[med-svn] [augustus] branch master updated (4312647 -> 93cc218)
Sascha Steinbiss
sascha at steinbiss.name
Thu Mar 31 22:16:33 UTC 2016
This is an automated email from the git hooks/post-receive script.
sascha-guest pushed a change to branch master
in repository augustus.
from 4312647 add ITP bug number
new 3d0e9ff add manpages contributed by upstream
new 0bf14a2 cosmetics in manpage
new 859dc5f exclude new binaries
new 34e8559 Imported Upstream version 3.2.2+dfsg
new 4ed7432 Merge tag 'upstream/3.2.2+dfsg'
new 4805a43 bump version
new 9e40fd7 remove manpages
new f3d54e8 update patches
new 129137b do not build aln2wig any more
new 93cc218 adjust file permissions
The 10 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 | 13 +-
Makefile | 18 +-
README-cgp.txt | 8 +-
README.TXT | 21 +-
auxprogs/aln2wig/Makefile | 10 +-
auxprogs/bam2hints/Makefile | 8 +-
auxprogs/bam2hints/bam2hints.cc | 2 +-
auxprogs/checkTargetSortedness/Makefile | 28 +-
.../checkTargetSortedness/checkTargetSortedness.c | 2 -
auxprogs/compileSpliceCands/Makefile | 4 +-
auxprogs/compileSpliceCands/chr21.fa | 962599 ++++++++++++++++++
auxprogs/compileSpliceCands/list.c | 10 +-
auxprogs/compileSpliceCands/out.gff | 2008 +
auxprogs/filterBam/Makefile | 2 +-
auxprogs/filterBam/src/Makefile | 21 +-
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/TODO.TXT | 13 +-
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/homGeneMapping/include/gene.hh | 4 +
auxprogs/homGeneMapping/include/projectio.hh | 0
auxprogs/homGeneMapping/src/Makefile | 102 +-
auxprogs/homGeneMapping/src/genome.cc | 61 +-
auxprogs/homGeneMapping/src/main.cc | 6 +-
auxprogs/joingenes/Makefile | 40 +-
auxprogs/joingenes/jg_ios.cpp | 63 +-
auxprogs/joingenes/jg_ios.h | 1 +
auxprogs/joingenes/jg_transcript.cpp | 442 +-
auxprogs/joingenes/jg_transcript.h | 103 +-
auxprogs/joingenes/joingenes.cpp | 5 +-
common.mk | 8 +-
config/cgp/log_reg_parameters_default.cfg | 4 +-
config/extrinsic/extrinsic.M.RM.PB.cfg | 57 +
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
.../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/coyote_tobacco_metapars.utr.cfg | 30 -
.../coyote_tobacco/coyote_tobacco_parameters.cfg | 145 -
.../coyote_tobacco_trans_shadow_partial_utr.pbl | 529 -
.../coyote_tobacco/coyote_tobacco_utr_probs.pbl | 4037 -
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/elegans/README.TXT | 3 -
config/species/elegans/elegans_exon_probs.pbl | 64243 --
config/species/elegans/elegans_igenic_probs.pbl | 27560 -
config/species/elegans/elegans_intron_probs.pbl | 21249 -
config/species/elegans/elegans_parameters.cfg | 115 -
config/species/elegans/elegans_weightmatrix.txt | 23 -
config/species/fly/fly_parameters.cgp.cfg | 30 +
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
config/species/maize/maize_splicefile.txt.gz | Bin
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 -
config/species/seahare/seahare_metapars.cfg | 48 -
config/species/seahare/seahare_parameters.cfg | 145 -
config/species/seahare/seahare_weightmatrix.txt | 23 -
.../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/volvox/volvox_exon_probs.pbl | 6641 +
config/species/volvox/volvox_igenic_probs.pbl | 2420 +
config/species/volvox/volvox_intron_probs.pbl | 6608 +
.../volvox_metapars.cfg} | 0
.../volvox_metapars.cgp.cfg} | 0
.../volvox_metapars.utr.cfg} | 0
.../volvox_parameters.cfg} | 56 +-
