3.5.0

List of changes from version 3.4.0 to 3.5.0 (until Sep 24th, 2022)

 - automatic testcases (short regression test) and long-running performance tests
 - added singularity definition file and instructions
 - fix of PP::ProfileReadError that occurred with new versions of libstdc++
 - fixed an issue with chromosomes that are larger than 2^31 bp (~2GB)
 - bugfixes in augustus, augustify and for BRAKER
 - common parameter definitions of pygustus and augustus
 - new species Vitis vinfera, Berviolum minutum, Hydra vulgaris, Skeletonema costatum, Pediculus humanus,
   Pycnopodia helianthoides, Dermasterias imbricata, Ricinus communis, Taeniopygia guttata, Branchiostoma floridae,
   Anopheles gambiae, Cryptosporidium hominis, Physcomitrium patens, Perkinsus marinus, Loa loa, Trypanosoma cruzi,
   Naegleria gruberi, Monosiga brevicollis, Cyclotella cryptica, Sclerotinia sclerotiorum, Paramecium tetraurelia,
   Xenopus tropicalis, Notospermus geniculatus, Chrysaora chesapeakei, sunflower
 - improved filterBam performance
 - make SeqLib API an alternative to the Bamtools API
 - improvements in augustify

New Contributors

• @nathanweeks made their first contribution in #235
• @smoe made their first contribution in #239
• @diekhans made their first contribution in #250
• @sestaton made their first contribution in #251
• @OnlineArts made their first contribution in #256
• @Gullumluvl made their first contribution in #265
• @paulmenzel made their first contribution in #271
• @prehensilecode made their first contribution in #321
• @douglasgscofield made their first contribution in #325

Full Changelog: v3.4.0...v3.5.0

3.4.0

List of changes from version 3.3.3 to 3.4.0 (until Dec 11th, 2020)
- enable making of a Debian package that includes the CGP functionality
- shortrunning (make test) and longrunning tests for monitoring functionality and performance
- drop dependency on static bam library, e.g. of bam2wig
- new program pp_simScore to score a protein against a protein profile (.prfl)
- new option --/CompPred/printExonCandsMSA=1 for CGP to produce MSAs of candidate coding regions
- new scripts augustify, fix_in_frame_stop_codon_genes.py
- new default: softmasking is assumed
- compile with CGP and ZIPINPUT support by default
- compile with SQLite and MySQL support for CGP (switch of by adding SQLite = false and MySQL = false to common.mk)
- new species Cassiopea xamachana, Ptychodera flava, Argopecten irridians, Nemopilema nomurai
Notospermus_geniculatus, Chrysaora chesapeakeij, Ectocarpus siliculosus, Trichoplax adhaerens,
Aurelia aurita, Rhopilema esculentum, Encephalitozoon cuniculi, Gonapodya prolifera, Dunaliella_salina
Sordaria macrospora, Sphaceloma murrayae, Vitrella brassicaformis, Monoraphidium neglectum, Raphidocelis subcapita,
Ostreococcus tauri, Ostreococcus sp. lucimarinus, Micromonas pusilla, Micromonas_commoda, Chlamydomonas eustigma,
Thalassiosira pseudonana, Pseudo-nitzschia multistriata, Phaeodactylum tricornutum, Fragilariopsis cylindrus,
Fistulifera solaris, Bathycoccus prasinos, Chloropicon primus
- added Windows Subsystem for Linux Installation documentation
- fixes of bugs, compiler warnings

3.3.3

List of changes from version 3.3.2 to 3.3.3 (until Sep 13th, 2019)
- docker container
- new script tfix_in_frame_stop_codon_genes.py that replaces genes where spliced in-frame stop codons were predicted
- new scripts: compare_masking.pl, merge_masking.pl
- new program bamToWig.py as alternarive to bam2wig C++ binary
- fix warnings on new GCC compiler (8.3)
- introduced unit tests of C++ code (make test)
- bugfixes (lex.cc, autoAug.pl)
- DIAMOND as alternative to BLAST in aa2nonred.pl

3.3.2

List of changes from version 3.3.1 to 3.3.2 (until Oct 5th, 2018)

• bugfixes in comparative augustus, utrrnaseq
• new species Chiloscyllium punctatum (bamboo shark), Scyliorhinus torazame (cat shark), Rhincodon typus (whale shark)
• updated comparative augustus (CGP) tutorial