Augustus: Source code changes report for 3.4.0 vs. 3.5.0

Summary:

The "Augustus" source code changed by about 39.4% and now consists of 2587 regular files (-55), 5 symbolic links (-4) and 353 directories (-25).

Related Informations:

See docs/HISTORY.TXT (Augustus 3.5.0).

Changes In Files (According File Type):

File Type	Total	Added	Removed	Changed
Header file	116	16	2	11
C program	9	0	1	2
C++ program	110	2	6	28
Patch	1	0	1	0
Perl module	3	0	0	0
Perl program	102	2	0	7
Python program	47	22	13	6
Shell program	9	2	3	1
Python compiled program	11	0	11	0
Configuration file	553	109	22	4
Executable file	22	0	22	0
JavaScript file	3	0	0	0
JSON file	197	29	8	1
Makefile	22	2	5	14
Man page	14	0	0	3
Module-Definition file	1	1	0	0
Symbolic link	12	3	8	0
Berkeley database	4	0	3	0
CSS style sheet	4	0	0	0
Data List	6	1	0	0
Doxygen file	1	0	0	0
Git file	3	1	1	0
HTML page	43	2	1	1
MS office document	3	0	0	0
Options file	1	0	0	0
TeX document	1	0	0	0
YAML file	3	2	0	0
Audio file	2	0	0	0
Data file	115	12	24	0
Image file	5	0	0	0
PDF file	9	0	0	0
Vector Image file	1	0	0	0
Directory	458	80	105	0
Archive	6	2	1	0
Information file	3	1	0	1
License	4	0	1	0
Readme file	103	28	3	12
Text file	1500	193	357	10
Other	42	10	6	0
Total Files	3549	520	604	101

Header Files (29 of 116):

Name	Status	Delta	Visual Diff
auxprogs/filterBam/src/bamtools/bamtools_sort.h	removed
auxprogs/filterBam/src/bamtools/bamtools_tool.h	removed
auxprogs/filterBam/src/headers/bamaccess.hh	added
auxprogs/filterBam/src/headers/bamseqlibaccess.hh	added
auxprogs/filterBam/src/headers/bamtoolsaccess.hh	added
auxprogs/filterBam/src/headers/filterBam.h	changed	63.7%	diff
include/compgenepred.hh	changed	5.3%	diff
include/contTimeMC.hh	changed	8.5%	diff
include/fasta.hh	changed	38.3%	diff
include/gene.hh	changed	12.5%	diff
include/hints.hh	changed	1.7%	diff
include/json.hpp	added
include/namgene.hh	changed	5.0%	diff
include/properties.hh	changed	53.6%	diff
include/randseqaccess.hh	changed	0.5%	diff
include/table_structure.h	changed	3.0%	diff
include/types.hh	changed	2.0%	diff
tests/short/auxprogs/filterbam/expected_results/example_paired.paired.sam	added
tests/short/auxprogs/filterbam/expected_results/example_paired.paired_maxIntronLen100.sam	added
tests/short/auxprogs/filterbam/expected_results/example_paired.paired_pairwiseAlignments.sam	added
tests/short/auxprogs/filterbam/expected_results/example_pairwise.paired_pairwiseAlignments.sam	added
tests/short/auxprogs/filterbam/expected_results/example_pairwise_calmd.best.sam	added
tests/short/auxprogs/filterbam/expected_results/example_pairwise_calmd.no_options.sam	added
tests/short/auxprogs/filterbam/expected_results/example_pairwise_calmd.paired_pairwiseAlignments.sa m	added
tests/short/auxprogs/filterbam/expected_results/example_pairwise_calmd.uniq.sam	added
tests/short/auxprogs/filterbam/expected_results/example_pairwise_calmd_seq_with_equalsigns.best.sam	added
tests/short/auxprogs/filterbam/expected_results/example_pairwise_calmd_seq_with_equalsigns.no_optio ns.sam	added
tests/short/auxprogs/filterbam/expected_results/example_pairwise_calmd_seq_with_equalsigns.paired_p airwiseAlignments.sam	added
tests/short/auxprogs/filterbam/expected_results/example_pairwise_calmd_seq_with_equalsigns.uniq.sam	added

C Programs (3 of 9):

Name	Status	Delta	Visual Diff
auxprogs/aln2wig/aln2wig.c	changed	88.5%	diff
auxprogs/compileSpliceCands/list.c	changed	0.6%	diff
auxprogs/joingenes/jg_transcript.cpp.backup	removed

C++ Programs (36 of 110):

Name	Status	Delta	Visual Diff
auxprogs/bam2hints/bam2hints.cc	changed	10.1%	diff
auxprogs/filterBam/src/BamSeqLibAccess.cc	added
auxprogs/filterBam/src/BamToolsAccess.cc	added
auxprogs/filterBam/src/filterBam.cc	changed	37.8%	diff
auxprogs/filterBam/src/functions/getReferenceLength.cc	removed
auxprogs/filterBam/src/functions/getReferenceName.cc	removed
auxprogs/filterBam/src/functions/initOptions.cc	changed	70.1%	diff
auxprogs/filterBam/src/functions/MatePairs.cc	changed	37.3%	diff
auxprogs/filterBam/src/functions/PairednessCoverage.cc	changed	36.5%	diff
auxprogs/filterBam/src/functions/printCigarOperations.cc	removed
auxprogs/filterBam/src/functions/printElapsedTime.cc	changed	28.2%	diff
auxprogs/filterBam/src/functions/SingleAlignment.cc	removed
auxprogs/filterBam/src/functions/sumDandIOperations.cc	removed
auxprogs/filterBam/src/functions/sumMandIOperations.cc	removed
auxprogs/joingenes/jg_ios.cpp	changed	0.7%	diff
src/augustus.cc	changed	7.8%	diff
src/compgenepred.cc	changed	1.6%	diff
src/contTimeMC.cc	changed	4.4%	diff
src/extrinsicinfo.cc	changed	0.4%	diff
src/fasta.cc	changed	14.1%	diff
src/genbank.cc	changed	0.9%	diff
src/gene.cc	changed	1.5%	diff
src/geneMSA.cc	changed	0.7%	diff
src/genomicMSA.cc	changed	0.2%	diff
src/hints.cc	changed	0.4%	diff
src/intronmodel.cc	changed	4.9%	diff
src/load2db.cc	changed	0.7%	diff
src/namgene.cc	changed	1.2%	diff
src/phylotree.cc	changed	3.3%	diff
src/pp_profile.cc	changed	0.2%	diff
src/properties.cc	changed	95.4%	diff
src/randseqaccess.cc	changed	1.8%	diff
src/unittests/codonevo_unittest.cc	changed	1.4%	diff
src/unittests/evo_unittest.cc	changed	20.3%	diff
src/unittests/fasta_unittest.cc	changed	2.3%	diff
src/vitmatrix.cc	changed	0.3%	diff

Patches (all 1):

Name	Status	Delta	Visual Diff
auxprogs/joingenes/issue182.patch	removed

Perl Programs (9 of 102):

