"Fossies" - the Fresh Open Source Software Archive  

Source code changes report for "augustus" between the packages
augustus-3.3.3.tar.gz and augustus-3.4.0.tar.gz

About: AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.

Summary:

The "augustus" source code changed by about 22.1% and now consists of 2642 regular files (+647), 9 symbolic links and 378 directories (+124).

Related Informations:

See docs/HISTORY.TXT (augustus 3.4.0).

Changes In Files (According File Type):

File TypeTotalAddedRemovedChanged
Header file 102 3 2 17
C program 10 1 1 2
C++ program 112 6 4 30
Patch 1 1 0 0
Perl module 3 0 0 1
Perl program 101 2 1 26
Python program 25 22 0 3
Shell program 7 2 0 0
Python compiled program 11 11 0 0
Configuration file 445 148 1 1
Executable file 23 11 1 7
JavaScript file 3 0 0 0
JSON file 168 41 0 0
Makefile 21 0 1 14
Man page 17 5 3 7
Symbolic link 9 0 0 0
Berkeley database 4 1 0 0
Compiled object 1 0 1 0
CSS style sheet 4 0 0 0
Data List 5 0 0 0
Doxygen file 1 0 0 0
Git file 3 1 1 0
HTML page 42 1 1 3
MS office document 4 1 1 0
Options file 1 0 0 0
TeX document 1 0 0 0
YAML file 1 1 0 0
Audio file 2 0 0 0
Data file 91 13 2 0
Image file 19 0 0 0
PDF file 9 0 0 0
Vector Image file 1 0 0 0
Directory 380 126 2 0
Archive 4 0 0 0
Information file 3 1 1 0
License 4 0 0 0
Readme file 77 37 2 3
Text file 1322 374 15 14
Other 33 3 1 0
Total Files307081241128



Header Files (22 of 102):

NameStatusDeltaVisual Diff
auxprogs/homGeneMapping/include/genome.hh changed 0.4% diff
include/alignment.hh changed 51.3% diff
include/codonevo.hh added
include/codonMSA.hh changed 3.5% diff
include/compgenepred.hh changed 100.0% diff
include/consensus.hh removed
include/contTimeMC.hh changed 52.1% diff
include/exon_seg.hh removed
include/exoncand.hh changed 0.8% diff
include/genbank.hh changed 14.6% diff
include/gene.hh changed 0.2% diff
include/geneMSA.hh changed 23.6% diff
include/genomicMSA.hh changed 12.3% diff
include/orthoexon.hh changed 0.9% diff
include/pp_hitseq.hh changed 0.8% diff
include/pp_profile.hh changed 100.0% diff
include/pp_simscore.hh added
include/properties.hh changed 12.3% diff
include/randseqaccess.hh changed 1.6% diff
include/tokenizer.hh added
include/types.hh changed 4.7% diff
include/vitmatrix.hh changed 1.4% diff

C Programs (4 of 10):

NameStatusDeltaVisual Diff
auxprogs/bam2wig/bam2wig.c changed 32.6% diff
auxprogs/checkTargetSortedness/checkTargetSortedness.c removed
auxprogs/compileSpliceCands/compileSpliceCands.c changed 5.9% diff
auxprogs/joingenes/jg_transcript.cpp.backup added

C++ Programs (40 of 112):

