File Changes for angie

v396_preview2 to v396_base (2020-03-23 to 2020-03-30) v396

• src/hg/makeDb/trackDb/virus/wuhCor1/description.html
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    19d834ec878db855e2da3fee9cef585ccdf17931 Thu Mar 26 10:56:09 2020 -0700
    Updating virus name to SARS-CoV-2.
• src/hg/makeDb/trackDb/virus/wuhCor1/ncbiGene.html
  • lines changed 1, context: html, text, full: html, text
    19d834ec878db855e2da3fee9cef585ccdf17931 Thu Mar 26 10:56:09 2020 -0700
    Updating virus name to SARS-CoV-2.
• src/hg/makeDb/trackDb/virus/wuhCor1/ncbiGeneBGP.html
  • lines changed 1, context: html, text, full: html, text
    19d834ec878db855e2da3fee9cef585ccdf17931 Thu Mar 26 10:56:09 2020 -0700
    Updating virus name to SARS-CoV-2.
• src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainClade.html
  • lines changed 60, context: html, text, full: html, text
    79deaabec43414458c195d8b4b3abce6d0e75cd6 Mon Mar 23 17:35:56 2020 -0700
    Fleshing out nextstrain track details (thanks for starting those, Max!) refs #25188
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    4cc83524b64cfedc3898c869ada91c3734b22aab Wed Mar 25 11:46:20 2020 -0700
    Added links from clades back to Nextstrain, and from description page to Nextstrain situation report pages that used the clades. refs #25188
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    8cd41d8051583a144e2405ee0df4c90bf92881ff Wed Mar 25 14:29:04 2020 -0700
    Tree terminology correction from David. refs #25188
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    fc7f1b9f5e16f4128f56760ac87a5649ee422b9d Thu Mar 26 15:07:25 2020 -0700
    Add TreeTime date and administrative division (location) info for clades to nextstrainClade. refs #25188
• src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainClades.html
  • lines changed 29, context: html, text, full: html, text
    79deaabec43414458c195d8b4b3abce6d0e75cd6 Mon Mar 23 17:35:56 2020 -0700
    Fleshing out nextstrain track details (thanks for starting those, Max!) refs #25188
• src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainGene.html
  • lines changed 26, context: html, text, full: html, text
    79deaabec43414458c195d8b4b3abce6d0e75cd6 Mon Mar 23 17:35:56 2020 -0700
    Fleshing out nextstrain track details (thanks for starting those, Max!) refs #25188
• src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainSamples.html
  • lines changed 97, context: html, text, full: html, text
    79deaabec43414458c195d8b4b3abce6d0e75cd6 Mon Mar 23 17:35:56 2020 -0700
    Fleshing out nextstrain track details (thanks for starting those, Max!) refs #25188
• src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainVars.html
  • lines changed 66, context: html, text, full: html, text
    79deaabec43414458c195d8b4b3abce6d0e75cd6 Mon Mar 23 17:35:56 2020 -0700
    Fleshing out nextstrain track details (thanks for starting those, Max!) refs #25188
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.nextstrain.ra
  • lines changed 2, context: html, text, full: html, text
    4cc83524b64cfedc3898c869ada91c3734b22aab Wed Mar 25 11:46:20 2020 -0700
    Added links from clades back to Nextstrain, and from description page to Nextstrain situation report pages that used the clades. refs #25188
• src/hg/utils/otto/nextstrainNcov/doUpdate.sh
  • lines changed 18, context: html, text, full: html, text
    7b7e13b225417cda1b010036bb13394a8c1e790c Mon Mar 23 18:13:36 2020 -0700
    Updating nextstrainNcov/doUpdate.sh to produce less output and be smarter about the true file date. refs #25188
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    35899dd8b6349db50dd77a92398d356d9d3be47b Tue Mar 24 15:16:01 2020 -0700
    Make doUpdate silent when ncov.json has not been updated since the last build. refs #25188
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    fc7f1b9f5e16f4128f56760ac87a5649ee422b9d Thu Mar 26 15:07:25 2020 -0700
    Add TreeTime date and administrative division (location) info for clades to nextstrainClade. refs #25188
• src/hg/utils/otto/nextstrainNcov/nextstrain.py
  • lines changed 37, context: html, text, full: html, text
    39a6a0080ab48990a02c59d21a1566d25a0103fe Wed Mar 25 15:28:33 2020 -0700
    Add sample date (just month and day; GISAID sample name ends in year) to sample labels in VCF (David request). refs #25188
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    3aec6ebceadc5dee647d4c1b294b3a3d81a391e6 Wed Mar 25 17:38:38 2020 -0700
    Clade variant list format change from David: ;-separated for different nodes, ,-sep for within node; also added amino acid changes when applicable. refs #25188
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    fc7f1b9f5e16f4128f56760ac87a5649ee422b9d Thu Mar 26 15:07:25 2020 -0700
    Add TreeTime date and administrative division (location) info for clades to nextstrainClade. refs #25188
• src/hg/utils/otto/nextstrainNcov/nextstrainClade.as
  • lines changed 1, context: html, text, full: html, text
    4b20c7547572d8795b5a6675c45e44491b23b42d Wed Mar 25 14:30:12 2020 -0700
    Clade variant terminology change from David. refs #25188
  • lines changed 5, context: html, text, full: html, text
    fc7f1b9f5e16f4128f56760ac87a5649ee422b9d Thu Mar 26 15:07:25 2020 -0700
    Add TreeTime date and administrative division (location) info for clades to nextstrainClade. refs #25188