Name	Status	Delta	Visual Diff
auxprogs/utrrnaseq/scripts/test_utr_wrapper.pl	changed	6.8%	diff
scripts/add_name_to_gff3.pl	changed	0.4%	diff
scripts/createAugustusJoblist.pl	changed	6.6%	diff
scripts/gff2gbSmallDNA.pl	changed	4.9%	diff
scripts/join_aug_pred.pl	changed	3.7%	diff
scripts/optimize_augustus.pl	changed	0.2%	diff
scripts/rename_species.pl	added
scripts/simplifyFastaHeaders.pl	changed	12.1%	diff
src/makedepend.pl	added

Python Programs (41 of 47):

Name	Status	Delta	Visual Diff
scripts/augustify.py	changed	42.2%	diff
scripts/extractAnno.py	changed	3.1%	diff
scripts/findRepetitiveProtSeqs.py	added
scripts/getAnnoFastaFromJoingenes.py	changed	1.3%	diff
scripts/stringtie2fa.py	added
tests/__init__.py	removed
tests/auxprogs/bam2wig/test_bam2wig.py	moved	44.5%	diff
tests/short/auxprogs/bam2wig/test_bam2wig.py	moved	44.5%	diff
tests/auxprogs/homGeneMapping/test_homGeneMapping.py	removed
tests/examples/__init__.py	moved	0.0%
tests/short/examples/__init__.py	moved	0.0%
tests/examples/aug_comparator.py	moved	0.0%
tests/short/utils/aug_comparator.py	moved	0.0%
tests/examples/aug_out_filter.py	moved	18.3%	diff
tests/short/utils/aug_out_filter.py	moved	18.3%	diff
tests/examples/create_default_config.py	moved	0.0%
tests/short/examples/create_default_config.py	moved	0.0%
tests/examples/testcases.py	removed
tests/longrunning/cgp/executeTestCGP.py	changed	1.7%	diff
tests/longrunning/extract_accuracy_values.py	changed	0.7%	diff
tests/longrunning/single_genome/test_single.py	changed	11.9%	diff
tests/short/__init__.py	added
tests/short/auxprogs/__init__.py	added
tests/short/auxprogs/bam2hints/__init__.py	added
tests/short/auxprogs/bam2hints/test_bam2hints.py	added
tests/short/auxprogs/bam2wig/__init__.py	added
tests/short/auxprogs/filterbam/__init__.py	added
tests/short/auxprogs/filterbam/test_filterbam.py	added
tests/short/auxprogs/homgenemapping/__init__.py	added
tests/short/auxprogs/homgenemapping/test_homgenemapping.py	added
tests/short/examples/test_examples.py	added
tests/short/execute_test.py	added
tests/utils/__init__.py	moved	0.0%
tests/short/utils/__init__.py	moved	0.0%
tests/utils/aug_argparse.py	removed
tests/utils/aug_assertions.py	moved	15.2%	diff
tests/short/utils/aug_assertions.py	moved	15.2%	diff
tests/utils/aug_path.py	moved	0.0%
tests/short/utils/aug_path.py	moved	0.0%
tests/utils/aug_process.py	moved	6.7%	diff
tests/short/utils/aug_process.py	moved	6.7%	diff

Shell Programs (6 of 9):

Name	Status	Delta	Visual Diff
auxprogs/filterBam/data/sam2bam.sh	removed
auxprogs/utrrnaseq/integration_test/test.sh	changed	27.9%	diff
tests/examples/buildTools	removed
tests/examples/installDependencies	removed
tests/pyclean.sh	added
tests/short/utils/installDependencies.sh	added

Python Compiled Programs (all 11):

Name	Status	Delta	Visual Diff
tests/__pycache__/__init__.cpython-38.pyc	removed
tests/examples/__pycache__/__init__.cpython-38.pyc	removed
tests/examples/__pycache__/aug_comparator.cpython-38.pyc	removed
tests/examples/__pycache__/aug_out_filter.cpython-38.pyc	removed
tests/examples_test/__pycache__/aug_comparator.cpython-38.pyc	removed
tests/examples_test/__pycache__/aug_out_filter.cpython-38.pyc	removed
tests/utils/__pycache__/__init__.cpython-38.pyc	removed
tests/utils/__pycache__/aug_argparse.cpython-38.pyc	removed
tests/utils/__pycache__/aug_assertions.cpython-38.pyc	removed
tests/utils/__pycache__/aug_path.cpython-38.pyc	removed
tests/utils/__pycache__/aug_process.cpython-38.pyc	removed

Configuration Files (135 of 553):