config/species/volvox/volvox_utr_probs.pbl | 4062 +
.../volvox_weightmatrix.txt} | 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
debian/changelog | 2 +-
debian/copyright | 11 +-
debian/mansrc/{aln2wig.1.adoc => aln2wig.1.adoc_} | 0
.../{curve2hints.1.adoc => curve2hints.1.adoc_} | 0
debian/mansrc/fastBlockSearch.1.adoc | 50 +
debian/mansrc/prepareAlign.1.adoc | 34 +
debian/patches/build_auxprogs | 203 +-
debian/patches/buildflags.patch | 79 +
debian/patches/keep_cflags | 2 +-
debian/patches/search_config_path | 2 +-
debian/patches/series | 5 +-
debian/rules | 26 +-
examples/autoAug/genome.fa.cidx | Bin 2121 -> 0 bytes
examples/autoAug/h.gff | 2 -
examples/database.db | Bin 10240 -> 0 bytes
examples/hsackI10.fa.gz | Bin 2164 -> 0 bytes
include/contTimeMC.hh | 51 +-
include/exoncand.hh | 13 +-
include/gene.hh | 15 +-
include/geneMSA.hh | 51 +-
include/graph.hh | 5 +
include/liftover.hh | 39 +-
include/orthoexon.hh | 42 +-
include/orthograph.hh | 13 +-
include/phylotree.hh | 6 +-
include/properties.hh | 4 +-
include/speciesgraph.hh | 1 +
include/statemodel.hh | 2 +-
include/types.hh | 6 +-
scripts/README.autoAug | 0
scripts/SplicedAlignment.pm | 0
scripts/autoRun.pathInfo | 0
scripts/blat2hints.pl | 2 +-
scripts/checkUTR | 0
scripts/evalCGP.pl | 27 +-
scripts/filterGenesIn_mRNAname.pl | 37 +-
scripts/gbrowse.conf | 0
scripts/getAnnoFasta.pl | 2 +
scripts/gff2ps_mycustom | 0
scripts/helpMod.pm | 0
scripts/optimize_augustus.pl | 6 +-
scripts/partition_gtf2gb.pl | 2 +-
scripts/simplifyFastaHeaders.pl | 4 +-
scripts/webserver-results.body | 0
scripts/webserver-results.head | 0
scripts/webserver-results.tail | 0
src/Makefile | 46 +-
src/alignment.cc | 6 +
src/cflags | 2 +-
src/compgenepred.cc | 177 +-
src/consensus.cc | 2 +-
src/contTimeMC.cc | 272 +-
src/cxxflags | 1 +
src/exon_seg.cc | 4 +-
src/exoncand.cc | 4 -
src/gene.cc | 2 +-
src/geneMSA.cc | 453 +-
src/graph.cc | 31 +-
src/introntrain.cc | 2 +-
src/load2sqlitedb.cc | 348 +
src/orthoexon.cc | 133 +-
src/orthograph.cc | 87 +-
src/phylotree.cc | 78 +-
src/pp_scoring.cc | 2 +-
src/properties.cc | 8 +-
src/speciesgraph.cc | 85 +-
src/types.cc | 21 +-
215 files changed, 986691 insertions(+), 166613 deletions(-)
create mode 100644 auxprogs/compileSpliceCands/chr21.fa
create mode 100644 auxprogs/compileSpliceCands/out.gff
mode change 100644 => 100755 auxprogs/filterBam/src/functions/MatePairs.cc
mode change 100644 => 100755 auxprogs/filterBam/src/functions/PairednessCoverage.cc
mode change 100644 => 100755 auxprogs/filterBam/src/functions/SingleAlignment.cc
mode change 100644 => 100755 auxprogs/filterBam/src/functions/getReferenceLength.cc
mode change 100644 => 100755 auxprogs/filterBam/src/functions/getReferenceName.cc
mode change 100644 => 100755 auxprogs/filterBam/src/functions/initOptions.cc
mode change 100644 => 100755 auxprogs/filterBam/src/functions/printCigarOperations.cc
mode change 100644 => 100755 auxprogs/filterBam/src/functions/printElapsedTime.cc
mode change 100644 => 100755 auxprogs/filterBam/src/functions/sumDandIOperations.cc
mode change 100644 => 100755 auxprogs/filterBam/src/functions/sumMandIOperations.cc
mode change 100644 => 100755 auxprogs/filterBam/src/headers/filterBam.h
mode change 100644 => 100755 auxprogs/homGeneMapping/examples/aln.hal
mode change 100644 => 100755 auxprogs/homGeneMapping/examples/gtffilenames.tbl
