File Changes for angie

v445_preview to v445_preview2 (2023-02-27 to 2023-03-06) v445

• src/hg/lib/variantProjector.c
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    1bb425f9fa71e6a0092954afb46e99886e9f3c08 Wed Mar 1 16:26:44 2023 -0800
    Add a check for a boundary condition that so far has appeared only in zebrafish: an insertion that lands (with HGVS right-shifting) at the boundary between an alignment block and *double-sided* gap, i.e. it's not a clean intron gap but instead has skipped over both genomic and transcript sequence. Due to the double-sided gap, vpTx start txOffset > end txOffset (not ==) so vpTxIsInsertion returns false but it's still an insertion in the genome so there is no vpTx->txRef. This was triggering an errAbort; head that off by returning NULL from vpTxSplitByRegion so we just call it complex_transcript_variant, which is all we can say when the transcript aligner is perhaps trying too hard. refs #29262
• src/hg/utils/otto/nextstrainNcov/nextstrain.py
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    8e96c1feec31b621eaae7748c43f6a8fb26bf4b5 Fri Mar 3 15:17:21 2023 -0800
    Fixing error that could lead to doubled counts, caught by Jonathan in code review, thanks! refs #30709
• src/hg/utils/otto/sarscov2phylo/branchSpecificMask.yml
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    f8d1ee9294ec18a6d876796a23632bfe5292a733 Thu Mar 2 16:57:35 2023 -0800
    Adding a couple more reversions in XBC, pointed out by @corneliusroemer in p-d 1100
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
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    84b64e86349ff055765d58c81cb99f856a6a09ba Thu Mar 2 16:55:00 2023 -0800
    Many new lineages, p-d v1.18.1 and beyond, some corrections & non-Pango labels. * Added B.1.1.529_dropout, BA.1_dropout, BA.2_dropout so I wouldn't have to move labels back manually in lineageTree for pangolin * Removed BA.5.2_no28330 since it's mostly not BA.5.2 (p-d issue 1640) * Corrections: - BQ.1.19: I had erroneously annotated this as BQ.1 > G22599C but it's BQ.1 > T23042C - CM.10: corrected allele for its reversion on 22995 - BN.3.1: I was missing the defining T23031C (S:F490S) at the end - CL.1: resolved some Ns that have cleared up with more sequences - BF.7.14: only S:C1243F is in p-d lineage_notes.txt, don't require G1085T - BA.5.2.50: broaden to not require C884T because it was missing from many seqs, p-d 1542 - BQ.1.1.7: add N to allow C29733T in path, not require reversion - XBF: broaden to not require G625T, p-d 1259
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    e77b309554b2756242db1f54214367d96ac0fc2b Fri Mar 3 15:18:56 2023 -0800
    Oops, missed that C26270T was reverted in CP.7.