Name	Status	Delta	Visual Diff
config/cgp/log_reg_parameters_trained.cfg	removed
config/species/aedes/aedes_parameters.cfg	changed	1.4%	diff
config/species/Anopheles_gambiae/Anopheles_gambiae_metapars.cfg	added
config/species/Anopheles_gambiae/Anopheles_gambiae_metapars.cgp.cfg	added
config/species/Anopheles_gambiae/Anopheles_gambiae_metapars.utr.cfg	added
config/species/Anopheles_gambiae/Anopheles_gambiae_parameters.cfg	added
config/species/Berviolum_minutum/Berviolum_minutum_metapars.cfg	added
config/species/Berviolum_minutum/Berviolum_minutum_metapars.cgp.cfg	added
config/species/Berviolum_minutum/Berviolum_minutum_metapars.utr.cfg	added
config/species/Berviolum_minutum/Berviolum_minutum_parameters.cfg	added
config/species/Branchiostoma_floridae/Branchiostoma_floridae_metapars.cfg	added
config/species/Branchiostoma_floridae/Branchiostoma_floridae_metapars.cgp.cfg	added
config/species/Branchiostoma_floridae/Branchiostoma_floridae_metapars.utr.cfg	added
config/species/Branchiostoma_floridae/Branchiostoma_floridae_parameters.cfg	added
config/species/Chrysaora_chesapeakeij/Chrysaora_chesapeakei_metapars.cfg	moved	0.0%
config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_metapars.cfg	moved	0.0%
config/species/Chrysaora_chesapeakeij/Chrysaora_chesapeakei_metapars.cgp.cfg	moved	0.0%
config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_metapars.cgp.cfg	moved	0.0%
config/species/Chrysaora_chesapeakeij/Chrysaora_chesapeakei_metapars.utr.cfg	moved	0.0%
config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_metapars.utr.cfg	moved	0.0%
config/species/Chrysaora_chesapeakeij/Chrysaora_chesapeakei_parameters.cfg	moved	0.0%
config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_parameters.cfg	moved	0.0%
config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_metapars.cfg	added
config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_metapars.cgp.cfg	added
config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_metapars.utr.cfg	added
config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_parameters.cfg	added
config/species/Cyclotella_cryptica/Cyclotella_cryptica_metapars.cfg	added
config/species/Cyclotella_cryptica/Cyclotella_cryptica_metapars.cgp.cfg	added
config/species/Cyclotella_cryptica/Cyclotella_cryptica_metapars.utr.cfg	added
config/species/Cyclotella_cryptica/Cyclotella_cryptica_parameters.cfg	added
config/species/Dermasterias_imbricata/Dermasterias_imbricata_metapars.cfg	added
config/species/Dermasterias_imbricata/Dermasterias_imbricata_metapars.cgp.cfg	added
config/species/Dermasterias_imbricata/Dermasterias_imbricata_metapars.utr.cfg	added
config/species/Dermasterias_imbricata/Dermasterias_imbricata_parameters.cfg	added
config/species/fusarium/fusarium_parameters.cfg	changed	1.2%	diff
config/species/human_longrunningtest_crf/human_longrunningtest_crf_metapars.cfg	removed
config/species/human_longrunningtest_crf/human_longrunningtest_crf_metapars.cgp.cfg	removed
config/species/human_longrunningtest_crf/human_longrunningtest_crf_metapars.utr.cfg	removed
config/species/human_longrunningtest_crf/human_longrunningtest_crf_parameters.cfg	removed
config/species/human_longrunningtest_hmm/human_longrunningtest_hmm_metapars.cfg	removed
config/species/human_longrunningtest_hmm/human_longrunningtest_hmm_metapars.cgp.cfg	removed
config/species/human_longrunningtest_hmm/human_longrunningtest_hmm_metapars.utr.cfg	removed
config/species/human_longrunningtest_hmm/human_longrunningtest_hmm_parameters.cfg	removed
config/species/Hydra_vulgaris/Hydra_vulgaris_metapars.cfg	added
config/species/Hydra_vulgaris/Hydra_vulgaris_metapars.cgp.cfg	added
config/species/Hydra_vulgaris/Hydra_vulgaris_metapars.utr.cfg	added
config/species/Hydra_vulgaris/Hydra_vulgaris_parameters.cfg	added
config/species/Leptasterias_sp/Leptasterias_sp_metapars.cfg	added
config/species/Leptasterias_sp/Leptasterias_sp_metapars.cgp.cfg	added
config/species/Leptasterias_sp/Leptasterias_sp_metapars.utr.cfg	added
config/species/Leptasterias_sp/Leptasterias_sp_parameters.cfg	added
config/species/Loa_loa/Loa_loa_metapars.cfg	added
config/species/Loa_loa/Loa_loa_metapars.cgp.cfg	added
config/species/Loa_loa/Loa_loa_metapars.utr.cfg	added
config/species/Loa_loa/Loa_loa_parameters.cfg	added
config/species/Monosiga_brevicollis/Monosiga_brevicollis_metapars.cfg	added
config/species/Monosiga_brevicollis/Monosiga_brevicollis_metapars.cgp.cfg	added
config/species/Monosiga_brevicollis/Monosiga_brevicollis_metapars.utr.cfg	added
config/species/Monosiga_brevicollis/Monosiga_brevicollis_parameters.cfg	added
config/species/Naegleria_gruberi/Naegleria_gruberi_metapars.cfg	added
config/species/Naegleria_gruberi/Naegleria_gruberi_metapars.cgp.cfg	added
config/species/Naegleria_gruberi/Naegleria_gruberi_metapars.utr.cfg	added
config/species/Naegleria_gruberi/Naegleria_gruberi_parameters.cfg	added
config/species/Notospermus_geniculatus/Notospermus_geniculatus_parameters.cfg	changed	17.5%	diff
config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_metapars.cfg	added
config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_metapars.cgp.cfg	added
config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_metapars.utr.cfg	added
config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_parameters.cfg	added
config/species/Pediculus_humanus/Pediculus_humanus_metapars.cfg	added
config/species/Pediculus_humanus/Pediculus_humanus_metapars.cgp.cfg	added
config/species/Pediculus_humanus/Pediculus_humanus_metapars.utr.cfg	added
config/species/Pediculus_humanus/Pediculus_humanus_parameters.cfg	added
config/species/Perkinsus_marinus/Perkinsus_marinus_metapars.cfg	added
config/species/Perkinsus_marinus/Perkinsus_marinus_metapars.cgp.cfg	added
config/species/Perkinsus_marinus/Perkinsus_marinus_metapars.utr.cfg	added
config/species/Perkinsus_marinus/Perkinsus_marinus_parameters.cfg	added
config/species/Physcomitrium_patens/Physcomitrium_patens_metapars.cfg	added
config/species/Physcomitrium_patens/Physcomitrium_patens_metapars.cgp.cfg	added
config/species/Physcomitrium_patens/Physcomitrium_patens_metapars.utr.cfg	added
config/species/Physcomitrium_patens/Physcomitrium_patens_parameters.cfg	added
config/species/Populus_trichocarpa/Populus_trichocarpa_metapars.cfg	added
config/species/Populus_trichocarpa/Populus_trichocarpa_metapars.cgp.cfg	added
config/species/Populus_trichocarpa/Populus_trichocarpa_metapars.utr.cfg	added
config/species/Populus_trichocarpa/Populus_trichocarpa_parameters.cfg	added
config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_metapars.cfg	added
config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_metapars.cgp.cfg	added
config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_metapars.utr.cfg	added
config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_parameters.cfg	added
config/species/Ricinus_communis/Ricinus_communis_metapars.cfg	added
config/species/Ricinus_communis/Ricinus_communis_metapars.cgp.cfg	added
config/species/Ricinus_communis/Ricinus_communis_metapars.utr.cfg	added
config/species/Ricinus_communis/Ricinus_communis_parameters.cfg	added
config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_metapars.cfg	added
config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_metapars.cgp.cfg	added
config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_metapars.utr.cfg	added
config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_parameters.cfg	added
config/species/sealamprey/sealamprey_parameters.cfg	changed	0.4%	diff
config/species/Skeletonema_costatum/Skeletonema_costatum_metapars.cfg	added
config/species/Skeletonema_costatum/Skeletonema_costatum_metapars.cgp.cfg	added
config/species/Skeletonema_costatum/Skeletonema_costatum_metapars.utr.cfg	added
config/species/Skeletonema_costatum/Skeletonema_costatum_parameters.cfg	added
config/species/sunflower/sunflower_metapars.cfg	added
config/species/sunflower/sunflower_metapars.cgp.cfg	added
config/species/sunflower/sunflower_metapars.utr.cfg	added
config/species/sunflower/sunflower_parameters.cfg	added
config/species/Taeniopygia_guttata/Taeniopygia_guttata_metapars.cfg	added
config/species/Taeniopygia_guttata/Taeniopygia_guttata_metapars.cgp.cfg	added
config/species/Taeniopygia_guttata/Taeniopygia_guttata_metapars.utr.cfg	added
config/species/Taeniopygia_guttata/Taeniopygia_guttata_parameters.cfg	added
config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_metapars.cfg	added
config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_metapars.cgp.cfg	added
config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_metapars.utr.cfg	added
config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_parameters.cfg	added
config/species/Vitis_vinifera/Vitis_vinifera_metapars.cfg	added
config/species/Vitis_vinifera/Vitis_vinifera_metapars.cgp.cfg	added
config/species/Vitis_vinifera/Vitis_vinifera_metapars.utr.cfg	added
config/species/Vitis_vinifera/Vitis_vinifera_parameters.cfg	added
config/species/Xenopus_tropicalis/Xenopus_tropicalis_metapars.cfg	added
config/species/Xenopus_tropicalis/Xenopus_tropicalis_metapars.cgp.cfg	added
config/species/Xenopus_tropicalis/Xenopus_tropicalis_metapars.utr.cfg	added
config/species/Xenopus_tropicalis/Xenopus_tropicalis_parameters.cfg	added
docs/tutorial-cgp/data/extrinsic-rnaseq.cfg	removed
doxygen.conf	added
tests/examples/expected_results/test_training_new_species/test_aug_dev_species/test_aug_dev_species _metapars.cfg	moved	0.0%
tests/short/examples/expected_results/test_training_new_species/test_aug_dev_species/test_aug_dev_species_metapars.cfg	moved	0.0%
tests/examples/expected_results/test_training_new_species/test_aug_dev_species/test_aug_dev_species _metapars.cgp.cfg	moved	0.0%
tests/short/examples/expected_results/test_training_new_species/test_aug_dev_species/test_aug_dev_species_metapars.cgp.cfg	moved	0.0%
tests/examples/expected_results/test_training_new_species/test_aug_dev_species/test_aug_dev_species _metapars.utr.cfg	moved	0.0%
tests/short/examples/expected_results/test_training_new_species/test_aug_dev_species/test_aug_dev_species_metapars.utr.cfg	moved	0.0%
tests/examples/expected_results/test_training_new_species/test_aug_dev_species/test_aug_dev_species _parameters.cfg	moved	0.0%
tests/short/examples/expected_results/test_training_new_species/test_aug_dev_species/test_aug_dev_species_parameters.cfg	moved	0.0%
tests/examples_test_results/test_training_new_species/test_aug_dev_species/test_aug_dev_species_met apars.cfg	removed
tests/examples_test_results/test_training_new_species/test_aug_dev_species/test_aug_dev_species_met apars.cgp.cfg	removed
tests/examples_test_results/test_training_new_species/test_aug_dev_species/test_aug_dev_species_met apars.utr.cfg	removed
tests/examples_test_results/test_training_new_species/test_aug_dev_species/test_aug_dev_species_par ameters.cfg	removed