NameStatusDeltaVisual Diff
auxprogs/homGeneMapping/src/genome.cc changed 0.1% diff
auxprogs/homGeneMapping/src/main.cc changed 1.9% diff
auxprogs/joingenes/jg_transcript.cpp changed 1.2% diff
src/alignment.cc changed 9.8% diff
src/augustus.cc changed 34.1% diff
src/codonevo.cc added
src/compgenepred.cc changed 86.0% diff
src/consensus.cc removed
src/consensusFinder.cc removed
src/contTimeMC.cc changed 62.4% diff
src/curve2hints.cc removed
src/espoca.cc changed 3.8% diff
src/etraining.cc changed 0.8% diff
src/exon_seg.cc removed
src/exoncand.cc changed 0.9% diff
src/exonmodel.cc changed 10.3% diff
src/exontrain.cc changed 0.05% diff
src/fastBlockSearch.cc changed 0.6% diff
src/genbank.cc changed 8.0% diff
src/gene.cc changed 0.6% diff
src/geneMSA.cc changed 9.3% diff
src/genomicMSA.cc changed 9.2% diff
src/getSeq.cc changed 15.2% diff
src/igenicmodel.cc changed 25.0% diff
src/load2db.cc changed 0.2% diff
src/load2sqlitedb.cc changed 1.0% diff
src/merkmal.cc changed 0.03% diff
src/orthoexon.cc changed 7.8% diff
src/orthograph.cc changed 1.8% diff
src/phylotree.cc changed 1.0% diff
src/pp_profile.cc changed 65.0% diff
src/pp_simscore.cc added
src/properties.cc changed 1.6% diff
src/randseqaccess.cc changed 2.1% diff
src/tokenizer.cc added
src/train_logReg_param.cc changed 23.0% diff
src/types.cc changed 3.9% diff
src/unittests/alignment_unittest.cc added
src/unittests/codonevo_unittest.cc added
src/unittests/evo_unittest.cc added

Patches (all 1):

NameStatusDeltaVisual Diff
auxprogs/joingenes/issue182.patch added

Perl Modules (1 of 3):

NameStatusDeltaVisual Diff
scripts/helpMod.pm changed 28.1% diff

Perl Programs (29 of 101):

NameStatusDeltaVisual Diff
auxprogs/utrrnaseq/scripts/gff2lst.pl changed 0.9% diff
auxprogs/utrrnaseq/scripts/test_utr_wrapper.pl changed 0.2% diff
docs/tutorial/data/gff2browser.pl changed 3.9% diff
docs/tutorial2018/BRAKER_v2.0.4+/align2hints.pl changed 0.1% diff
scripts/aa2nonred.pl changed 9.7% diff
scripts/add_name_to_gff3.pl added
scripts/autoAug.pl changed 23.9% diff
scripts/autoAugPred.pl changed 23.8% diff
scripts/autoAugTrain.pl changed 15.1% diff
scripts/blat2gbrowse.pl changed 41.3% diff
scripts/blat2hints.pl changed 63.6% diff
scripts/block2prfl.pl changed 0.3% diff
scripts/compare_masking.pl changed 1.3% diff
scripts/createAugustusJoblist.pl changed 1.3% diff
scripts/del_from_prfl.pl changed 1.1% diff
scripts/filter-ppx.pl changed 8.2% diff
scripts/filterGenesIn_mRNAname.pl changed 1.7% diff
scripts/fix_joingenes_gtf.pl changed 21.2% diff
scripts/get_loci_from_gb.pl added
scripts/gff2gbSmallDNA.pl changed 9.8% diff
scripts/gtf2gff.pl changed 1.9% diff
scripts/merge_masking.pl changed 1.3% diff
scripts/moveParameters.pl changed 44.4% diff
scripts/msa2prfl.pl changed 0.2% diff
scripts/optimize_augustus.pl changed 3.0% diff
scripts/prints2prfl.pl changed 0.3% diff
scripts/ratewig.pl removed
scripts/writeResultsPage.pl changed 31.9% diff
scripts/yaml2gff.1.4.pl changed 5.2% diff

Python Programs (all 25):

