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satta pushed a change to branch upstream
in repository augustus.
from 6746895 Imported Upstream version 3.2.2+dfsg
new 591ea5c New upstream version 3.2.3+dfsg
new cd27ed4 New upstream version 3.2.3+dfsg
The 2 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 | 7 +
Makefile | 2 +-
README-cgp.txt | 2 +-
README.TXT | 11 +-
auxprogs/bam2wig/Makefile | 12 +-
auxprogs/bam2wig/bam2wig.c | 2 +-
auxprogs/homGeneMapping/README.TXT | 23 +-
auxprogs/homGeneMapping/include/gene.hh | 54 +-
auxprogs/homGeneMapping/include/genome.hh | 57 +-
auxprogs/homGeneMapping/include/projectio.hh | 14 +-
.../homGeneMapping/include}/sqliteDB.hh | 6 -
auxprogs/homGeneMapping/src/Makefile | 19 +-
auxprogs/homGeneMapping/src/gene.cc | 197 +-
auxprogs/homGeneMapping/src/genome.cc | 645 +-
auxprogs/homGeneMapping/src/main.cc | 94 +-
auxprogs/homGeneMapping/src/sqliteDB.cc | 115 +
auxprogs/joingenes/jg_ios.cpp | 1108 +-
auxprogs/joingenes/jg_ios.h | 4 +-
auxprogs/joingenes/jg_transcript.cpp | 3018 +--
auxprogs/joingenes/jg_transcript.h | 942 +-
auxprogs/joingenes/joingenes.cpp | 682 +-
common.mk | 8 +-
config/cgp/log_reg_parameters_primates.cfg | 25 +
config/extrinsic/cgp.extrinsic.cfg | 74 -
config/extrinsic/extrinsic-cgp.cfg | 119 +
.../coyote_tobacco/coyote_tobacco_exon_probs.pbl | 6591 ++++++
.../coyote_tobacco/coyote_tobacco_igenic_probs.pbl | 2420 +++
.../coyote_tobacco/coyote_tobacco_intron_probs.pbl | 7191 +++++++
.../coyote_tobacco_metapars.cfg} | 0
.../coyote_tobacco_metapars.utr.cfg} | 0
.../coyote_tobacco_parameters.cfg} | 64 +-
.../coyote_tobacco_trans_shadow_partial_utr.pbl} | 0
.../coyote_tobacco/coyote_tobacco_utr_probs.pbl | 4037 ++++
.../coyote_tobacco_weightmatrix.txt} | 0
.../japaneselamprey/japaneselamprey_exon_probs.pbl | 20253 +++++++++++++++++++
.../japaneselamprey_igenic_probs.pbl | 9680 +++++++++
.../japaneselamprey_intron_probs.pbl | 13746 +++++++++++++
.../japaneselamprey_metapars.cfg} | 0
.../japaneselamprey_metapars.utr.cfg} | 0
.../japaneselamprey_parameters.cfg} | 52 +-
.../japaneselamprey_weightmatrix.txt} | 0
config/species/schistosoma2/README.TXT | 7 +
.../sealamprey_exon_probs.pbl} | 0
.../sealamprey_igenic_probs.pbl} | 0
.../sealamprey_intron_probs.pbl} | 0
.../sealamprey_metapars.cfg} | 0
.../sealamprey_parameters.cfg} | 22 +-
.../sealamprey_weightmatrix.txt} | 0
docs/espoca/README | 52 +
docs/espoca/example.fa | 25 +
docs/espoca/tree.nwk | 1 +
include/codonMSA.hh | 40 +
include/contTimeMC.hh | 11 +-
include/geneMSA.hh | 8 +-
include/igenicmodel.hh | 4 +-
include/orthoexon.hh | 14 +-
include/properties.hh | 3 +-
include/sqliteDB.hh | 7 +-
include/types.hh | 5 +-
mansrc/aln2wig.1 | 47 +
mansrc/aln2wig.1.adoc | 29 +
mansrc/augustus.1 | 180 +
mansrc/augustus.1.adoc | 85 +
mansrc/bam2hints.1 | 120 +
mansrc/bam2hints.1.adoc | 75 +
mansrc/checkTargetSortedness.1 | 35 +
mansrc/checkTargetSortedness.1.adoc | 23 +
mansrc/consensusFinder.1 | 77 +
