Published March 2, 2023
| Version v0.7.0
Software
Open
ktmeaton/ncov-recombinant: v0.7.0 - Recursive Recombinants
Description
Notes
This is a minor release aimed towards a nextclade
dataset upgrade from 2022-10-27
to 2023-01-09
which adds nomenclature for newly designated recombinants XBH
- XBP
. This release also adds initial support for the detection of "recursive recombination" including XBL
and XBN
which are recombinants of XBB
.
A comprehensive test summary report can be downloaded directly with: ncov-recombinant_v0.6.1_v0.7.0.zip or viewed at the following link once the release is complete.
Documentation- Issue #24: Create documentation on Read The Docs
- Issue #210: Handle numeric strain names.
- Issue #185: Simplify creation of the pango-lineage nomenclature phylogeny to use the lineage_notes.txt file and the pango_aliasor library.
- Issue #195: Add bypass to intermission allele ratio for edge cases.
- Issue #204: Add special handling for XBB sequenced with ARTIC v4.1 and dropout regions.
- Issue #205: Add new column
parents_conflict
to indicate whether the reported lineages from covSPECTRUM conflict with the reported parental clades from `sc2rf. - Issue #213: Add
XBK
to auto-pass lineages. - Issue #222: Add new parameter
--gisaid-access-key
tosc2rf
andsc2rf_recombinants
. - Issue #229: Fix bug where auto-pass lineages are missing when exclude_negatives is set to true.
- Issue #231: Fix bug where 'null' lineages in covSPECTRUM caused error in
sc2rf
postprocess. - The order of the
postprocessing.py
was rearranged to have more comprehensive details for auto-pass lineages. - Add
XAN
to auto-pass lineages.
- Issue #209: Restrict the palette for
rbd_level
to the range of0:12
. - Issue #218: Fix bug concerning data fragmentation with large numbers of sequences.
- Issue #221: Remove parameter
--singletons
in favor of--min-cluster-size
to control cluster size in plots. - Issue #224: Fix bug where plot crashed with extremely large datasets.
- Combine
plot
andplot_historical
into one snakemake rule. Also at custom patternplot_NX
(ex.plot_N10
) to adjust min cluster size.
- Combine
report
andreport_historical
into one snakemake rule.
- Issue #225: Fix bug where false negatives passed validation because the status column wasn't checked.
- Issue #217:
XBB.1.5
- Issue #196:
XBF
- Issue #206:
XBG
- Issue #196:
XBH
- Issue #199:
XBJ
- Issue #213:
XBK
- Issue #219:
XBL
- Issue #215:
XBM
- Issue #197:
XBN
- Issue #203:
proposed1305
- Issue #208:
proposed1340
- Issue #212:
proposed1425
- Issue #214:
proposed1440
- Issue #216:
proposed1444
- Issue #220:
proposed1576
c279f1e4
docs: add changelog for v0.7.02964b4a1
docs: update notes to include 1576 proposed issuefdc874ab
docs: add test summary package for v0.7.03f3d4438
docs: update docs v0.7.078696b36
script: add bug fix to sc2rf postprocess for #231403777a0
script: lint plotting script2a09c783
script: fix sc2rf postprocess bug in duplicate removald44d5f90
data: add XBP to controls-gisaid4293439c
profile: add controls-gisaid to virusseq builds91d6fb89
defaults: update nextclade dataset to 2023-02-01630b2cd5
resources: update49e6f598
profile: add virusseq profile7e586d1d
script: add extra logic for auto-passing lineages0ebe5e9c
script: fix bug in report where it didn't check that plots existed25b2f243
docs: update developers guide914d933f
defaults: add XBN to controls-gisaid and validation8eaf08a9
data: restore controls-gisaid strain listfa123009
script: defragment plot for 2185f24f695
dataset: update controls-gisaid strain listefc5aab7
defaults: update validation to fix XBH dropout- See CHANGELOG.md for additional commits.
Files
ktmeaton/ncov-recombinant-v0.7.0.zip
Files
(5.5 MB)
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Additional details
Related works
- Is supplement to
- https://github.com/ktmeaton/ncov-recombinant/tree/v0.7.0 (URL)