NameStatusDeltaVisual Diff
scripts/augustify.py added
scripts/bamToWig.py changed 0.8% diff
scripts/executeTestCGP.py added
scripts/extractAnno.py added
scripts/fix_in_frame_stop_codon_genes.py changed 9.8% diff
scripts/getAnnoFastaFromJoingenes.py changed 6.7% diff
tests/__init__.py added
tests/auxprogs/bam2wig/test_bam2wig.py added
tests/auxprogs/homGeneMapping/test_homGeneMapping.py added
tests/examples/__init__.py added
tests/examples/aug_comparator.py added
tests/examples/aug_out_filter.py added
tests/examples/create_default_config.py added
tests/examples/testcases.py added
tests/longrunning/cgp/executeTestCGP.py added
tests/longrunning/check_latest_commit_influx.py added
tests/longrunning/extract_accuracy_values.py added
tests/longrunning/lr_util.py added
tests/longrunning/single_genome/test_single.py added
tests/longrunning/write_to_influx.py added
tests/utils/__init__.py added
tests/utils/aug_argparse.py added
tests/utils/aug_assertions.py added
tests/utils/aug_path.py added
tests/utils/aug_process.py added

Shell Programs (2 of 7):

NameStatusDeltaVisual Diff
tests/examples/buildTools added
tests/examples/installDependencies added

Python Compiled Programs (all 11):

NameStatusDeltaVisual Diff
tests/__pycache__/__init__.cpython-38.pyc added
tests/examples/__pycache__/__init__.cpython-38.pyc added
tests/examples/__pycache__/aug_comparator.cpython-38.pyc added
tests/examples/__pycache__/aug_out_filter.cpython-38.pyc added
tests/examples_test/__pycache__/aug_comparator.cpython-38.pyc added
tests/examples_test/__pycache__/aug_out_filter.cpython-38.pyc added
tests/utils/__pycache__/__init__.cpython-38.pyc added
tests/utils/__pycache__/aug_argparse.cpython-38.pyc added
tests/utils/__pycache__/aug_assertions.cpython-38.pyc added
tests/utils/__pycache__/aug_path.cpython-38.pyc added
tests/utils/__pycache__/aug_process.cpython-38.pyc added

Configuration Files (150 of 445):

