All File Changes

v353_base to v354_preview (2017-08-07 to 2017-08-14) v354

• src/hg/hgCollection/hgCollection.c
  • lines changed 29, context: html, text, full: html, text
    a5b512a7a022c72d644b843b88f8d0e6c990a5cf Fri Aug 11 14:49:58 2017 -0700
    move to jstree, first pass at Cath's spec
• src/hg/hgTables/mainPage.c
  • lines changed 1, context: html, text, full: html, text
    91a5433b04d68f18947c959bc335c290bf24c556 Mon Aug 7 16:57:47 2017 -0700
    Minor edit to GTF output TB drop-down and adding url to FAQ in TB usage GTF blurb, refs #257
• src/hg/hgTables/usage.c
  • lines changed 3, context: html, text, full: html, text
    91a5433b04d68f18947c959bc335c290bf24c556 Mon Aug 7 16:57:47 2017 -0700
    Minor edit to GTF output TB drop-down and adding url to FAQ in TB usage GTF blurb, refs #257
  • lines changed 1, context: html, text, full: html, text
    bb7b0e40468f5c9bf19aba7834a72199a9e30e45 Mon Aug 7 17:02:17 2017 -0700
    Minor lowercase edit to TB GTF usage, refs #257
• src/hg/hgTracks/barChartTrack.c
  • lines changed 72, context: html, text, full: html, text
    18114c799ed1df9bc555b832ca21008c5bb63b45 Wed Jul 26 11:02:54 2017 -0700
    Add autoscale feature. refs #19867
  • lines changed 40, context: html, text, full: html, text
    21bf4f713e944af4e8810544d68c441510ea85a3 Wed Jul 26 16:31:01 2017 -0700
    Add support for maxHeightPixels in trackDb and UI of barChart type tracks. refs #19872
  • lines changed 10, context: html, text, full: html, text
    ed768f7644e7de01fbfa83c1a8f17129ed3305d1 Tue Aug 1 10:13:34 2017 -0700
    Minor code cleanup. refs #19872
  • lines changed 3, context: html, text, full: html, text
    a79ca8843be0fbe1b0c59167db1aa9e4b487a07e Wed Aug 9 12:45:32 2017 -0700
    Fixes to maxHeightPixels support in barChart UI. refs #19872
• src/hg/hgVai/hgVai.c
  • lines changed 47, context: html, text, full: html, text
    de29d745d32fb04a5187fb5998cc94bbb9bf41a4 Wed Aug 9 13:39:59 2017 -0700
    Add optional HGVS output to annoGratorGpVar and hgVai. Since annoGratorGpVar is genePred-based, it can't yet take advantage of variantProjector's full PSL+CDS+sequence support, so when transcripts don't align cleanly to genome, HGVS c./n./p. output may be incorrect. refs #19968
• src/hg/hgVarAnnogrator/hgVarAnnogrator.c
  • lines changed 1, context: html, text, full: html, text
    de29d745d32fb04a5187fb5998cc94bbb9bf41a4 Wed Aug 9 13:39:59 2017 -0700
    Add optional HGVS output to annoGratorGpVar and hgVai. Since annoGratorGpVar is genePred-based, it can't yet take advantage of variantProjector's full PSL+CDS+sequence support, so when transcripts don't align cleanly to genome, HGVS c./n./p. output may be incorrect. refs #19968
• src/hg/htdocs/FAQ/FAQdownloads.html
  • lines changed 14, context: html, text, full: html, text
    66244bd54def30df6443a79f7a72a913f31d6447 Tue Aug 8 12:57:26 2017 -0700
    Adding summary of TB GTF limitations, refs #257
• src/hg/htdocs/admin/maintenance.html
  • lines changed 5, context: html, text, full: html, text
    56d020d8fd2a2aca2a3e4f6bebdab520b3f20363 Wed Aug 9 16:00:16 2017 -0700
    Adding red font requested by Brian, no refs
• src/hg/htdocs/contacts.html