Executable Files (all 22):

Name	Status	Delta	Visual Diff
auxprogs/aln2wig/aln2wig	removed
auxprogs/bam2hints/bam2hints	removed
auxprogs/bam2wig/bam2wig	removed
auxprogs/compileSpliceCands/compileSpliceCands	removed
auxprogs/homGeneMapping/src/homGeneMapping	removed
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config/parameters/aug_cmdln_parameters.json	added
config/species/Anopheles_gambiae/Anopheles_gambiae_igenic_probs.pbl	added
config/species/Berviolum_minutum/Berviolum_minutum_igenic_probs.pbl	added
config/species/Branchiostoma_floridae/Branchiostoma_floridae_igenic_probs.pbl	added
config/species/Chrysaora_chesapeakeij/Chrysaora_chesapeakei_igenic_probs.pbl	moved	0.0%
config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_igenic_probs.pbl	moved	0.0%
config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_igenic_probs.pbl	added
config/species/Cyclotella_cryptica/Cyclotella_cryptica_igenic_probs.pbl	added
config/species/Dermasterias_imbricata/Dermasterias_imbricata_igenic_probs.pbl	added
config/species/human_longrunningtest_crf/human_longrunningtest_crf_igenic_probs.pbl	removed
config/species/human_longrunningtest_crf/human_longrunningtest_crf_igenic_probs.pbl.HMM	removed
config/species/human_longrunningtest_crf/human_longrunningtest_crf_igenic_probs.pbl1	removed
config/species/human_longrunningtest_hmm/human_longrunningtest_hmm_igenic_probs.pbl	removed
config/species/Hydra_vulgaris/Hydra_vulgaris_igenic_probs.pbl	added
config/species/Leptasterias_sp/Leptasterias_sp_igenic_probs.pbl	added
config/species/Loa_loa/Loa_loa_igenic_probs.pbl	added
config/species/Monosiga_brevicollis/Monosiga_brevicollis_igenic_probs.pbl	added
config/species/Naegleria_gruberi/Naegleria_gruberi_igenic_probs.pbl	added
config/species/Notospermus_geniculatus/Notospermus_geniculatus_igenic_probs.pbl	changed	100.0%	diff
config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_igenic_probs.pbl	added
config/species/Pediculus_humanus/Pediculus_humanus_igenic_probs.pbl	added
config/species/Perkinsus_marinus/Perkinsus_marinus_igenic_probs.pbl	added
config/species/Physcomitrium_patens/Physcomitrium_patens_igenic_probs.pbl	added
config/species/Populus_trichocarpa/Populus_trichocarpa_igenic_probs.pbl	added
config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_igenic_probs.pbl	added
config/species/Ricinus_communis/Ricinus_communis_igenic_probs.pbl	added
config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_igenic_probs.pbl	added
config/species/Skeletonema_costatum/Skeletonema_costatum_igenic_probs.pbl	added
config/species/sunflower/sunflower_igenic_probs.pbl	added
config/species/Taeniopygia_guttata/Taeniopygia_guttata_igenic_probs.pbl	added
config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_igenic_probs.pbl	added
config/species/Vitis_vinifera/Vitis_vinifera_igenic_probs.pbl	added
config/species/Xenopus_tropicalis/Xenopus_tropicalis_igenic_probs.pbl	added
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config/species/Pycnopodia_helianthoides	added
config/species/Ricinus_communis	added
config/species/Sclerotinia_sclerotiorum	added
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config/species/Xenopus_tropicalis	added
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config/species/Taeniopygia_guttata/README.txt	added
config/species/Trypanosoma_cruzi/README.txt	added
config/species/Vitis_vinifera/README.txt	added
docs/.ipynb_checkpoints/README-cgp-checkpoint.md	removed
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docs/tutorial2018/README_augustus.TXT	changed	0.1%	diff
README.md	changed	62.1%	diff
scripts/README.autoAug	changed	0.6%	diff
tests/longrunning/cgp/README.TXT	changed	100.0%	diff
tests/longrunning/single_genome/README.TXT	changed	100.0%	diff
tests/short/README.md	added

Text Files (560 of 1500):

