[med-svn] [augustus] branch upstream updated (cd27ed4 -> fbc59e8)

Sascha Steinbiss satta at debian.org
Tue Jul 18 09:00:16 UTC 2017


This is an automated email from the git hooks/post-receive script.

satta pushed a change to branch upstream
in repository augustus.

      from  cd27ed4   New upstream version 3.2.3+dfsg
       new  fbc59e8   New upstream version 3.3+dfsg

The 1 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
 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 +-
 226 files changed, 139261 insertions(+), 2105 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

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/augustus.git



More information about the debian-med-commit mailing list