NameStatusDeltaVisual Diff
config/cgp/cgp_param_21features_accuracy_largerGrid.convDivCorrect.cfg added
config/cgp/log_reg_parameters_trained.cfg added
config/extrinsic/extrinsic.MPE.cfg changed 67.7% diff
config/species/Argopecten_irradians/Argopecten_irradians_metapars.cfg added
config/species/Argopecten_irradians/Argopecten_irradians_metapars.cgp.cfg added
config/species/Argopecten_irradians/Argopecten_irradians_metapars.utr.cfg added
config/species/Argopecten_irradians/Argopecten_irradians_parameters.cfg added
config/species/Aurelia_aurita/Aurelia_aurita_metapars.cfg added
config/species/Aurelia_aurita/Aurelia_aurita_metapars.cgp.cfg added
config/species/Aurelia_aurita/Aurelia_aurita_metapars.utr.cfg added
config/species/Aurelia_aurita/Aurelia_aurita_parameters.cfg added
config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_metapars.cfg added
config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_metapars.cgp.cfg added
config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_metapars.utr.cfg added
config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_parameters.cfg added
config/species/Cassiopea_xamachana/Cassiopea_xamachana_metapars.cfg added
config/species/Cassiopea_xamachana/Cassiopea_xamachana_metapars.cgp.cfg added
config/species/Cassiopea_xamachana/Cassiopea_xamachana_metapars.utr.cfg added
config/species/Cassiopea_xamachana/Cassiopea_xamachana_parameters.cfg added
config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_metapars.cfg added
config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_metapars.cgp.cfg added
config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_metapars.utr.cfg added
config/species/Chlamydomonas_eustigma/Chlamydomonas_eustigma_parameters.cfg added
config/species/Chloropicon_primus/Chloropicon_primus_metapars.cfg added
config/species/Chloropicon_primus/Chloropicon_primus_metapars.cgp.cfg added
config/species/Chloropicon_primus/Chloropicon_primus_metapars.utr.cfg added
config/species/Chloropicon_primus/Chloropicon_primus_parameters.cfg added
config/species/Chrysaora_chesapeakeij/Chrysaora_chesapeakei_metapars.cfg added
config/species/Chrysaora_chesapeakeij/Chrysaora_chesapeakei_metapars.cgp.cfg added
config/species/Chrysaora_chesapeakeij/Chrysaora_chesapeakei_metapars.utr.cfg added
config/species/Chrysaora_chesapeakeij/Chrysaora_chesapeakei_parameters.cfg added
config/species/Dunaliella_salina/Dunaliella_salina_metapars.cfg added
config/species/Dunaliella_salina/Dunaliella_salina_metapars.cgp.cfg added
config/species/Dunaliella_salina/Dunaliella_salina_metapars.utr.cfg added
config/species/Dunaliella_salina/Dunaliella_salina_parameters.cfg added
config/species/Ectocarpus_siliculosus/Ectocarpus_siliculosus_metapars.cfg added
config/species/Ectocarpus_siliculosus/Ectocarpus_siliculosus_metapars.cgp.cfg added
config/species/Ectocarpus_siliculosus/Ectocarpus_siliculosus_metapars.utr.cfg added
config/species/Ectocarpus_siliculosus/Ectocarpus_siliculosus_parameters.cfg added
config/species/Encephalitozoon_cuniculi/Encephalitozoon_cuniculi_metapars.cfg added
config/species/Encephalitozoon_cuniculi/Encephalitozoon_cuniculi_metapars.cgp.cfg added
config/species/Encephalitozoon_cuniculi/Encephalitozoon_cuniculi_metapars.utr.cfg added
config/species/Encephalitozoon_cuniculi/Encephalitozoon_cuniculi_parameters.cfg added
config/species/Fistulifera_solaris/Fistulifera_solaris_metapars.cfg added
config/species/Fistulifera_solaris/Fistulifera_solaris_metapars.cgp.cfg added
config/species/Fistulifera_solaris/Fistulifera_solaris_metapars.utr.cfg added
config/species/Fistulifera_solaris/Fistulifera_solaris_parameters.cfg added
config/species/Fragilariopsis_cylindrus_CCMP1102/Fragilariopsis_cylindrus_CCMP1102_metapars.cfg added
config/species/Fragilariopsis_cylindrus_CCMP1102/Fragilariopsis_cylindrus_CCMP1102_metapars.cgp.cfg added
config/species/Fragilariopsis_cylindrus_CCMP1102/Fragilariopsis_cylindrus_CCMP1102_metapars.utr.cfg added
config/species/Fragilariopsis_cylindrus_CCMP1102/Fragilariopsis_cylindrus_CCMP1102_parameters.cfg added
config/species/gigaspora_margarita/gigaspora_margarita_metapars.cfg added
