File Changes for angie

v432_preview2 to v432_base (2022-05-31 to 2022-06-06) v432

• src/hg/utils/faToVcf/faToVcf.c
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    6212068bffa294be01c27e5e34f7b51def22f25a Tue Apr 12 17:58:51 2022 -0700
    Treat '-' bases as 'N' when counting differing bases between ref and input seq for -maxDiff.
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
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    4b526917c44114d3d9fa18e6dd31bee769b5a24f Mon Apr 4 09:44:28 2022 -0700
    Added proposed482. G210T in XS and proposed446 needs to be masked for pangolin. XD samples should have 29742; some do, some don't, so mask that in (HT Cornelius Roemer). Added miscRecombOrContam to prevent non-XM descendants of XM branch from being labeled XM (HT Cornelius Roemer).
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    046b5de9f797d101b1de3bf677fc7249672a9779 Thu Apr 14 09:48:12 2022 -0700
    Added BA.4, BA.5, BA.2.11, BA.2.12, BA.2.12.1, BA.2.3.2, BA.2.10.1, AY.112.3 (pango-designation v1.3). Added BA.2.9.1, BA.2.13, BA.1.20, BA.1.21, BA.1.21.1, BA.1.14.1, BA.1.14.2, BA.1.15.2, AY.122.6, AY.127.3 (pango-designation v1.4).
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    7d3899630ebc8e51b5ba9724645a7e2c5ec9cab5 Thu Apr 14 13:00:43 2022 -0700
    Renamed proposed478 to XT. Added new lineages BA.1.1.17, BA.1.16.2, BA.2.14, BA.2.15, BA.2.16, AY.4.2.5, AY.33.2, and AY.39.4 [which will be renamed to AY.134 in v1.6] (pango-designation v1.5).
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    0bdcc5b4d14cf7a66c4d1ce677de340a36a82949 Wed Apr 20 11:14:58 2022 -0700
    Mask some additional sites for proposed437 -- addition of a new sequence caused some shifting around. Rename miscRecombOrContam to miscBA1BA2Post17k and add more misc labels to cover not-quite-the-designated-recombinant branches.
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    c7b124d26dc2d6df9116b1ab73b871ea48b6e8ba Fri Apr 22 16:56:18 2022 -0700
    Renamed AY.39.4 to AY.134. Added new lineages BA.1.22, BA.1.1.18, BA.2.3.3, BA.2.3.4, BA.2.9.2, BA.2.17-34, BA.2.25.1, XU and AY.39.1.4 - pango-designation v1.7
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    9c35703727c4430d37385dfc2245224c34e4c8ec Fri Apr 22 20:00:52 2022 -0700
    Added new lineage BA.3.1 - pango-designation v1.8
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    0c307351d389eef43c1f8e6157319a64fc7dde6b Mon May 2 09:33:55 2022 -0700
    Don't require C2455T for B.1.640; new back-mutation-penalizing matOptimize puts it on the branches to B.1.640.1 and B.1.640.2.
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    7b5cc8d266fb8f0fe6bd3205aa9ecc0c5216b3ef Mon May 9 17:21:59 2022 -0700
    Changes since release 1.8: BA.2.3.3 withdrawn; BA.2.12.1 broadened; BA.2.13 tweaked for change in order of mutations; new lineages BA.2.23.1, BA.2.35-39. Also added markers for several proposed lineages.
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    8332e557ae10b5c28591af7a3f534ebfb237934b Tue May 10 11:20:38 2022 -0700
    Renamed proposed569 to BA.2.10.2 and proposed542 to BA.2.40.1, with its parent node as BA.2.40.
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    3a55344530eb4be149af6c7995fa0757c887afc7 Thu May 12 20:43:37 2022 -0700
    Renamed proposed463 to XV, proposed586 to BA.2.41 and proposed591 to XW. Added proposed606 and proposed607.
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    ba77c7da2bff16677e7d42484a74aac9c645e9f2 Fri May 13 14:21:05 2022 -0700
    Move definition of BA.2.41 to where I would expect to find it. We are now up to pango-designation v1.9.
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    491248ae0a0495930849ee36c56163cd07168eca Tue May 17 13:28:36 2022 -0700
    Tweak to B.1.637.1 for more back-mutation-averse matOptimize.
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    a67eeb144dcd0ff90df4de1ad726ea7b34b82a6c Fri May 27 09:39:44 2022 -0700
    Added new post-v1.9 lineages AY.98.1.1, BA.2.10.3, BA.2.42-45, BA.4.1; renamed proposed606 to XY. Added proposed636-7. Removed masked reversions from BA.2.13 since those have been cleaned up.
• src/lib/linefile.c
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    48d497b991b74998ee79dfb1276235b0930863be Tue May 31 09:43:07 2022 -0700
    Increase hardcoded line size limit in linefile.c; the Newick-formatted SARS-CoV-2 tree with 10 million sequences breaks this limit. If/when we approach 20 million this may need to be redoubled.