  • lines changed 1, context: html, text, full: html, text
    7f89f5035d98c3467d0335fb190ed2bf1e459cbf Thu Aug 10 09:58:29 2017 -0700
    adding reference to public hubs for the genome-www list
• src/hg/htdocs/goldenPath/help/query.html
  • lines changed 4, context: html, text, full: html, text
    b52736a9195fe5eac309ca9f47c092a92dcf20c0 Thu Aug 10 11:31:32 2017 -0700
    Expanding HGVS examples and adding a tag to section, goldenPath/help/query.html#HGVS ref #18372
• src/hg/htdocs/inc/hgCollection.html
  • lines changed 41, context: html, text, full: html, text
    a5b512a7a022c72d644b843b88f8d0e6c990a5cf Fri Aug 11 14:49:58 2017 -0700
    move to jstree, first pass at Cath's spec
• src/hg/htdocs/staff.html
  • lines changed 10, context: html, text, full: html, text
    605b618ae59480d74c11e2a8184984a61b057299 Tue Aug 8 13:58:57 2017 -0700
    moved Donna and Luvina to alumni, fixed Jairo's name
  • lines changed 9, context: html, text, full: html, text
    a046da4b1f4bd092d6b118640544565b5e1ee77e Tue Aug 8 14:07:34 2017 -0700
    corrected project afiliation, as needed
  • lines changed 12, context: html, text, full: html, text
    afe7543bf717a2cf2f695ca94f09b614b21667e6 Tue Aug 8 14:14:18 2017 -0700
    edited titles and removed specialties
  • lines changed 4, context: html, text, full: html, text
    6e073ba943bae78951dc730043eca73e60b0b6a2 Tue Aug 8 14:26:02 2017 -0700
    added Paris and Alexa
  • lines changed 1, context: html, text, full: html, text
    8c51b8c4d802b56c5994e23d0c5f60e65c9158d5 Tue Aug 8 14:28:03 2017 -0700
    fixing space
• src/hg/inc/annoGratorGpVar.h
  • lines changed 3, context: html, text, full: html, text
    de29d745d32fb04a5187fb5998cc94bbb9bf41a4 Wed Aug 9 13:39:59 2017 -0700
    Add optional HGVS output to annoGratorGpVar and hgVai. Since annoGratorGpVar is genePred-based, it can't yet take advantage of variantProjector's full PSL+CDS+sequence support, so when transcripts don't align cleanly to genome, HGVS c./n./p. output may be incorrect. refs #19968
• src/hg/inc/barChartUi.h
  • lines changed 2, context: html, text, full: html, text
    18114c799ed1df9bc555b832ca21008c5bb63b45 Wed Jul 26 11:02:54 2017 -0700
    Add autoscale feature. refs #19867
  • lines changed 8, context: html, text, full: html, text
    21bf4f713e944af4e8810544d68c441510ea85a3 Wed Jul 26 16:31:01 2017 -0700
    Add support for maxHeightPixels in trackDb and UI of barChart type tracks. refs #19872
  • lines changed 4, context: html, text, full: html, text
    a79ca8843be0fbe1b0c59167db1aa9e4b487a07e Wed Aug 9 12:45:32 2017 -0700
    Fixes to maxHeightPixels support in barChart UI. refs #19872
• src/hg/inc/cart.h
  • lines changed 7, context: html, text, full: html, text
    a79ca8843be0fbe1b0c59167db1aa9e4b487a07e Wed Aug 9 12:45:32 2017 -0700
    Fixes to maxHeightPixels support in barChart UI. refs #19872
• src/hg/inc/hdb.h
  • lines changed 7, context: html, text, full: html, text
    37977956905d588f73ee5f635fae2f609cb40842 Wed Aug 9 12:52:00 2017 -0700
    Assorted little util functions in support of adding HGVS output to hgVai -- refs #19968
• src/hg/inc/hgHgvs.h
  • lines changed 43, context: html, text, full: html, text