mansrc/consensusFinder.1.adoc | 47 +
mansrc/curve2hints.1 | 77 +
mansrc/curve2hints.1.adoc | 47 +
mansrc/etraining.1 | 41 +
mansrc/etraining.1.adoc | 28 +
mansrc/fastBlockSearch.1 | 85 +
mansrc/fastBlockSearch.1.adoc | 45 +
mansrc/filterBam.1 | 165 +
mansrc/filterBam.1.adoc | 87 +
mansrc/homGeneMapping.1 | 151 +
mansrc/homGeneMapping.1.adoc | 81 +
mansrc/joingenes.1 | 199 +
mansrc/joingenes.1.adoc | 83 +
mansrc/make.doc | 2 +
mansrc/prepareAlign.1 | 51 +
mansrc/prepareAlign.1.adoc | 31 +
scripts/gtf2bed.pl | 259 +
scripts/gtf2gff.pl | 36 +-
scripts/hal2maf_split.pl | 19 +-
scripts/join_mult_hints.pl | 2 +-
scripts/selectLongestORFs.pl | 20 -
scripts/splitMfasta.pl | 2 +-
scripts/transMap2hints.pl | 136 +-
src/Makefile | 15 +-
src/augustus.cc | 6 +-
src/codonMSA.cc | 146 +
src/compgenepred.cc | 14 +-
src/contTimeMC.cc | 371 +-
src/cxxflags | 2 +-
src/espoca.cc | 174 +
src/gene.cc | 3 +-
src/geneMSA.cc | 187 +-
src/igenicmodel.cc | 14 +-
src/load2sqlitedb.cc | 79 +-
src/orthoexon.cc | 43 +-
src/orthograph.cc | 16 +
src/parser/parse.cc | 7 +-
src/phylotree.cc | 40 +-
src/properties.cc | 61 +-
src/{properties.cc => properties.cc.backup} | 23 +-
src/{properties.cc => properties.cc.orig} | 25 +-
src/randseqaccess.cc | 16 +-
src/remove_PATH_MAX.patch | 71 +
src/scanner/lex.cc | 301 +-
src/scanner/lexer | 3 +-
src/scanner/scannerbase.h | 16 +-
src/sqliteDB.cc | 24 +-
src/types.cc | 19 +-
116 files changed, 71631 insertions(+), 3883 deletions(-)
mode change 100755 => 100644 auxprogs/homGeneMapping/include/projectio.hh
copy {include => auxprogs/homGeneMapping/include}/sqliteDB.hh (92%)
create mode 100644 auxprogs/homGeneMapping/src/sqliteDB.cc
create mode 100644 config/cgp/log_reg_parameters_primates.cfg
delete mode 100644 config/extrinsic/cgp.extrinsic.cfg
create mode 100644 config/extrinsic/extrinsic-cgp.cfg
create mode 100644 config/species/coyote_tobacco/coyote_tobacco_exon_probs.pbl
create mode 100644
config/species/coyote_tobacco/coyote_tobacco_igenic_probs.pbl
create mode 100644
config/species/coyote_tobacco/coyote_tobacco_intron_probs.pbl
copy
config/species/{Conidiobolus_coronatus/Conidiobolus_coronatus_metapars.cfg =>
coyote_tobacco/coyote_tobacco_metapars.cfg} (100%)
copy
config/species/{Conidiobolus_coronatus/Conidiobolus_coronatus_metapars.utr.cfg
=> coyote_tobacco/coyote_tobacco_metapars.utr.cfg} (100%)
copy config/species/{bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig1
=> coyote_tobacco/coyote_tobacco_parameters.cfg} (74%)
mode change 100755 => 100644
copy config/species/{human/human_trans_shadow_partial_utr.pbl =>
coyote_tobacco/coyote_tobacco_trans_shadow_partial_utr.pbl} (100%)
create mode 100644 config/species/coyote_tobacco/coyote_tobacco_utr_probs.pbl
rename config/species/{lamprey/lamprey_weightmatrix.txt =>
coyote_tobacco/coyote_tobacco_weightmatrix.txt} (100%)
create mode 100644
config/species/japaneselamprey/japaneselamprey_exon_probs.pbl
create mode 100644
