- edited description
[ X ] Immcantation https://bitbucket.org/kleinstein/immcantation/issues/90/update-changeo-10xsh-to-match-the-new (@ssnn )
[ X ] Tutorials: Review all figures are present and correctly placed.
[ > ] Tutorials. Would be nice, but could go to next release: Remove common intro technical parts (how to get and use container, how to use jupyter notebooks…) and make a specific section or notebook with this, that we can reference to from all other notebooks. This is for easier maintenance. Include in this refactoring the README file in https://bitbucket.org/kleinstein/immcantation/src/master/training/.
[ > ] Pipelines: rhesus. See Changeo issue 194. ~February 2021 (https://www.imgt.org/IMGTinformation/creations/#2021)) IMGT introduced two new codons into the alignment of Rhesus IGH (15A and 26A), along with a large number of gene name changes. If you work with V-quest or High V-Quest, you will see the additional codons in alignment of the results. I don't think IgBLAST has done any updates to rhesus_monkey.ndm.imgt to account for the two new codons, at least I have not seen this changes in the release notes, so probably best to use IMGT for the alignments. Because of the new positions, Change-O can't find the second cysteine in the expected location. Can use --partial to avoid this check (if will use https://bitbucket.org/kleinstein/changeo/src/8a3ba4cdcf78b3a2f93132da529a18ad5ab90595/bin/MakeDb.py#lines-226:231, as opposed to the strict checks https://bitbucket.org/kleinstein/changeo/src/8a3ba4cdcf78b3a2f93132da529a18ad5ab90595/bin/MakeDb.py#lines-194:224). But downstream analysis that rely on the location of the CDRs, are also impacted. (@ssnn )
[x] pRESTO: Is branch makedb-airr ready to be merged?
[ > ] Change-O: CreateGermlines.py does not generate full germline upon -g full option (@Kenneth Hoehn )
[ x ] Change-O #188: it needs testing - for both the C-region parsing and MakeDb-airr command. I also need to extract the C region alignment positions, but that should be minor. I can probably merge it now though.
[ x ] Change-O: Another thing that should be in a changeo release is changing the default validation behavior of MakeDb to be something between the current default and --partial (V/J gene check but without the CDR3 position check). Because the IMGT gapping difference for mouse TRA and rhesus IGL is generating a lot of single-cell emails. ? It would be nice to have in the coming release. But if there is too much work left to do, we can leave it for an early December release.
[ x ] Scoper: Added some performance improvements. groupGenes improvements for next release.
[ x ] Website: Add scoper, dowser, Noah, and fix alakazam.
[ x ] alakazam: can readFastQ function be moved to another branch? We will try remove BioC dependency in next release.
[ x ] shazam: chimera filter plot function (Noah)