mode change 100644 => 100755 auxprogs/homGeneMapping/examples/gtfs/chicken.gtf
mode change 100644 => 100755 auxprogs/homGeneMapping/examples/gtfs/cow.gtf
mode change 100644 => 100755 auxprogs/homGeneMapping/examples/gtfs/human.gtf
mode change 100644 => 100755 auxprogs/homGeneMapping/examples/gtfs/human.hints.gff
mode change 100644 => 100755 auxprogs/homGeneMapping/examples/gtfs/mouse.gtf
mode change 100644 => 100755 auxprogs/homGeneMapping/examples/gtfs/mouse.hints.gff
mode change 100644 => 100755 auxprogs/homGeneMapping/examples/make.doc
mode change 100644 => 100755 auxprogs/homGeneMapping/include/projectio.hh
create mode 100644 config/extrinsic/extrinsic.M.RM.PB.cfg
mode change 100644 => 100755 config/profile/blosum55.qij
mode change 100644 => 100755 config/profile/blosum62.qij
mode change 100644 => 100755 config/species/ancylostoma_ceylanicum/README.TXT
mode change 100644 => 100755 config/species/bombus_impatiens1/bombus_impatiens1_exon_probs.pbl.withoutCRF
mode change 100644 => 100755 config/species/bombus_impatiens1/bombus_impatiens1_igenic_probs.pbl.withoutCRF
mode change 100644 => 100755 config/species/bombus_impatiens1/bombus_impatiens1_intron_probs.pbl.withoutCRF
mode change 100644 => 100755 config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig1
mode change 100644 => 100755 config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig2
mode change 100644 => 100755 config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig3
mode change 100644 => 100755 config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig4
mode change 100644 => 100755 config/species/bombus_impatiens1/bombus_impatiens1_parameters.cfg.orig5
mode change 100644 => 100755 config/species/bombus_terrestris2/bombus_terrestris2_exon_probs.pbl.withoutCRF
mode change 100644 => 100755 config/species/bombus_terrestris2/bombus_terrestris2_igenic_probs.pbl.withoutCRF
mode change 100644 => 100755 config/species/bombus_terrestris2/bombus_terrestris2_intron_probs.pbl.withoutCRF
mode change 100644 => 100755 config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig1
mode change 100644 => 100755 config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig2
mode change 100644 => 100755 config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig3
mode change 100644 => 100755 config/species/bombus_terrestris2/bombus_terrestris2_parameters.cfg.orig4
mode change 100644 => 100755 config/species/brugia/brugia_splicefile
mode change 100644 => 100755 config/species/c_elegans_trsk/c_elegans_trsk_exon_probs.pbl.withoutCRF
mode change 100644 => 100755 config/species/c_elegans_trsk/c_elegans_trsk_igenic_probs.pbl.withoutCRF
mode change 100644 => 100755 config/species/c_elegans_trsk/c_elegans_trsk_intron_probs.pbl.withoutCRF
mode change 100644 => 100755 config/species/camponotus_floridanus/README.TXT
mode change 100644 => 100755 config/species/chicken/README.TXT
delete mode 100644 config/species/coyote_tobacco/coyote_tobacco_exon_probs.pbl
delete mode 100644 config/species/coyote_tobacco/coyote_tobacco_igenic_probs.pbl
delete mode 100644 config/species/coyote_tobacco/coyote_tobacco_intron_probs.pbl
delete mode 100644 config/species/coyote_tobacco/coyote_tobacco_metapars.utr.cfg
delete mode 100644 config/species/coyote_tobacco/coyote_tobacco_parameters.cfg