    de29d745d32fb04a5187fb5998cc94bbb9bf41a4 Wed Aug 9 13:39:59 2017 -0700
    Add optional HGVS output to annoGratorGpVar and hgVai. Since annoGratorGpVar is genePred-based, it can't yet take advantage of variantProjector's full PSL+CDS+sequence support, so when transcripts don't align cleanly to genome, HGVS c./n./p. output may be incorrect. refs #19968
• src/hg/inc/hui.h
  • lines changed 1, context: html, text, full: html, text
    4b6ac84870c1f19f651aae4feb3089d415a05e6f Wed Aug 9 13:57:57 2017 -0700
    adding file missing in last commit
• src/hg/inc/indelShift.h
  • lines changed 39, context: html, text, full: html, text
    61647b42c0de4b0d11abf375cd713cb28758a954 Wed Aug 9 12:53:14 2017 -0700
    New lib modules in support of adding HGVS output to hgVai: - seqWindow: generic interface to fetch portions of a sequence - indelShift: slide to the left or right of an ambiguous alignment range (e.g. AG to AGAGAG) - variantProjector: use PSL+CDS to project a genomic variant to a transcript variant; project transcript variant to protein variant refs #19968
• src/hg/inc/seqWindow.h
  • lines changed 53, context: html, text, full: html, text
    61647b42c0de4b0d11abf375cd713cb28758a954 Wed Aug 9 12:53:14 2017 -0700
    New lib modules in support of adding HGVS output to hgVai: - seqWindow: generic interface to fetch portions of a sequence - indelShift: slide to the left or right of an ambiguous alignment range (e.g. AG to AGAGAG) - variantProjector: use PSL+CDS to project a genomic variant to a transcript variant; project transcript variant to protein variant refs #19968
• src/hg/inc/variantProjector.h
  • lines changed 121, context: html, text, full: html, text
    61647b42c0de4b0d11abf375cd713cb28758a954 Wed Aug 9 12:53:14 2017 -0700
    New lib modules in support of adding HGVS output to hgVai: - seqWindow: generic interface to fetch portions of a sequence - indelShift: slide to the left or right of an ambiguous alignment range (e.g. AG to AGAGAG) - variantProjector: use PSL+CDS to project a genomic variant to a transcript variant; project transcript variant to protein variant refs #19968
• src/hg/inc/wiggle.h
  • lines changed 4, context: html, text, full: html, text
    21bf4f713e944af4e8810544d68c441510ea85a3 Wed Jul 26 16:31:01 2017 -0700
    Add support for maxHeightPixels in trackDb and UI of barChart type tracks. refs #19872
  • lines changed 4, context: html, text, full: html, text
    a79ca8843be0fbe1b0c59167db1aa9e4b487a07e Wed Aug 9 12:45:32 2017 -0700
    Fixes to maxHeightPixels support in barChart UI. refs #19872
• src/hg/js/hgCollection.js
  • lines changed 339, context: html, text, full: html, text
    a5b512a7a022c72d644b843b88f8d0e6c990a5cf Fri Aug 11 14:49:58 2017 -0700
    move to jstree, first pass at Cath's spec
• src/hg/js/utils.js
  • lines changed 19, context: html, text, full: html, text
    18114c799ed1df9bc555b832ca21008c5bb63b45 Wed Jul 26 11:02:54 2017 -0700
    Add autoscale feature. refs #19867
• src/hg/lib/annoFormatVep.c
  • lines changed 29, context: html, text, full: html, text
    de29d745d32fb04a5187fb5998cc94bbb9bf41a4 Wed Aug 9 13:39:59 2017 -0700