config/species/japaneselamprey/japaneselamprey_igenic_probs.pbl
create mode 100644
config/species/japaneselamprey/japaneselamprey_intron_probs.pbl
copy
config/species/{Conidiobolus_coronatus/Conidiobolus_coronatus_metapars.cfg =>
japaneselamprey/japaneselamprey_metapars.cfg} (100%)
copy config/species/{generic/generic_metapars.utr.cfg =>
japaneselamprey/japaneselamprey_metapars.utr.cfg} (100%)
copy config/species/{generic/generic_parameters.cfg =>
japaneselamprey/japaneselamprey_parameters.cfg} (76%)
copy
config/species/{Conidiobolus_coronatus/Conidiobolus_coronatus_weightmatrix.txt
=> japaneselamprey/japaneselamprey_weightmatrix.txt} (100%)
create mode 100644 config/species/schistosoma2/README.TXT
rename config/species/{lamprey/lamprey_exon_probs.pbl =>
sealamprey/sealamprey_exon_probs.pbl} (100%)
rename config/species/{lamprey/lamprey_igenic_probs.pbl =>
sealamprey/sealamprey_igenic_probs.pbl} (100%)
rename config/species/{lamprey/lamprey_intron_probs.pbl =>
sealamprey/sealamprey_intron_probs.pbl} (100%)
rename config/species/{lamprey/lamprey_metapars.cfg =>
sealamprey/sealamprey_metapars.cfg} (100%)
rename config/species/{lamprey/lamprey_parameters.cfg =>
sealamprey/sealamprey_parameters.cfg} (87%)
copy
config/species/{Conidiobolus_coronatus/Conidiobolus_coronatus_weightmatrix.txt
=> sealamprey/sealamprey_weightmatrix.txt} (100%)
create mode 100644 docs/espoca/README
create mode 100644 docs/espoca/example.fa
create mode 100644 docs/espoca/tree.nwk
create mode 100644 include/codonMSA.hh
create mode 100644 mansrc/aln2wig.1
create mode 100644 mansrc/aln2wig.1.adoc
create mode 100644 mansrc/augustus.1
create mode 100644 mansrc/augustus.1.adoc
create mode 100644 mansrc/bam2hints.1
create mode 100644 mansrc/bam2hints.1.adoc
create mode 100644 mansrc/checkTargetSortedness.1
create mode 100644 mansrc/checkTargetSortedness.1.adoc
create mode 100644 mansrc/consensusFinder.1
create mode 100644 mansrc/consensusFinder.1.adoc
create mode 100644 mansrc/curve2hints.1
create mode 100644 mansrc/curve2hints.1.adoc
create mode 100644 mansrc/etraining.1
create mode 100644 mansrc/etraining.1.adoc
create mode 100644 mansrc/fastBlockSearch.1
create mode 100644 mansrc/fastBlockSearch.1.adoc
create mode 100644 mansrc/filterBam.1
create mode 100644 mansrc/filterBam.1.adoc
create mode 100644 mansrc/homGeneMapping.1
create mode 100644 mansrc/homGeneMapping.1.adoc
create mode 100644 mansrc/joingenes.1
create mode 100644 mansrc/joingenes.1.adoc
create mode 100644 mansrc/make.doc
create mode 100644 mansrc/prepareAlign.1
create mode 100644 mansrc/prepareAlign.1.adoc
create mode 100755 scripts/gtf2bed.pl
delete mode 100755 scripts/selectLongestORFs.pl
create mode 100644 src/codonMSA.cc
create mode 100644 src/espoca.cc
copy src/{properties.cc => properties.cc.backup} (96%)
copy src/{properties.cc => properties.cc.orig} (96%)
create mode 100644 src/remove_PATH_MAX.patch
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