delete mode 100644 config/species/coyote_tobacco/coyote_tobacco_trans_shadow_partial_utr.pbl
delete mode 100644 config/species/coyote_tobacco/coyote_tobacco_utr_probs.pbl
mode change 100644 => 100755 config/species/culex/culex_exon_probs.pbl.wech
mode change 100644 => 100755 config/species/culex/culex_igenic_probs.pbl.wech
mode change 100644 => 100755 config/species/culex/culex_intron_probs.pbl.wech
delete mode 100644 config/species/elegans/README.TXT
delete mode 100644 config/species/elegans/elegans_exon_probs.pbl
delete mode 100644 config/species/elegans/elegans_igenic_probs.pbl
delete mode 100644 config/species/elegans/elegans_intron_probs.pbl
delete mode 100644 config/species/elegans/elegans_parameters.cfg
delete mode 100644 config/species/elegans/elegans_weightmatrix.txt
create mode 100644 config/species/fly/fly_parameters.cgp.cfg
mode change 100644 => 100755 config/species/galdieria/galdieria_splicefile
mode change 100644 => 100755 config/species/honeybee1/honeybee1_exon_probs.pbl.withoutCRF
mode change 100644 => 100755 config/species/honeybee1/honeybee1_igenic_probs.pbl.withoutCRF
mode change 100644 => 100755 config/species/honeybee1/honeybee1_intron_probs.pbl.withoutCRF
mode change 100644 => 100755 config/species/honeybee1/honeybee1_parameters.cfg.orig1
mode change 100644 => 100755 config/species/human/README.TXT
mode change 100644 => 100755 config/species/maize/maize_splicefile.txt.gz
mode change 100644 => 100755 config/species/pneumocystis/README.TXT
mode change 100644 => 100755 config/species/rice/README.TXT
mode change 100644 => 100755 config/species/s_aureus/README.TXT
mode change 100644 => 100755 config/species/schistosoma/schistosoma_parameters.cfg.opt
delete mode 100644 config/species/seahare/seahare_exon_probs.pbl
delete mode 100644 config/species/seahare/seahare_exon_probs.pbl.withoutCRF
delete mode 100644 config/species/seahare/seahare_igenic_probs.pbl
delete mode 100644 config/species/seahare/seahare_igenic_probs.pbl.withoutCRF
delete mode 100644 config/species/seahare/seahare_intron_probs.pbl
delete mode 100644 config/species/seahare/seahare_intron_probs.pbl.withoutCRF
delete mode 100644 config/species/seahare/seahare_metapars.cfg
delete mode 100644 config/species/seahare/seahare_parameters.cfg
delete mode 100644 config/species/seahare/seahare_weightmatrix.txt
mode change 100644 => 100755 config/species/tribolium2012/tribolium2012_exon_probs.pbl.HMM
mode change 100644 => 100755 config/species/tribolium2012/tribolium2012_exon_probs.pbl1
mode change 100644 => 100755 config/species/tribolium2012/tribolium2012_exon_probs.pbl2
mode change 100644 => 100755 config/species/tribolium2012/tribolium2012_exon_probs.pbl3
mode change 100644 => 100755 config/species/tribolium2012/tribolium2012_exon_probs.pbl4
mode change 100644 => 100755 config/species/tribolium2012/tribolium2012_igenic_probs.pbl.HMM
mode change 100644 => 100755 config/species/tribolium2012/tribolium2012_igenic_probs.pbl1
mode change 100644 => 100755 config/species/tribolium2012/tribolium2012_igenic_probs.pbl2
mode change 100644 => 100755 config/species/tribolium2012/tribolium2012_igenic_probs.pbl3
mode change 100644 => 100755 config/species/tribolium2012/tribolium2012_igenic_probs.pbl4
mode change 100644 => 100755 config/species/tribolium2012/tribolium2012_intron_probs.pbl.HMM
mode change 100644 => 100755 config/species/tribolium2012/tribolium2012_intron_probs.pbl1