    Add optional HGVS output to annoGratorGpVar and hgVai. Since annoGratorGpVar is genePred-based, it can't yet take advantage of variantProjector's full PSL+CDS+sequence support, so when transcripts don't align cleanly to genome, HGVS c./n./p. output may be incorrect. refs #19968
• src/hg/lib/annoGratorGpVar.c
  • lines changed 230, context: html, text, full: html, text
    de29d745d32fb04a5187fb5998cc94bbb9bf41a4 Wed Aug 9 13:39:59 2017 -0700
    Add optional HGVS output to annoGratorGpVar and hgVai. Since annoGratorGpVar is genePred-based, it can't yet take advantage of variantProjector's full PSL+CDS+sequence support, so when transcripts don't align cleanly to genome, HGVS c./n./p. output may be incorrect. refs #19968
• src/hg/lib/barChartUi.c
  • lines changed 40, context: html, text, full: html, text
    18114c799ed1df9bc555b832ca21008c5bb63b45 Wed Jul 26 11:02:54 2017 -0700
    Add autoscale feature. refs #19867
  • lines changed 29, context: html, text, full: html, text
    21bf4f713e944af4e8810544d68c441510ea85a3 Wed Jul 26 16:31:01 2017 -0700
    Add support for maxHeightPixels in trackDb and UI of barChart type tracks. refs #19872
  • lines changed 21, context: html, text, full: html, text
    a79ca8843be0fbe1b0c59167db1aa9e4b487a07e Wed Aug 9 12:45:32 2017 -0700
    Fixes to maxHeightPixels support in barChart UI. refs #19872
  • lines changed 5, context: html, text, full: html, text
    353c944fde8bc6cb69b56eb6caa80a20a5c60921 Wed Aug 9 12:51:33 2017 -0700
    Disable autoScale feature for now. MaxHeightPixels seems enough for now to address user scaling issues, and autoScale is confusing. refs #19867
  • lines changed 3, context: html, text, full: html, text
    516063c68ea96a492cf8f4c971498f99cdce838a Wed Aug 9 13:09:18 2017 -0700
    Relabel for clarity. refs #19872
• src/hg/lib/cart.c
  • lines changed 106, context: html, text, full: html, text
    a79ca8843be0fbe1b0c59167db1aa9e4b487a07e Wed Aug 9 12:45:32 2017 -0700
    Fixes to maxHeightPixels support in barChart UI. refs #19872
• src/hg/lib/hdb.c
  • lines changed 39, context: html, text, full: html, text
    37977956905d588f73ee5f635fae2f609cb40842 Wed Aug 9 12:52:00 2017 -0700
    Assorted little util functions in support of adding HGVS output to hgVai -- refs #19968
• src/hg/lib/hgHgvs.c
  • lines changed 692, context: html, text, full: html, text
    de29d745d32fb04a5187fb5998cc94bbb9bf41a4 Wed Aug 9 13:39:59 2017 -0700
    Add optional HGVS output to annoGratorGpVar and hgVai. Since annoGratorGpVar is genePred-based, it can't yet take advantage of variantProjector's full PSL+CDS+sequence support, so when transcripts don't align cleanly to genome, HGVS c./n./p. output may be incorrect. refs #19968
  • lines changed 40, context: html, text, full: html, text
    904b4e4ad971a5be51a26dee4809efbe9c7b6430 Thu Aug 10 13:22:26 2017 -0700
    Support XM_/XR_/XP_ accs in HGVS position search. Generate correct HGVS p.*ext terms for stop codon loss. refs #19968
• src/hg/lib/hgHgvsParse.c
  • lines changed 3, context: html, text, full: html, text
    812dec9c5d8a5c947bd30442feae4a4449f50257 Wed Aug 9 13:41:58 2017 -0700
    Oops, forgot to handle '=' in hgvsParseNucleotideChange.