config/species/gigaspora_margarita/gigaspora_margarita_metapars.cgp.cfg added
config/species/gigaspora_margarita/gigaspora_margarita_metapars.utr.cfg added
config/species/gigaspora_margarita/gigaspora_margarita_parameters.cfg added
config/species/gigaspora_margarita/gth.cfg added
config/species/Gonapodya_prolifera/Gonapodya_prolifera_metapars.cfg added
config/species/Gonapodya_prolifera/Gonapodya_prolifera_metapars.cgp.cfg added
config/species/Gonapodya_prolifera/Gonapodya_prolifera_metapars.utr.cfg added
config/species/Gonapodya_prolifera/Gonapodya_prolifera_parameters.cfg added
config/species/human_longrunningtest_crf/human_longrunningtest_crf_metapars.cfg added
config/species/human_longrunningtest_crf/human_longrunningtest_crf_metapars.cgp.cfg added
config/species/human_longrunningtest_crf/human_longrunningtest_crf_metapars.utr.cfg added
config/species/human_longrunningtest_crf/human_longrunningtest_crf_parameters.cfg added
config/species/human_longrunningtest_hmm/human_longrunningtest_hmm_metapars.cfg added
config/species/human_longrunningtest_hmm/human_longrunningtest_hmm_metapars.cgp.cfg added
config/species/human_longrunningtest_hmm/human_longrunningtest_hmm_metapars.utr.cfg added
config/species/human_longrunningtest_hmm/human_longrunningtest_hmm_parameters.cfg added
config/species/hymenolepis_microstoma/hymenolepis_microstoma_metapars.cfg added
config/species/hymenolepis_microstoma/hymenolepis_microstoma_metapars.cgp.cfg added
config/species/hymenolepis_microstoma/hymenolepis_microstoma_metapars.utr.cfg added
config/species/hymenolepis_microstoma/hymenolepis_microstoma_parameters.cfg added
config/species/Micromonas_commoda/Micromonas_commoda_metapars.cfg added
config/species/Micromonas_commoda/Micromonas_commoda_metapars.cgp.cfg added
config/species/Micromonas_commoda/Micromonas_commoda_metapars.utr.cfg added
config/species/Micromonas_commoda/Micromonas_commoda_parameters.cfg added
config/species/Micromonas_pusilla/Micromonas_pusilla_metapars.cfg added
config/species/Micromonas_pusilla/Micromonas_pusilla_metapars.cgp.cfg added
config/species/Micromonas_pusilla/Micromonas_pusilla_metapars.utr.cfg added
config/species/Micromonas_pusilla/Micromonas_pusilla_parameters.cfg added
config/species/Monoraphidium_neglectum/Monoraphidium_neglectum_metapars.cfg added
config/species/Monoraphidium_neglectum/Monoraphidium_neglectum_metapars.cgp.cfg added
config/species/Monoraphidium_neglectum/Monoraphidium_neglectum_metapars.utr.cfg added
config/species/Monoraphidium_neglectum/Monoraphidium_neglectum_parameters.cfg added
config/species/Nemopilema_nomurai/Nemopilema_nomurai_metapars.cfg added
config/species/Nemopilema_nomurai/Nemopilema_nomurai_metapars.cgp.cfg added
config/species/Nemopilema_nomurai/Nemopilema_nomurai_metapars.utr.cfg added
config/species/Nemopilema_nomurai/Nemopilema_nomurai_parameters.cfg added
config/species/Notospermus_geniculatus/Notospermus_geniculatus_metapars.cfg added
config/species/Notospermus_geniculatus/Notospermus_geniculatus_metapars.cgp.cfg added
config/species/Notospermus_geniculatus/Notospermus_geniculatus_metapars.utr.cfg added
config/species/Notospermus_geniculatus/Notospermus_geniculatus_parameters.cfg added
config/species/Ostreococcus_sp_lucimarinus/Ostreococcus_sp_lucimarinus_metapars.cfg added
config/species/Ostreococcus_sp_lucimarinus/Ostreococcus_sp_lucimarinus_metapars.cgp.cfg added
config/species/Ostreococcus_sp_lucimarinus/Ostreococcus_sp_lucimarinus_metapars.utr.cfg added
config/species/Ostreococcus_sp_lucimarinus/Ostreococcus_sp_lucimarinus_parameters.cfg added
config/species/Ostreococcus_tauri/Ostreococcus_tauri_metapars.cfg added
config/species/Ostreococcus_tauri/Ostreococcus_tauri_metapars.cgp.cfg added
config/species/Ostreococcus_tauri/Ostreococcus_tauri_metapars.utr.cfg added
config/species/Ostreococcus_tauri/Ostreococcus_tauri_parameters.cfg added
config/species/Phaeodactylum_tricornutum/Phaeodactylum_tricornutum_metapars.cfg added
config/species/Phaeodactylum_tricornutum/Phaeodactylum_tricornutum_metapars.cgp.cfg added
config/species/Phaeodactylum_tricornutum/Phaeodactylum_tricornutum_metapars.utr.cfg added