Name	Status	Delta	Visual Diff
auxprogs/filterBam/data/example_data.about.txt	changed	2.2%	diff
auxprogs/homGeneMapping/Dockerfile	changed	15.6%	diff
auxprogs/utrrnaseq/Debug/src/Compute_UTRs.d	removed
auxprogs/utrrnaseq/Debug/src/Coord_Transform.d	removed
auxprogs/utrrnaseq/Debug/src/Genomic_Data.d	removed
auxprogs/utrrnaseq/Debug/src/main.d	removed
auxprogs/utrrnaseq/Debug/src/Splice_Sites.d	removed
auxprogs/utrrnaseq/Debug/src/Supporting_Methods.d	removed
auxprogs/utrrnaseq/Debug/src/Test.d	removed
auxprogs/utrrnaseq/Debug/src/UTRs.d	removed
auxprogs/utrrnaseq/input/human-chr19/lib1.introns.ff.gff	added
auxprogs/utrrnaseq/input/human-chr19/ref-introns.gff	added
auxprogs/utrrnaseq/input/human-chr19/repeats.gff	added
auxprogs/utrrnaseq/input/human-chr19/start_stop.gff	added
auxprogs/utrrnaseq/input/human-chr19/trimmed-wig/trimmed.sf.wig	added
auxprogs/utrrnaseq/input/human-chr19/trimmed-wig/trimmed01_singleton.gsnap.ffs.wig	added
auxprogs/utrrnaseq/input/human-chr19/trimmed-wig/trimmed05.blat.sf.wig	added
auxprogs/utrrnaseq/input/human-chr19/trimmed05.blat.sf.gff	added
auxprogs/utrrnaseq/input/human-chr19/trimmed05.blat.sf.gtag.gff	added
config/parameters/AUG_CMDLN_PARAMETERS.md	added
config/species/Anopheles_gambiae/Anopheles_gambiae_exon_probs.pbl	added
config/species/Anopheles_gambiae/Anopheles_gambiae_intron_probs.pbl	added
config/species/Anopheles_gambiae/Anopheles_gambiae_weightmatrix.txt	added
config/species/Berviolum_minutum/Berviolum_minutum_exon_probs.pbl	added
config/species/Berviolum_minutum/Berviolum_minutum_intron_probs.pbl	added
config/species/Berviolum_minutum/Berviolum_minutum_weightmatrix.txt	added
config/species/Branchiostoma_floridae/Branchiostoma_floridae_exon_probs.pbl	added
config/species/Branchiostoma_floridae/Branchiostoma_floridae_intron_probs.pbl	added
config/species/Branchiostoma_floridae/Branchiostoma_floridae_weightmatrix.txt	added
config/species/Chrysaora_chesapeakeij/Chrysaora_chesapeakei_exon_probs.pbl	moved	0.0%
config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_exon_probs.pbl	moved	0.0%
config/species/Chrysaora_chesapeakeij/Chrysaora_chesapeakei_intron_probs.pbl	moved	0.0%
config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_intron_probs.pbl	moved	0.0%
config/species/Chrysaora_chesapeakeij/Chrysaora_chesapeakei_weightmatrix.txt	moved	0.0%
config/species/Chrysaora_chesapeakei/Chrysaora_chesapeakei_weightmatrix.txt	moved	0.0%
config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_exon_probs.pbl	added
config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_intron_probs.pbl	added
config/species/Cryptosporidium_hominis/Cryptosporidium_hominis_weightmatrix.txt	added
config/species/Cyclotella_cryptica/Cyclotella_cryptica_exon_probs.pbl	added
config/species/Cyclotella_cryptica/Cyclotella_cryptica_intron_probs.pbl	added
config/species/Cyclotella_cryptica/Cyclotella_cryptica_weightmatrix.txt	added
config/species/Dermasterias_imbricata/Dermasterias_imbricata_exon_probs.pbl	added
config/species/Dermasterias_imbricata/Dermasterias_imbricata_intron_probs.pbl	added
config/species/Dermasterias_imbricata/Dermasterias_imbricata_weightmatrix.txt	added
config/species/human_longrunningtest_crf/human_longrunningtest_crf_exon_probs.pbl	removed
config/species/human_longrunningtest_crf/human_longrunningtest_crf_exon_probs.pbl.HMM	removed
config/species/human_longrunningtest_crf/human_longrunningtest_crf_exon_probs.pbl1	removed
config/species/human_longrunningtest_crf/human_longrunningtest_crf_intron_probs.pbl	removed
config/species/human_longrunningtest_crf/human_longrunningtest_crf_intron_probs.pbl.HMM	removed
config/species/human_longrunningtest_crf/human_longrunningtest_crf_intron_probs.pbl1	removed
config/species/human_longrunningtest_crf/human_longrunningtest_crf_utr_probs.pbl	removed
config/species/human_longrunningtest_crf/human_longrunningtest_crf_weightmatrix.txt	removed
config/species/human_longrunningtest_hmm/human_longrunningtest_hmm_exon_probs.pbl	removed
config/species/human_longrunningtest_hmm/human_longrunningtest_hmm_intron_probs.pbl	removed
config/species/human_longrunningtest_hmm/human_longrunningtest_hmm_utr_probs.pbl	removed
config/species/human_longrunningtest_hmm/human_longrunningtest_hmm_weightmatrix.txt	removed
config/species/Hydra_vulgaris/Hydra_vulgaris_exon_probs.pbl	added
config/species/Hydra_vulgaris/Hydra_vulgaris_intron_probs.pbl	added
config/species/Hydra_vulgaris/Hydra_vulgaris_weightmatrix.txt	added
config/species/Leptasterias_sp/Leptasterias_sp_exon_probs.pbl	added
config/species/Leptasterias_sp/Leptasterias_sp_intron_probs.pbl	added
config/species/Leptasterias_sp/Leptasterias_sp_weightmatrix.txt	added
config/species/Loa_loa/Loa_loa_exon_probs.pbl	added
config/species/Loa_loa/Loa_loa_intron_probs.pbl	added
config/species/Loa_loa/Loa_loa_weightmatrix.txt	added
config/species/Monosiga_brevicollis/Monosiga_brevicollis_exon_probs.pbl	added
config/species/Monosiga_brevicollis/Monosiga_brevicollis_intron_probs.pbl	added
config/species/Monosiga_brevicollis/Monosiga_brevicollis_weightmatrix.txt	added
config/species/Naegleria_gruberi/Naegleria_gruberi_exon_probs.pbl	added
config/species/Naegleria_gruberi/Naegleria_gruberi_intron_probs.pbl	added
config/species/Naegleria_gruberi/Naegleria_gruberi_weightmatrix.txt	added
config/species/Notospermus_geniculatus/Notospermus_geniculatus_exon_probs.pbl	changed	100.0%	diff
config/species/Notospermus_geniculatus/Notospermus_geniculatus_intron_probs.pbl	changed	100.0%	diff
config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_exon_probs.pbl	added
config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_intron_probs.pbl	added
config/species/Paramecium_tetraurelia/Paramecium_tetraurelia_weightmatrix.txt	added
config/species/Pediculus_humanus/Pediculus_humanus_exon_probs.pbl	added
config/species/Pediculus_humanus/Pediculus_humanus_intron_probs.pbl	added
config/species/Pediculus_humanus/Pediculus_humanus_weightmatrix.txt	added
config/species/Perkinsus_marinus/Perkinsus_marinus_exon_probs.pbl	added
config/species/Perkinsus_marinus/Perkinsus_marinus_intron_probs.pbl	added
config/species/Perkinsus_marinus/Perkinsus_marinus_weightmatrix.txt	added
config/species/Physcomitrium_patens/Physcomitrium_patens_exon_probs.pbl	added
config/species/Physcomitrium_patens/Physcomitrium_patens_intron_probs.pbl	added
config/species/Physcomitrium_patens/Physcomitrium_patens_weightmatrix.txt	added
config/species/Populus_trichocarpa/Populus_trichocarpa_exon_probs.pbl	added
config/species/Populus_trichocarpa/Populus_trichocarpa_intron_probs.pbl	added
config/species/Populus_trichocarpa/Populus_trichocarpa_parameters.cfg~	added
config/species/Populus_trichocarpa/Populus_trichocarpa_weightmatrix.txt	added
config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_exon_probs.pbl	added
config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_intron_probs.pbl	added
config/species/Pycnopodia_helianthoides/Pycnopodia_helianthoides_weightmatrix.txt	added
config/species/Ricinus_communis/Ricinus_communis_exon_probs.pbl	added
config/species/Ricinus_communis/Ricinus_communis_intron_probs.pbl	added
config/species/Ricinus_communis/Ricinus_communis_weightmatrix.txt	added
config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_exon_probs.pbl	added
config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_intron_probs.pbl	added
config/species/Sclerotinia_sclerotiorum/Sclerotinia_sclerotiorum_weightmatrix.txt	added
config/species/Skeletonema_costatum/Skeletonema_costatum_exon_probs.pbl	added
config/species/Skeletonema_costatum/Skeletonema_costatum_intron_probs.pbl	added
config/species/Skeletonema_costatum/Skeletonema_costatum_weightmatrix.txt	added
config/species/sunflower/sunflower_exon_probs.pbl	added
config/species/sunflower/sunflower_intron_probs.pbl	added
config/species/sunflower/sunflower_weightmatrix.txt	added
config/species/Taeniopygia_guttata/Taeniopygia_guttata_exon_probs.pbl	added
config/species/Taeniopygia_guttata/Taeniopygia_guttata_intron_probs.pbl	added
config/species/Taeniopygia_guttata/Taeniopygia_guttata_weightmatrix.txt	added
config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_exon_probs.pbl	added
config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_intron_probs.pbl	added
config/species/Trypanosoma_cruzi/Trypanosoma_cruzi_weightmatrix.txt	added
config/species/Vitis_vinifera/Vitis_vinifera_exon_probs.pbl	added
config/species/Vitis_vinifera/Vitis_vinifera_intron_probs.pbl	added
config/species/Vitis_vinifera/Vitis_vinifera_weightmatrix.txt	added
config/species/Xenopus_tropicalis/Xenopus_tropicalis_exon_probs.pbl	added
config/species/Xenopus_tropicalis/Xenopus_tropicalis_intron_probs.pbl	added
config/species/Xenopus_tropicalis/Xenopus_tropicalis_weightmatrix.txt	added
Dockerfile	changed	35.1%	diff
docs/.ipynb_checkpoints/ABOUT-checkpoint.md	removed
docs/.ipynb_checkpoints/CONTACT-checkpoint.md	removed
docs/.ipynb_checkpoints/EXONCAND-MSAS-CGP-checkpoint.md	removed
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examples/cgp12way/out101run/rn6.cgp.SHIFTED.gff	removed
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examples/cgp12way/out118run/bosTau8.cgp.SHIFTED.gff	removed
examples/cgp12way/out118run/canFam3.cgp.SHIFTED.gff	removed
examples/cgp12way/out118run/dasNov3.cgp.SHIFTED.gff	removed
examples/cgp12way/out118run/echTel2.cgp.SHIFTED.gff	removed
examples/cgp12way/out118run/galGal4.cgp.SHIFTED.gff	removed
examples/cgp12way/out118run/hg38.cgp.SHIFTED.gff	removed
examples/cgp12way/out118run/loxAfr3.cgp.SHIFTED.gff	removed
examples/cgp12way/out118run/mm10.cgp.SHIFTED.gff	removed
examples/cgp12way/out118run/monDom5.cgp.SHIFTED.gff	removed
examples/cgp12way/out118run/oryCun2.cgp.SHIFTED.gff	removed
examples/cgp12way/out118run/rheMac3.cgp.SHIFTED.gff	removed
examples/cgp12way/out118run/rn6.cgp.SHIFTED.gff	removed
examples/cgp12way/out27result/out.runTest	removed
examples/cgp12way/out27run/bosTau8.cgp.SHIFTED.gff	removed
examples/cgp12way/out27run/canFam3.cgp.SHIFTED.gff	removed
examples/cgp12way/out27run/dasNov3.cgp.SHIFTED.gff	removed
examples/cgp12way/out27run/echTel2.cgp.SHIFTED.gff	removed
examples/cgp12way/out27run/galGal4.cgp.SHIFTED.gff	removed
examples/cgp12way/out27run/hg38.cgp.SHIFTED.gff	removed
examples/cgp12way/out27run/loxAfr3.cgp.SHIFTED.gff	removed
examples/cgp12way/out27run/mm10.cgp.SHIFTED.gff	removed
examples/cgp12way/out27run/monDom5.cgp.SHIFTED.gff	removed
examples/cgp12way/out27run/oryCun2.cgp.SHIFTED.gff	removed
examples/cgp12way/out27run/rheMac3.cgp.SHIFTED.gff	removed
