File Changes for angie

v409_preview to v409_preview2 (2021-01-04 to 2021-01-11) v409

• src/hg/hgPhyloPlace/phyloPlace.c
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    55d15bfd5b19c9755b8385df51cd002a61e2baf6 Mon Jan 4 18:04:38 2021 -0800
    When writing custom tracks, attribute public vs. GISAID sequences correctly.
• src/hg/hgPhyloPlace/phyloPlace.h
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    55d15bfd5b19c9755b8385df51cd002a61e2baf6 Mon Jan 4 18:04:38 2021 -0800
    When writing custom tracks, attribute public vs. GISAID sequences correctly.
• src/hg/hgPhyloPlace/writeCustomTracks.c
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    55d15bfd5b19c9755b8385df51cd002a61e2baf6 Mon Jan 4 18:04:38 2021 -0800
    When writing custom tracks, attribute public vs. GISAID sequences correctly.
• src/hg/hgTracks/vcfTrack.c
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    2ebfbfc9042e880ad0cdda1643d4ec57621579df Mon Jan 4 18:03:11 2021 -0800
    Warn about empty tree file and avoid seg fault.
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    6301b9d4214f464863531b4af0e0ba2c0f6106b4 Wed Jan 6 20:33:39 2021 -0800
    Increase branch width for VCF+tree display; it was really hard to follow branches with the narrow width. Russ asked to make it configurable; for now, just make it wider.
• src/hg/makeDb/doc/wuhCor1/phylogenetics.txt
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    244a07ffab7f03e9dadc8419c14f3685246860a9 Tue Jan 5 00:47:01 2021 -0800
    Adding B.1.1.7 (US) track. refs #26753
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    4f0cb5be8dce2a3a1e070e23c8a150c375a6e979 Tue Jan 5 10:47:57 2021 -0800
    lineageB_1_1_7_US update: replace EPI_ IDs with GenBank IDs so we can share more sequences in VCF. refs #26753
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    55de0a7d0d285d4be07cd15958db764d8ed3f6ed Tue Jan 5 16:26:01 2021 -0800
    Adding New York B.1.1.7 sequence, updating GenBank links in description. refs #26753
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    04d2dd20a61dd65b51611024d31c04078276c6b3 Thu Jan 7 17:14:09 2021 -0800
    A little cleanup of some inconsistent names and a stray rev-strand sequence in preparation for rolling out incrementally updated trees of public sequences.
• src/hg/makeDb/trackDb/virus/wuhCor1/lineageB_1_1_7_US.html
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    244a07ffab7f03e9dadc8419c14f3685246860a9 Tue Jan 5 00:47:01 2021 -0800
    Adding B.1.1.7 (US) track. refs #26753
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    55de0a7d0d285d4be07cd15958db764d8ed3f6ed Tue Jan 5 16:26:01 2021 -0800
    Adding New York B.1.1.7 sequence, updating GenBank links in description. refs #26753
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    bf4c0a38e64577aa9a4ade7efc43ab705ce2c1a1 Wed Jan 6 17:12:58 2021 -0800
    Updating link for subtree with NY and San Diego sequences. refs #26753
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    09525abd6d4ced09add79f0d1e6c0475ef0fd7ab Thu Jan 7 17:13:00 2021 -0800
    No need to refer to the genome-test version of hgPhyloPlace now that the tree has been updated on the RR, thanks Lou! refs #26753, #26774
• src/hg/makeDb/trackDb/virus/wuhCor1/sarsCov2Phylo.html
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    f52368a9198ad15b260ca56301a2a0baf653267b Mon Jan 4 18:00:09 2021 -0800
    Updating reference for Pangolin lineage nomenclature.
• src/hg/makeDb/trackDb/virus/wuhCor1/sarsCov2PhyloPub.html
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    f52368a9198ad15b260ca56301a2a0baf653267b Mon Jan 4 18:00:09 2021 -0800
    Updating reference for Pangolin lineage nomenclature.
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
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    244a07ffab7f03e9dadc8419c14f3685246860a9 Tue Jan 5 00:47:01 2021 -0800
    Adding B.1.1.7 (US) track. refs #26753
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    f260f5d365a4c2eee0148ea35df12ff14995a48c Tue Jan 5 13:00:12 2021 -0800
    David suggests emphasizing in the longLabel that this track includes deletions unlike other tracks. refs #26753
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    55de0a7d0d285d4be07cd15958db764d8ed3f6ed Tue Jan 5 16:26:01 2021 -0800
    Adding New York B.1.1.7 sequence, updating GenBank links in description. refs #26753
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    cd7f64050304b673a80b0e3eeb748bba67780b97 Thu Jan 7 17:15:34 2021 -0800
    Add correct release date for pennant icon mouseover. refs #26753
• src/hg/utils/otto/sarscov2phylo/updateIdMapping.sh
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    b9b84244ae9fbfa6d81c92028634be26e8a5898f Tue Jan 5 00:50:55 2021 -0800
    Prevent redundant seqToEpi lines from nextmeta cobbled together from old nextmeta plus manually downloaded sequences.
• src/lib/udc.c
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    fafc064148fba3ad1efdb726b3ac3fdd0784d4e1 Mon Jan 4 18:02:21 2021 -0800
    When a file has a single line of content with no newline, return the content instead of NULL.