[med-svn] [augustus] branch master updated (2712ce5 -> 33a0420)
Sascha Steinbiss
satta at debian.org
Sun Dec 11 11:07:21 UTC 2016
This is an automated email from the git hooks/post-receive script.
satta pushed a change to branch master
in repository augustus.
from 2712ce5 dch -r
new 591ea5c New upstream version 3.2.3+dfsg
new a0ab861 Merge tag 'upstream/3.2.3+dfsg'
new cd27ed4 New upstream version 3.2.3+dfsg
new b41cf3b Merge tag 'upstream/3.2.3+dfsg'
new 953cde7 new Debian version
new 8392a29 d/copyright: adjust Files-Excluded
new f9648ce drop unused overrides
new 0dfffa1 add spelling patch
new 07663df use upstream provided man pages
new d144130 use debhelper 10
new fc2612a add patch header
new 33a0420 finalise d/changelog
The 12 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
debian/augustus-data.lintian-overrides | 2 -
debian/augustus-doc.lintian-overrides | 2 -
debian/changelog | 12 +
debian/compat | 2 +-
debian/control | 2 +-
debian/copyright | 8 +-
debian/manpages | 2 +-
debian/patches/buildflags.patch | 18 +-
debian/patches/keep_cflags | 2 +-
debian/patches/search_config_path | 2 +-
debian/patches/series | 2 +-
debian/patches/spelling | 246 -
debian/patches/spelling.patch | 132 +
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 +
.../aln2wig.1.adoc_ => mansrc/aln2wig.1.adoc | 0
mansrc/augustus.1 | 180 +
{debian/mansrc => mansrc}/augustus.1.adoc | 2 +-
mansrc/bam2hints.1 | 120 +
{debian/mansrc => mansrc}/bam2hints.1.adoc | 0
mansrc/checkTargetSortedness.1 | 35 +
.../mansrc => mansrc}/checkTargetSortedness.1.adoc | 0
mansrc/consensusFinder.1 | 77 +
{debian/mansrc => mansrc}/consensusFinder.1.adoc | 0
mansrc/curve2hints.1 | 77 +
.../curve2hints.1.adoc | 0
mansrc/etraining.1 | 41 +
{debian/mansrc => mansrc}/etraining.1.adoc | 0
mansrc/fastBlockSearch.1 | 85 +
{debian/mansrc => mansrc}/fastBlockSearch.1.adoc | 31 +-
mansrc/filterBam.1 | 165 +
{debian/mansrc => mansrc}/filterBam.1.adoc | 0
mansrc/homGeneMapping.1 | 151 +
{debian/mansrc => mansrc}/homGeneMapping.1.adoc | 0
mansrc/joingenes.1 | 199 +
{debian/mansrc => mansrc}/joingenes.1.adoc | 0
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 +-
.../remove_PATH_MAX.patch | 145 +-
src/scanner/lex.cc | 301 +-
src/scanner/lexer | 3 +-
src/scanner/scannerbase.h | 16 +-
src/sqliteDB.cc | 24 +-
src/types.cc | 19 +-
129 files changed, 71174 insertions(+), 4249 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%)
delete mode 100644 debian/augustus-data.lintian-overrides
delete mode 100644 debian/augustus-doc.lintian-overrides
delete mode 100644 debian/patches/spelling
create mode 100644 debian/patches/spelling.patch
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
copy debian/mansrc/aln2wig.1.adoc_ => mansrc/aln2wig.1.adoc (100%)
create mode 100644 mansrc/augustus.1
copy {debian/mansrc => mansrc}/augustus.1.adoc (98%)
create mode 100644 mansrc/bam2hints.1
copy {debian/mansrc => mansrc}/bam2hints.1.adoc (100%)
create mode 100644 mansrc/checkTargetSortedness.1
copy {debian/mansrc => mansrc}/checkTargetSortedness.1.adoc (100%)
create mode 100644 mansrc/consensusFinder.1
copy {debian/mansrc => mansrc}/consensusFinder.1.adoc (100%)
create mode 100644 mansrc/curve2hints.1
copy debian/mansrc/curve2hints.1.adoc_ => mansrc/curve2hints.1.adoc (100%)
create mode 100644 mansrc/etraining.1
copy {debian/mansrc => mansrc}/etraining.1.adoc (100%)
create mode 100644 mansrc/fastBlockSearch.1
copy {debian/mansrc => mansrc}/fastBlockSearch.1.adoc (69%)
create mode 100644 mansrc/filterBam.1
copy {debian/mansrc => mansrc}/filterBam.1.adoc (100%)
create mode 100644 mansrc/homGeneMapping.1
copy {debian/mansrc => mansrc}/homGeneMapping.1.adoc (100%)
create mode 100644 mansrc/joingenes.1
copy {debian/mansrc => mansrc}/joingenes.1.adoc (100%)
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%)
copy debian/patches/avoid_PATH_MAX.patch => src/remove_PATH_MAX.patch (82%)
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