[med-svn] [augustus] 02/12: Merge tag 'upstream/3.2.3+dfsg'
Sascha Steinbiss
satta at debian.org
Sun Dec 11 11:07:23 UTC 2016
This is an automated email from the git hooks/post-receive script.
satta pushed a commit to branch master
in repository augustus.
commit a0ab861a404084fca01ebf8a02524ca79895732e
Merge: 2712ce5 591ea5c
Author: Sascha Steinbiss <satta at debian.org>
Date: Sat Dec 10 09:07:42 2016 +0000
Merge tag 'upstream/3.2.3+dfsg'
Upstream version 3.2.3+dfsg
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} | 8 +-
.../coyote_tobacco/coyote_tobacco_metapars.utr.cfg | 30 +
.../coyote_tobacco_parameters.cfg} | 99 +-
.../coyote_tobacco_trans_shadow_partial_utr.pbl | 529 +
.../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} | 8 +-
.../japaneselamprey_metapars.utr.cfg | 30 +
.../japaneselamprey_parameters.cfg} | 81 +-
.../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/getSeq | Bin 0 -> 33872520 bytes
src/igenicmodel.cc | 14 +-
src/load2sqlitedb | Bin 0 -> 2534880 bytes
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 +-
118 files changed, 72263 insertions(+), 3920 deletions(-)
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