examples/cgp12way/out27run/rn6.cgp.SHIFTED.gff	removed
examples/cgp12way/out30result/out.runTest	removed
examples/cgp12way/out30run/bosTau8.cgp.SHIFTED.gff	removed
examples/cgp12way/out30run/canFam3.cgp.SHIFTED.gff	removed
examples/cgp12way/out30run/dasNov3.cgp.SHIFTED.gff	removed
examples/cgp12way/out30run/echTel2.cgp.SHIFTED.gff	removed
examples/cgp12way/out30run/galGal4.cgp.SHIFTED.gff	removed
examples/cgp12way/out30run/hg38.cgp.SHIFTED.gff	removed
examples/cgp12way/out30run/loxAfr3.cgp.SHIFTED.gff	removed
examples/cgp12way/out30run/mm10.cgp.SHIFTED.gff	removed
examples/cgp12way/out30run/monDom5.cgp.SHIFTED.gff	removed
examples/cgp12way/out30run/oryCun2.cgp.SHIFTED.gff	removed
examples/cgp12way/out30run/rheMac3.cgp.SHIFTED.gff	removed
examples/cgp12way/out30run/rn6.cgp.SHIFTED.gff	removed
examples/cgp12way/out47result/out.runTest	removed
examples/cgp12way/out47run/bosTau8.cgp.SHIFTED.gff	removed
examples/cgp12way/out47run/canFam3.cgp.SHIFTED.gff	removed
examples/cgp12way/out47run/dasNov3.cgp.SHIFTED.gff	removed
examples/cgp12way/out47run/echTel2.cgp.SHIFTED.gff	removed
examples/cgp12way/out47run/galGal4.cgp.SHIFTED.gff	removed
examples/cgp12way/out47run/hg38.cgp.SHIFTED.gff	removed
examples/cgp12way/out47run/loxAfr3.cgp.SHIFTED.gff	removed
examples/cgp12way/out47run/mm10.cgp.SHIFTED.gff	removed
examples/cgp12way/out47run/monDom5.cgp.SHIFTED.gff	removed
examples/cgp12way/out47run/oryCun2.cgp.SHIFTED.gff	removed
examples/cgp12way/out47run/rheMac3.cgp.SHIFTED.gff	removed
examples/cgp12way/out47run/rn6.cgp.SHIFTED.gff	removed
examples/cgp12way/out54result/out.runTest	removed
examples/cgp12way/out54run/bosTau8.cgp.SHIFTED.gff	removed
examples/cgp12way/out54run/canFam3.cgp.SHIFTED.gff	removed
examples/cgp12way/out54run/dasNov3.cgp.SHIFTED.gff	removed
examples/cgp12way/out54run/echTel2.cgp.SHIFTED.gff	removed
examples/cgp12way/out54run/galGal4.cgp.SHIFTED.gff	removed
examples/cgp12way/out54run/hg38.cgp.SHIFTED.gff	removed
examples/cgp12way/out54run/loxAfr3.cgp.SHIFTED.gff	removed
examples/cgp12way/out54run/mm10.cgp.SHIFTED.gff	removed
examples/cgp12way/out54run/monDom5.cgp.SHIFTED.gff	removed
examples/cgp12way/out54run/oryCun2.cgp.SHIFTED.gff	removed
examples/cgp12way/out54run/rheMac3.cgp.SHIFTED.gff	removed
examples/cgp12way/out54run/rn6.cgp.SHIFTED.gff	removed
examples/cgp12way/out57result/out.runTest	removed
examples/cgp12way/out57run/bosTau8.cgp.SHIFTED.gff	removed
examples/cgp12way/out57run/canFam3.cgp.SHIFTED.gff	removed
examples/cgp12way/out57run/dasNov3.cgp.SHIFTED.gff	removed
examples/cgp12way/out57run/echTel2.cgp.SHIFTED.gff	removed
examples/cgp12way/out57run/galGal4.cgp.SHIFTED.gff	removed
examples/cgp12way/out57run/hg38.cgp.SHIFTED.gff	removed
examples/cgp12way/out57run/loxAfr3.cgp.SHIFTED.gff	removed
examples/cgp12way/out57run/mm10.cgp.SHIFTED.gff	removed
examples/cgp12way/out57run/monDom5.cgp.SHIFTED.gff	removed
examples/cgp12way/out57run/oryCun2.cgp.SHIFTED.gff	removed
examples/cgp12way/out57run/rheMac3.cgp.SHIFTED.gff	removed
examples/cgp12way/out57run/rn6.cgp.SHIFTED.gff	removed
examples/cgp12way/out80result/out.runTest	removed
examples/cgp12way/out80run/bosTau8.cgp.SHIFTED.gff	removed
examples/cgp12way/out80run/canFam3.cgp.SHIFTED.gff	removed
examples/cgp12way/out80run/dasNov3.cgp.SHIFTED.gff	removed
examples/cgp12way/out80run/echTel2.cgp.SHIFTED.gff	removed
examples/cgp12way/out80run/galGal4.cgp.SHIFTED.gff	removed
examples/cgp12way/out80run/hg38.cgp.SHIFTED.gff	removed
examples/cgp12way/out80run/loxAfr3.cgp.SHIFTED.gff	removed
examples/cgp12way/out80run/mm10.cgp.SHIFTED.gff	removed
examples/cgp12way/out80run/monDom5.cgp.SHIFTED.gff	removed
examples/cgp12way/out80run/oryCun2.cgp.SHIFTED.gff	removed
examples/cgp12way/out80run/rheMac3.cgp.SHIFTED.gff	removed
examples/cgp12way/out80run/rn6.cgp.SHIFTED.gff	removed
examples/cgp12way/out86result/out.runTest	removed
examples/cgp12way/out86run/bosTau8.cgp.SHIFTED.gff	removed
examples/cgp12way/out86run/canFam3.cgp.SHIFTED.gff	removed
examples/cgp12way/out86run/dasNov3.cgp.SHIFTED.gff	removed
examples/cgp12way/out86run/echTel2.cgp.SHIFTED.gff	removed
examples/cgp12way/out86run/galGal4.cgp.SHIFTED.gff	removed
examples/cgp12way/out86run/hg38.cgp.SHIFTED.gff	removed
examples/cgp12way/out86run/loxAfr3.cgp.SHIFTED.gff	removed
examples/cgp12way/out86run/mm10.cgp.SHIFTED.gff	removed
examples/cgp12way/out86run/monDom5.cgp.SHIFTED.gff	removed
examples/cgp12way/out86run/oryCun2.cgp.SHIFTED.gff	removed
examples/cgp12way/out86run/rheMac3.cgp.SHIFTED.gff	removed
examples/cgp12way/out86run/rn6.cgp.SHIFTED.gff	removed
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examples/chr2L/genes.gb.train	added
examples/chr2L/hints.gff	added
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mansrc/bam2hints.1.adoc	changed	13.3%	diff
mansrc/filterBam.1.adoc	changed	85.0%	diff
src/cxxflags	removed
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tests/short/examples/expected_results/test_cgp_with_db_mysql/pred/bosTau4.cgp.filtered.gff	moved	0.0%
tests/examples/expected_results/test_cgp_with_db_mysql/pred/galGal3.cgp.filtered.gff	moved	0.0%
tests/short/examples/expected_results/test_cgp_with_db_mysql/pred/galGal3.cgp.filtered.gff	moved	0.0%
tests/examples/expected_results/test_cgp_with_db_mysql/pred/hg19.cgp.filtered.gff	moved	0.0%
tests/short/examples/expected_results/test_cgp_with_db_mysql/pred/hg19.cgp.filtered.gff	moved	0.0%
tests/examples/expected_results/test_cgp_with_db_mysql/pred/mm9.cgp.filtered.gff	moved	0.0%
tests/short/examples/expected_results/test_cgp_with_db_mysql/pred/mm9.cgp.filtered.gff	moved	0.0%
tests/examples/expected_results/test_cgp_with_db_mysql_hints/pred/bosTau4.cgp.filtered.gff	moved	0.0%
tests/short/examples/expected_results/test_cgp_with_db_mysql_hints/pred/bosTau4.cgp.filtered.gff	moved	0.0%
tests/examples/expected_results/test_cgp_with_db_mysql_hints/pred/galGal3.cgp.filtered.gff	moved	0.0%
tests/short/examples/expected_results/test_cgp_with_db_mysql_hints/pred/galGal3.cgp.filtered.gff	moved	0.0%
tests/examples/expected_results/test_cgp_with_db_mysql_hints/pred/hg19.cgp.filtered.gff	moved	0.0%
tests/short/examples/expected_results/test_cgp_with_db_mysql_hints/pred/hg19.cgp.filtered.gff	moved	0.0%
tests/examples/expected_results/test_cgp_with_db_mysql_hints/pred/mm9.cgp.filtered.gff	moved	0.0%
tests/short/examples/expected_results/test_cgp_with_db_mysql_hints/pred/mm9.cgp.filtered.gff	moved	0.0%
tests/examples/expected_results/test_format_and_error_out/augustus.gff3	moved	0.1%	diff
tests/short/examples/expected_results/test_format_and_error_out/augustus.gff3	moved	0.1%	diff
tests/examples/expected_results/test_hints_MPE/aug_hints_MPE.gff	moved	0.0%
tests/short/examples/expected_results/test_hints_MPE/aug_hints_MPE.gff	moved	0.0%
tests/examples/expected_results/test_training_new_species/test_aug_dev_species/test_aug_dev_species _exon_probs.pbl	moved	0.0%
tests/short/examples/expected_results/test_training_new_species/test_aug_dev_species/test_aug_dev_species_exon_probs.pbl	moved	0.0%
tests/examples/expected_results/test_training_new_species/test_aug_dev_species/test_aug_dev_species _intron_probs.pbl	moved	0.0%
tests/short/examples/expected_results/test_training_new_species/test_aug_dev_species/test_aug_dev_species_intron_probs.pbl	moved	0.0%
tests/examples/expected_results/test_training_new_species/test_aug_dev_species/test_aug_dev_species _weightmatrix.txt	moved	0.0%
tests/short/examples/expected_results/test_training_new_species/test_aug_dev_species/test_aug_dev_species_weightmatrix.txt	moved	0.0%
tests/examples/expected_results/test_utr_on/aug_utr_on.gff	moved	0.0%
tests/short/examples/expected_results/test_utr_on/aug_utr_on.gff	moved	0.0%
tests/examples_test/data/tmp/chr2L.sm.fa	removed
tests/examples_test_results/test_ab_initio_prediction/augustus.gff	removed
tests/examples_test_results/test_cgp/bosTau4.cgp.filtered.gff	removed
tests/examples_test_results/test_cgp/galGal3.cgp.filtered.gff	removed
tests/examples_test_results/test_cgp/hg19.cgp.filtered.gff	removed
tests/examples_test_results/test_cgp/mm9.cgp.filtered.gff	removed
tests/examples_test_results/test_cgp/output.txt	removed
tests/examples_test_results/test_cgp_with_db/pred/bosTau4.cgp.filtered.gff	removed
tests/examples_test_results/test_cgp_with_db/pred/galGal3.cgp.filtered.gff	removed
tests/examples_test_results/test_cgp_with_db/pred/hg19.cgp.filtered.gff	removed
tests/examples_test_results/test_cgp_with_db/pred/mm9.cgp.filtered.gff	removed
tests/examples_test_results/test_cgp_with_db_hints/pred/bosTau4.cgp.filtered.gff	removed
tests/examples_test_results/test_cgp_with_db_hints/pred/galGal3.cgp.filtered.gff	removed
tests/examples_test_results/test_cgp_with_db_hints/pred/hg19.cgp.filtered.gff	removed
tests/examples_test_results/test_cgp_with_db_hints/pred/mm9.cgp.filtered.gff	removed
tests/examples_test_results/test_format_and_error_out/augustus.gff3	removed
tests/examples_test_results/test_hints_MPE/aug_hints_MPE.gff	removed
tests/examples_test_results/test_training_new_species/test_aug_dev_species/test_aug_dev_species_exo n_probs.pbl	removed
tests/examples_test_results/test_training_new_species/test_aug_dev_species/test_aug_dev_species_int ron_probs.pbl	removed
tests/examples_test_results/test_training_new_species/test_aug_dev_species/test_aug_dev_species_wei ghtmatrix.txt	removed
tests/examples_test_results/test_utr_on/aug_utr_on.gff	removed
tests/short/auxprogs/bam2hints/expected_results/test.intron.gff	added
tests/short/auxprogs/filterbam/expected_results/commonGeneFile.txt	added
tests/short/auxprogs/filterbam/expected_results/example_single.best.sam	added
tests/short/auxprogs/filterbam/expected_results/example_single.minCover99.sam	added
tests/short/auxprogs/filterbam/expected_results/example_single.no_minCover.sam	added
tests/short/auxprogs/filterbam/expected_results/example_single.no_minId.sam	added
tests/short/auxprogs/filterbam/expected_results/example_single.no_minId_no_minCover.sam	added
tests/short/auxprogs/filterbam/expected_results/example_single.no_options.sam	added
tests/short/auxprogs/filterbam/expected_results/example_single.noIntrons.sam	added
tests/short/auxprogs/filterbam/expected_results/example_single.noIntrons_insertLimit15.sam	added
tests/short/auxprogs/filterbam/expected_results/example_single.not_paired.sam	added
tests/short/auxprogs/filterbam/expected_results/example_single.uniq.sam	added
tests/short/auxprogs/filterbam/expected_results/example_single.uniqThresh1_1.sam	added
tests/short/auxprogs/filterbam/expected_results/pairBedFile.bed	added

