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commit a0ab861a404084fca01ebf8a02524ca79895732e Merge: 2712ce5 591ea5c Author: Sascha Steinbiss <[email protected]> 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(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/augustus.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