• src/hg/lib/hui.c
  • lines changed 2, context: html, text, full: html, text
    21bf4f713e944af4e8810544d68c441510ea85a3 Wed Jul 26 16:31:01 2017 -0700
    Add support for maxHeightPixels in trackDb and UI of barChart type tracks. refs #19872
  • lines changed 2, context: html, text, full: html, text
    7b25ffaf74c9fdba348090b37245c6b44131c72f Wed Aug 9 11:23:25 2017 -0700
    making scoreLabel work with bigBed, refs #19514
• src/hg/lib/indelShift.c
  • lines changed 217, context: html, text, full: html, text
    61647b42c0de4b0d11abf375cd713cb28758a954 Wed Aug 9 12:53:14 2017 -0700
    New lib modules in support of adding HGVS output to hgVai: - seqWindow: generic interface to fetch portions of a sequence - indelShift: slide to the left or right of an ambiguous alignment range (e.g. AG to AGAGAG) - variantProjector: use PSL+CDS to project a genomic variant to a transcript variant; project transcript variant to protein variant refs #19968
• src/hg/lib/makefile
  • lines changed 5, context: html, text, full: html, text
    61647b42c0de4b0d11abf375cd713cb28758a954 Wed Aug 9 12:53:14 2017 -0700
    New lib modules in support of adding HGVS output to hgVai: - seqWindow: generic interface to fetch portions of a sequence - indelShift: slide to the left or right of an ambiguous alignment range (e.g. AG to AGAGAG) - variantProjector: use PSL+CDS to project a genomic variant to a transcript variant; project transcript variant to protein variant refs #19968
• src/hg/lib/seqWindow.c
  • lines changed 141, context: html, text, full: html, text
    61647b42c0de4b0d11abf375cd713cb28758a954 Wed Aug 9 12:53:14 2017 -0700
    New lib modules in support of adding HGVS output to hgVai: - seqWindow: generic interface to fetch portions of a sequence - indelShift: slide to the left or right of an ambiguous alignment range (e.g. AG to AGAGAG) - variantProjector: use PSL+CDS to project a genomic variant to a transcript variant; project transcript variant to protein variant refs #19968
• src/hg/lib/tests/expected/annoGrator/pgSnpKgDbToGpFx.txt
  • lines changed 1, context: html, text, full: html, text
    de29d745d32fb04a5187fb5998cc94bbb9bf41a4 Wed Aug 9 13:39:59 2017 -0700
    Add optional HGVS output to annoGratorGpVar and hgVai. Since annoGratorGpVar is genePred-based, it can't yet take advantage of variantProjector's full PSL+CDS+sequence support, so when transcripts don't align cleanly to genome, HGVS c./n./p. output may be incorrect. refs #19968
• src/hg/lib/variantProjector.c
  • lines changed 662, context: html, text, full: html, text
    61647b42c0de4b0d11abf375cd713cb28758a954 Wed Aug 9 12:53:14 2017 -0700
    New lib modules in support of adding HGVS output to hgVai: - seqWindow: generic interface to fetch portions of a sequence - indelShift: slide to the left or right of an ambiguous alignment range (e.g. AG to AGAGAG) - variantProjector: use PSL+CDS to project a genomic variant to a transcript variant; project transcript variant to protein variant refs #19968
  • lines changed 31, context: html, text, full: html, text
    904b4e4ad971a5be51a26dee4809efbe9c7b6430 Thu Aug 10 13:22:26 2017 -0700
    Support XM_/XR_/XP_ accs in HGVS position search. Generate correct HGVS p.*ext terms for stop codon loss. refs #19968
• src/hg/lib/wiggleCart.c
  • lines changed 20, context: html, text, full: html, text
    21bf4f713e944af4e8810544d68c441510ea85a3 Wed Jul 26 16:31:01 2017 -0700
    Add support for maxHeightPixels in trackDb and UI of barChart type tracks. refs #19872
  • lines changed 1, context: html, text, full: html, text
    10a3419b1e2f2da5893c65d3c3b65c8553ecf450 Tue Aug 8 14:06:41 2017 -0700
    Support for max height.
