Release notes for vadr SARS-CoV-2 models:

Download site:
https://ftp.ncbi.nlm.nih.gov/pub/nawrocki/vadr-models/sarscov2

Bitbucket repo:
https://bitbucket.org/nawrockie/vadr-models-sarscov2

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1.3-2:   [Nov 2021]: Reverted to using a single reference model for
         SARS-CoV-2: NC_045512 (removed NC_045512-MW422255,
         NC_045512-MW809059, NC_045512-del28254). Also:

           - many problems in stem_loop.1 (reference positions
             29728..29768) no longer cause a sequence to fail
             but stem_loop.1 will become a misc_feature in the output
             .tbl files.
           - added the ORF6 protein and nucleocapsid phosphoprotein
             from MW809059 to the blastx protein database for
             NC_045512. 

         Because there is now only 1 model, there is no need for
         mapping between models with the
         vadr-map-two-complete-model.pl script or sarscov2.mmap files
         introduced in version 1.3-1.

         Additional changes that will affect vadr 1.4 (not yet
         released) but have no impact when used with vadr 1.3:
          - stem_loop.1 will be allowed to be completely deleted
            without causing a sequence to fail
          - any indfstrn alert in the region of reference positions
            5737..5772 will be ignored (not reported)

1.3-1:   [Aug 2021]: Changed the CDS and gene features with gene
         qualifier values of 'ORF3a', 'ORF6', 'ORF7a', 'ORF7b', and
         'ORF10' so that most fatal alerts in those features do not
         cause a sequence to FAIL by adding the string
         'misc_not_failure:"1"' to their 'FEATURE' lines in the
         sarscov2.minfo file. This was done for all 4 models. This is
         the *only* change to models made between 1.2-2 and 1.3-1.
         Also adds sarscov2.mmap file for use with
         vadr-map-model-coords.pl and vadr-map-two-complete-model.pl
         scripts in vadr miniscripts/ directory. See 00README.txt for
         example usage. 

1.2-2:   [April 2021]: Added NC_045512-MW809059 model, did not change
         any of the existing 3 models.

         4 total models
         Model 1: NC_045512          (same as from 1.2-1)
         Model 2: NC_045512-del28254 (same as from 1.2-1)
         Model 3: NC_045512-MW422255 (same as from 1.2-1)
         Model 4: NC_045512-MW809059 (description below)
         
         NC_045512-MW809059 model is identical to sequence MW809059
         except for the following changes:

         - the model was extended past the 5' and 3' ends of MW809059
           to include the 5' and 3' ends of NC_045512, by adding 2nt
           from NC_045512 at the 5' end and 50nt from NC_045512 at the
           3' end.
         - the stem_loop feature Coronavirus 3' stem-loop II-like
           motif (s2m) present in NC_045512 is not expected or
           annotated by this model
         - the blastx protein validation stage blast db includes the 
           NC_045512 ORF6 and nucleocapsid phosphoprotein proteins as
           well as the MW809059 versions of those proteins. This allows 
           sequences that match best to the NC_045512-MW809059 model 
           that do or do not have the del:27205:3 and/or del:28278:3
           deletions to pass.

1.2-1:   [March 2021]: identical to 1.1.3-1 but files renamed from
         'NC_045512' to 'sarscov2' to reflect that there is more than
         just a single RefSeq model now. Also some formatting changes
         relative to 1.1.3-1 required for use with vadr 1.2. NO
         CHANGES TO ACTUAL MODELS OR MODEL PARAMETERS.

1.1.3-1: [Feb 2021]: 3 total models
         Model 1: NC_045512 (same as from 1.1-1 and 1.1.2-1)
         Model 2: NC_045512-del28254 which is identical to NC_045512
           but has position 28254 deleted, which extends ORF8
           by 4 amino acids. 
         Model 3: NC_045512-MW422255: renamed from MW422255-NC_045512
           from v1.1.2-1 (but same model except for different name).
           This model was renamed to avoid a problem with score
           tie-breaks for sequences that match equally well to
           NC_045512 and MW422255.
         
         A new attribute was added to the .minfo files for ORF8 of the
         two NC_045512* models that allow it to be annotated as a
         misc_feature instead of as a CDS, in which case a protein
         record will not be created from it in GenBank. This
         misc_feature-ization is only possible with vadr v1.1.3 or
         later and occurs if the ORF8 region is flagged with certain
         types of errors (e.g. invalid start/stop codons). See the
         vadr documentation on github or email eric.nawrocki@nih.gov
         for more information.

         Note that the 54 other (non-SARS-CoV-2) coronaviridae models
         from v1.1.2-1 were removed in interest of making the model
         tarball file smaller. If you're interested in those models,
         download the v1.1.2-1 file which includes them.

1.1.2-1: [Jan 2021]: 56 total models (same set as 1.1-1) plus
         MW422255-NCC_045512. NOTE that NC_045512-d28254 and
         NC_045512-T27915 the two models added in 1.1.2-1 are not
         included in this model library. The new model exists in 
         both 'NC_045512.cm' and 'corona.cm.

         MW422255-NCC_045512: identical to sequence MW422255 except
         for the following changes:

         - the model was extended past the 5' and 3' ends of MW422255
           to include the 5' and 3' ends of NC_045512. 

         - the 8 Ns in MW422255 were replaced with the NC_045512
           nucleotide at the corresponding position.

1.1-1:   [Apr 2020]: 55 total models (same set as 1.0.2dev-{5,4,3})
         - updates blast database files to blast db format 5 for use 
           with updated blast version (v2.10.0+); all previous model
           files included blast db format 4 (v.2.9.0+)
         - adds corona.hmm and NC_045512.hmm file for hmmer-based
           protein validation
         - NO CHANGES TO MODELS THEMSELVES (corona.cm, NC_045512.cm
           corona.minfo and NC_045512.minfo unchanged)

vadr-models-55-1.0.2-dev-5: [Apr 2020]:
         - adds blastn nucleotide databases (e.g. corona.fa.*)
           for use with v-annotate.pl -s option.
         - renames vadr.NC_045512.stem_loops.{cm*,minfo} to
           NC_045512.{cm*,minfo}
         - renames vadr.corona.NC_045512.stem_loops.{cm*,minfo} to
           corona.{cm*,minfo}
         - removes vadr.NC_045512.{cm*,minfo} (these models lacked
           stem_loop info for NC_045512)
         - removes vadr.corona.{cm*,minfo} (these models lacked
           stem_loop info for NC_045512)
         - NO CHANGES TO RENAMED MODELS THEMSELVES other than renaming
           them

vadr-models-55-1.0.2-dev-4: [Apr 2020]:
         - only differences between this set of models and
           vadr-models-corona-55-1.0.2dev-3 is the four files with the
           .minfo suffix. Those four files have been changed *only* as
           follows: 
           * 'orf1ab' (v3) replaced with 'ORF1ab' (v4) 
           * 'orf1a' (v3) replaced with 'ORF1a' (v4)
           These changes reflect updates to the NC_045512.2 RefSeq
           annotation.

vadr-models-corona-55-1.0.2-dev-3 [Mar 2020]:
         - only difference between this set of models and
           vadr-models-corona-55-1.0.2dev-2 is addition of mat_peptide
           features for orf1a not currently in the YP_009725295
           protein linked from the NC_045512 RefSeq.

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contact: eric.nawrocki@nih.gov