mode change 100644 => 100755 config/species/tribolium2012/tribolium2012_intron_probs.pbl2
mode change 100644 => 100755 config/species/tribolium2012/tribolium2012_intron_probs.pbl3
mode change 100644 => 100755 config/species/tribolium2012/tribolium2012_intron_probs.pbl4
mode change 100644 => 100755 config/species/tribolium2012/tribolium2012_parameters.cfg.orig1
mode change 100644 => 100755 config/species/tribolium2012/tribolium2012_parameters.cfg.orig2
mode change 100644 => 100755 config/species/tribolium2012/tribolium2012_parameters.cfg.orig3
mode change 100644 => 100755 config/species/tribolium2012/tribolium2012_parameters.cfg.orig4
mode change 100644 => 100755 config/species/tribolium2012/tribolium2012_parameters.cfg.orig5
mode change 100644 => 100755 config/species/tribolium2012/tribolium2012_parameters.cfg.orig6
mode change 100644 => 100755 config/species/tribolium2012/tribolium2012_parameters.cfg.orig7
mode change 100644 => 100755 config/species/tribolium2012/tribolium2012_utr_probs.pbl.HMM
mode change 100644 => 100755 config/species/verticillium_longisporum1/verticillium_longisporum1_parameters.cfg.orig1
create mode 100644 config/species/volvox/volvox_exon_probs.pbl
create mode 100644 config/species/volvox/volvox_igenic_probs.pbl
create mode 100644 config/species/volvox/volvox_intron_probs.pbl
rename config/species/{coyote_tobacco/coyote_tobacco_metapars.cfg => volvox/volvox_metapars.cfg} (100%)
copy config/species/{generic/generic_metapars.cgp.cfg => volvox/volvox_metapars.cgp.cfg} (100%)
rename config/species/{seahare/seahare_metapars.utr.cfg => volvox/volvox_metapars.utr.cfg} (100%)
copy config/species/{generic/generic_parameters.cfg => volvox/volvox_parameters.cfg} (76%)
create mode 100644 config/species/volvox/volvox_utr_probs.pbl
rename config/species/{coyote_tobacco/coyote_tobacco_weightmatrix.txt => volvox/volvox_weightmatrix.txt} (100%)
mode change 100644 => 100755 config/species/zebrafish/README.TXT
mode change 100644 => 100755 config/species/zebrafish/zebrafish_exon_probs.pbl.HMM
mode change 100644 => 100755 config/species/zebrafish/zebrafish_igenic_probs.pbl.HMM
mode change 100644 => 100755 config/species/zebrafish/zebrafish_intron_probs.pbl.HMM
rename debian/mansrc/{aln2wig.1.adoc => aln2wig.1.adoc_} (100%)
rename debian/mansrc/{curve2hints.1.adoc => curve2hints.1.adoc_} (100%)
create mode 100644 debian/mansrc/fastBlockSearch.1.adoc
create mode 100644 debian/mansrc/prepareAlign.1.adoc
create mode 100644 debian/patches/buildflags.patch
delete mode 100644 examples/autoAug/genome.fa.cidx
delete mode 100644 examples/autoAug/h.gff
delete mode 100644 examples/database.db
delete mode 100644 examples/hsackI10.fa.gz
mode change 100644 => 100755 scripts/README.autoAug
mode change 100644 => 100755 scripts/SplicedAlignment.pm
mode change 100644 => 100755 scripts/autoRun.pathInfo
mode change 100644 => 100755 scripts/checkUTR
mode change 100644 => 100755 scripts/gbrowse.conf
mode change 100644 => 100755 scripts/gff2ps_mycustom
mode change 100644 => 100755 scripts/helpMod.pm
mode change 100644 => 100755 scripts/webserver-results.body
mode change 100644 => 100755 scripts/webserver-results.head
mode change 100644 => 100755 scripts/webserver-results.tail
create mode 100644 src/cxxflags
create mode 100644 src/load2sqlitedb.cc
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