config/species/Phaeodactylum_tricornutum/Phaeodactylum_tricornutum_parameters.cfg added
config/species/Pseudo-nitzschia_multistriata/Pseudo-nitzschia_multistriata_metapars.cfg added
config/species/Pseudo-nitzschia_multistriata/Pseudo-nitzschia_multistriata_metapars.cgp.cfg added
config/species/Pseudo-nitzschia_multistriata/Pseudo-nitzschia_multistriata_metapars.utr.cfg added
config/species/Pseudo-nitzschia_multistriata/Pseudo-nitzschia_multistriata_parameters.cfg added
config/species/Ptychodera_flava/Ptychodera_flava_metapars.cfg added
config/species/Ptychodera_flava/Ptychodera_flava_metapars.cgp.cfg added
config/species/Ptychodera_flava/Ptychodera_flava_metapars.utr.cfg added
config/species/Ptychodera_flava/Ptychodera_flava_parameters.cfg added
config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_metapars.cfg added
config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_metapars.cgp.cfg added
config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_metapars.utr.cfg added
config/species/Raphidocelis_subcapitata/Raphidocelis_subcapitata_parameters.cfg added
config/species/Rhopilema_esculentum/Rhopilema_esculentum_metapars.cfg added
config/species/Rhopilema_esculentum/Rhopilema_esculentum_metapars.cgp.cfg added
config/species/Rhopilema_esculentum/Rhopilema_esculentum_metapars.utr.cfg added
config/species/Rhopilema_esculentum/Rhopilema_esculentum_parameters.cfg added
config/species/Sordaria_macrospora/Sordaria_macrospora_metapars.cfg added
config/species/Sordaria_macrospora/Sordaria_macrospora_metapars.cgp.cfg added
config/species/Sordaria_macrospora/Sordaria_macrospora_metapars.utr.cfg added
config/species/Sordaria_macrospora/Sordaria_macrospora_parameters.cfg added
config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_metapars.cfg added
config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_metapars.cgp.cfg added
config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_metapars.utr.cfg added
config/species/Sphaceloma_murrayae/Sphaceloma_murrayae_parameters.cfg added
config/species/Thalassiosira_pseudonana_CCMP1335/Thalassiosira_pseudonana_CCMP1335_metapars.cfg added
config/species/Thalassiosira_pseudonana_CCMP1335/Thalassiosira_pseudonana_CCMP1335_metapars.cgp.cfg added
config/species/Thalassiosira_pseudonana_CCMP1335/Thalassiosira_pseudonana_CCMP1335_metapars.utr.cfg added
config/species/Thalassiosira_pseudonana_CCMP1335/Thalassiosira_pseudonana_CCMP1335_parameters.cfg added
config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_metapars.cfg added
config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_metapars.cgp.cfg added
config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_metapars.utr.cfg added
config/species/Trichoplax_adhaerens/Trichoplax_adhaerens_parameters.cfg added
config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_metapars.cfg added
config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_metapars.cgp.cfg added
config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_metapars.utr.cfg added
config/species/Vitrella_brassicaformis/Vitrella_brassicaformis_parameters.cfg added
config/species/Xiphophorus_maculatus/Xiphophorus_maculatus_parameters.cfg added
doxygen.conf removed
tests/examples/expected_results/test_training_new_species/test_aug_dev_species/test_aug_dev_species
_metapars.cfg
added
tests/examples/expected_results/test_training_new_species/test_aug_dev_species/test_aug_dev_species
_metapars.cgp.cfg
added
tests/examples/expected_results/test_training_new_species/test_aug_dev_species/test_aug_dev_species
_metapars.utr.cfg
added
tests/examples/expected_results/test_training_new_species/test_aug_dev_species/test_aug_dev_species
_parameters.cfg
added
tests/examples_test_results/test_training_new_species/test_aug_dev_species/test_aug_dev_species_met
apars.cfg
added
tests/examples_test_results/test_training_new_species/test_aug_dev_species/test_aug_dev_species_met
apars.cgp.cfg
added
tests/examples_test_results/test_training_new_species/test_aug_dev_species/test_aug_dev_species_met
apars.utr.cfg
added
tests/examples_test_results/test_training_new_species/test_aug_dev_species/test_aug_dev_species_par
ameters.cfg
added