Other Files (16 of 42):

Name	Status	Delta
auxprogs/filterBam/data/dummy.best.bam	removed
auxprogs/filterBam/data/dummy.merged.bam	removed
auxprogs/filterBam/data/single.bam	removed
docs/tutorial2015/results/rnaseq.bam	added
docs/tutorial2015/results/rnaseq.bam.bai	added
tests/auxprogs/bam2wig/test_files/test.s.bam	moved	0.0%
tests/short/auxprogs/bam2wig/test_files/test.s.bam	moved	0.0%
tests/examples/expected_results/test_format_and_error_out/augustus.err	moved	0.0%
tests/short/examples/expected_results/test_format_and_error_out/augustus.err	moved	0.0%
tests/examples_test_results/test_format_and_error_out/augustus.err	removed
tests/short/auxprogs/bam2hints/test_files/test.s.sorted.bam	added
tests/short/auxprogs/filterbam/test_files/example_paired.bam	added
tests/short/auxprogs/filterbam/test_files/example_pairwise.bam	added
tests/short/auxprogs/filterbam/test_files/example_pairwise_calmd.bam	added
tests/short/auxprogs/filterbam/test_files/example_pairwise_calmd_seq_with_equalsigns.bam	added
tests/short/auxprogs/filterbam/test_files/example_single.bam	added

