => 100644 config/species/zebrafish/README.TXT
mode change 100755 => 100644 config/species/zebrafish/zebrafish_exon_probs.pbl.HMM
mode change 100755 => 100644 config/species/zebrafish/zebrafish_igenic_probs.pbl.HMM
mode change 100755 => 100644 config/species/zebrafish/zebrafish_intron_probs.pbl.HMM
create mode 100644 examples/autoAug/genome.fa.cidx
create mode 100644 examples/autoAug/h.gff
create mode 100644 examples/database.db
create mode 100644 examples/hsackI10.fa.gz
create mode 100644 include/train_logReg_param.hh
mode change 100755 => 100644 scripts/README.autoAug
mode change 100755 => 100644 scripts/SplicedAlignment.pm
mode change 100755 => 100644 scripts/autoRun.pathInfo
mode change 100755 => 100644 scripts/checkUTR
create mode 100755 scripts/eval_dualdecomp.pl
mode change 100755 => 100644 scripts/filterGenesIn_mRNAname.pl
create mode 100644 scripts/filterGenesIn_mRNAname.pl.patch
mode change 100755 => 100644 scripts/gbrowse.conf
mode change 100755 => 100644 scripts/gff2ps_mycustom
copy scripts/{gtf2gff.pl => gtf2gff.pl.origexit} (97%)
mode change 100755 => 100644 scripts/helpMod.pm
mode change 100755 => 100644 scripts/webserver-results.body
mode change 100755 => 100644 scripts/webserver-results.head
mode change 100755 => 100644 scripts/webserver-results.tail
create mode 100644 src/emptyalirow.patch
delete mode 100644 src/properties.cc.backup
delete mode 100644 src/properties.cc.orig
delete mode 100644 src/remove_PATH_MAX.patch
create mode 100644 src/train_logReg_param.cc
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