Executable Files (19 of 23):

NameStatusDeltaVisual Diff
auxprogs/aln2wig/aln2wig added
auxprogs/bam2hints/bam2hints added
auxprogs/bam2wig/bam2wig added
auxprogs/compileSpliceCands/compileSpliceCands added
auxprogs/homGeneMapping/src/homGeneMapping changed 71.5% diff
auxprogs/joingenes/joingenes added
auxprogs/utrrnaseq/Debug/utrrnaseq added
bin/aln2wig changed 37.5% diff
bin/augustus changed skipped
bin/bam2hints changed 38.6% diff
bin/bam2wig changed skipped
bin/compileSpliceCands added
bin/etraining changed skipped
bin/fastBlockSearch changed skipped
bin/filterBam changed 90.7% diff
bin/getSeq added
bin/homGeneMapping changed 71.5% diff
bin/joingenes changed 87.7% diff
bin/load2db added
bin/load2sqlitedb added
bin/pp_simScore added
bin/prepareAlign changed 37.8% diff
bin/utrrnaseq removed

JSON Files (41 of 168):

NameStatusDeltaVisual Diff
config/species/Argopecten_irradians/Argopecten_irradians_igenic_probs.pbl added
config/species/Aurelia_aurita/Aurelia_aurita_igenic_probs.pbl added
config/species/Bathycoccus_prasinos/Bathycoccus_prasinos_igenic_probs.pbl added
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tests/examples_test_results/test_cgp_with_db/pred/bosTau4.cgp.filtered.gff added
tests/examples_test_results/test_cgp_with_db/pred/galGal3.cgp.filtered.gff added
tests/examples_test_results/test_cgp_with_db/pred/hg19.cgp.filtered.gff added
tests/examples_test_results/test_cgp_with_db/pred/mm9.cgp.filtered.gff added
tests/examples_test_results/test_cgp_with_db_hints/pred/bosTau4.cgp.filtered.gff added
tests/examples_test_results/test_cgp_with_db_hints/pred/galGal3.cgp.filtered.gff added
tests/examples_test_results/test_cgp_with_db_hints/pred/hg19.cgp.filtered.gff added
tests/examples_test_results/test_cgp_with_db_hints/pred/mm9.cgp.filtered.gff added
tests/examples_test_results/test_format_and_error_out/augustus.gff3 added
tests/examples_test_results/test_hints_MPE/aug_hints_MPE.gff added
tests/examples_test_results/test_training_new_species/test_aug_dev_species/test_aug_dev_species_exo
n_probs.pbl
added
tests/examples_test_results/test_training_new_species/test_aug_dev_species/test_aug_dev_species_int
ron_probs.pbl
added
tests/examples_test_results/test_training_new_species/test_aug_dev_species/test_aug_dev_species_wei
ghtmatrix.txt
added
tests/examples_test_results/test_utr_on/aug_utr_on.gff added

Other Files (4 of 33):

NameStatusDeltaVisual Diff
auxprogs/bam2wig/test.s.bam moved 0.0%
tests/auxprogs/bam2wig/test_files/test.s.bam
tests/examples/expected_results/test_format_and_error_out/augustus.err added
tests/examples_test_results/test_format_and_error_out/augustus.err added

Packages Compared:

augustus-3.3.3.tar.gz
augustus-3.4.0.tar.gz


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