Commits for angie

v355_base to v356_preview (2017-09-18 to 2017-09-25) v356

c20579fc7c537c1736650125c5d264357d2cfa78 Mon Sep 18 13:15:16 2017 -0700

• Big search & replace: use https instead of http for NCBI URLs. refs #17793
  • src/hg/cirm/cdw/cdwSummary/cdwSummary - lines changed 3, context: html, text, full: html, text
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a0c8e5e673c15848e6f9ab33e7e77f32c641d995 Mon Sep 18 14:38:57 2017 -0700

• Big search & replace: use https instead of http for NCBI URLs. refs #17793
  • python/lib/ucscGb/externalData/geo/soft.py - lines changed 1, context: html, text, full: html, text
  • python/lib/ucscGb/externalData/geo/submission.py - lines changed 1, context: html, text, full: html, text
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447843e8a6310fa7a837c2f1790dea8a093e9cf7 Wed Sep 20 13:20:53 2017 -0700

• NCBI RefSeq: link out to MGI IDs for mouse. Use the human-specific hgnc column of ncbiRefSeqLink table. In hgc, if contents of hgnc start with "MGI:" then label as MGI instead of HGNC. In ncbiRefSeqOther bigBed, omit extra columns that have no values (like OMIM and HGNC for mouse, and MGI for human); auto-generate ncbiRefSeqOther.as accordingly. refs #18997
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8713ca7b27e952757501d687a3b48b9ec42f932e Thu Sep 21 11:02:25 2017 -0700

• Oops, 0 is a valid limit on how many bases we're allowed to shift; make INDEL_SHIFT_NO_MAX negative.
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bf2b4ab1b621fbcddc5b00c40616fdda09681942 Thu Sep 21 11:15:57 2017 -0700

• Peter Causey-Freeman (VariantValidator.org) convinced me that Mutalyzer is overconfident in assigning p.= to variants in UTR, introns etc; safer to go with p.?.
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bb1de08ea64e41b63cb861913f65712c29607e11 Fri Sep 22 15:51:49 2017 -0700

• Updating urls for MGI ID.
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1ffd9a045c83c4b4a90493323e4dc3d3ac677f31 Fri Sep 22 16:07:10 2017 -0700

• When start codon is lost, HGVS p. should be p.? because there may or may not be something that rescues the protein like a downstream in-frame start codon.
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0164f9e45e1d8777bf20e4d34113afe80d9c9619 Fri Sep 22 16:51:46 2017 -0700

• Broadening accession regexes so they also include NP_ -- mouse uses NP_ for chrM unlike human which uses YP_. refs #18997
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