Packages Compared:

augustus-3.4.0.tar.gz
Augustus-3.5.0.tar.gz

"Fossies" - the Fresh Open Source Software Archive

Source code changes report for "Augustus" between the packages
augustus-3.4.0.tar.gz and Augustus-3.5.0.tar.gz

Summary:

Related Informations:

Changes In Files (According File Type):

Header Files (29 of 116):

C Programs (3 of 9):

C++ Programs (36 of 110):

Patches (all 1):

Perl Programs (9 of 102):

Python Programs (41 of 47):

Shell Programs (6 of 9):

Python Compiled Programs (all 11):

Configuration Files (135 of 553):

Executable Files (all 22):

JSON Files (38 of 197):

Makefiles (21 of 22):

Man Pages (3 of 14):

Module-Definition Files (all 1):

Symbolic Links (11 of 12):

Berkeley Databases (3 of 4):

Data Lists (1 of 6):

Git Files (2 of 3):

HTML Pages (4 of 43):

YAML Files (2 of 3):

Data Files (36 of 115):

Directories (185 of 458):

Archives (3 of 6):

Information Files (2 of 3):

Licenses (1 of 4):

Readme Files (43 of 103):

Text Files (560 of 1500):

Other Files (16 of 42):

Packages Compared:

"Fossies" - the Fresh Open Source Software Archive

Source code changes report for "Augustus" between the packagesaugustus-3.4.0.tar.gz and Augustus-3.5.0.tar.gz

Summary:

Related Informations:

Changes In Files (According File Type):

Header Files (29 of 116):

C Programs (3 of 9):

C++ Programs (36 of 110):

Patches (all 1):

Perl Programs (9 of 102):

Python Programs (41 of 47):

Shell Programs (6 of 9):

Python Compiled Programs (all 11):

Configuration Files (135 of 553):

Executable Files (all 22):

JSON Files (38 of 197):

Makefiles (21 of 22):

Man Pages (3 of 14):

Module-Definition Files (all 1):

Symbolic Links (11 of 12):

Berkeley Databases (3 of 4):

Data Lists (1 of 6):

Git Files (2 of 3):

HTML Pages (4 of 43):

YAML Files (2 of 3):

Data Files (36 of 115):

Directories (185 of 458):

Archives (3 of 6):

Information Files (2 of 3):

Licenses (1 of 4):

Readme Files (43 of 103):

Text Files (560 of 1500):

Other Files (16 of 42):

Packages Compared:

Source code changes report for "Augustus" between the packages
augustus-3.4.0.tar.gz and Augustus-3.5.0.tar.gz