  • lines changed 98, context: html, text, full: html, text
    a79ca8843be0fbe1b0c59167db1aa9e4b487a07e Wed Aug 9 12:45:32 2017 -0700
    Fixes to maxHeightPixels support in barChart UI. refs #19872
  • lines changed 3, context: html, text, full: html, text
    efc5d694c63bb43de24814a20506798fb60b73ae Wed Aug 9 14:49:54 2017 -0700
    wiggleCart: Use theCart arg instead of global cart because not all mains define cart.
• src/hg/makeDb/doc/calJac3.txt
  • lines changed 116, context: html, text, full: html, text
    0c7a167d16c3f38a4a4f1dd0401c174d6457a709 Thu Aug 10 07:33:10 2017 -0700
    run up lastz chainNet panTro5 rheMac8 calJac3 per user request refs #19942
• src/hg/makeDb/doc/hg38/hg38.txt
  • lines changed 26, context: html, text, full: html, text
    7ec257cf5c0c902ca0dcefe0467929c9269f584a Tue Aug 8 10:05:51 2017 -0700
    Updating docs for refSeq FuncElems track, refs #19638
• src/hg/makeDb/doc/hg38/hg38Patch11.txt
  • lines changed 973, context: html, text, full: html, text
    fd3afb9bf651cb88e5a7ffb8eaf0172b02097894 Tue Aug 8 21:49:55 2017 -0700
    starting hg38 patch11 build refs #19665
  • lines changed 96, context: html, text, full: html, text
    f819efbf989664e74bc50f66a7b0ee90c3979ec8 Wed Aug 9 09:31:08 2017 -0700
    patch11 hg38 ready to go refs #19665
• src/hg/makeDb/doc/mm10.txt
  • lines changed 20, context: html, text, full: html, text
    7ec257cf5c0c902ca0dcefe0467929c9269f584a Tue Aug 8 10:05:51 2017 -0700
    Updating docs for refSeq FuncElems track, refs #19638
  • lines changed 7, context: html, text, full: html, text
    10e87001f0ed512b4896f8ad342bd6a683868d01 Tue Aug 8 21:52:46 2017 -0700
    adding gorGor5 lastz chainNet per user request refs #19942
• src/hg/makeDb/doc/panTro5/lastzRuns.txt
  • lines changed 74, context: html, text, full: html, text
    0c7a167d16c3f38a4a4f1dd0401c174d6457a709 Thu Aug 10 07:33:10 2017 -0700
    run up lastz chainNet panTro5 rheMac8 calJac3 per user request refs #19942
• src/hg/makeDb/trackDb/criGri/criGri1/crispr.html
  • lines changed 3, context: html, text, full: html, text
    ca085aae2412b02df4c5f999175d3940292fcdbc Wed Aug 9 08:56:21 2017 -0700
    Changing 'crispor.org' to the name of the tool 'CRISPOR' since the link doesn't go to crispor.org. I am also changing 20mer to 20-mer. refs #19514
  • lines changed 3, context: html, text, full: html, text
    f37d33372ff833f41675a166403ba5a1d29c1735 Wed Aug 9 09:38:35 2017 -0700
    Changing more '20mer' to '20-mer' on the track description page. Updating the bigBedToBed command to use this assembly, refs #19514
  • lines changed 2, context: html, text, full: html, text
    dfd453fee611e646e6eae02620747a73474a8a3c Wed Aug 9 11:42:26 2017 -0700
    Changing a few words to make the sentence flow better, refs #19514
  • lines changed 4, context: html, text, full: html, text
    fc0e423f203888246aaf0bee37947afd9fb18fb4 Wed Aug 9 12:47:15 2017 -0700
    Adding a space between 'base pairs'. Changing mentions of 'crispor' to the program name: CRISPOR. refs #19514
  • lines changed 9, context: html, text, full: html, text
    d00c3163e1ff25a32f6a94e5da0ee0e46d5b7211 Wed Aug 9 13:17:25 2017 -0700
    Changing 'crispor.org' to the URL it redirects to and adding target=_blank to links so they open on a new page. Refs #19514
  • lines changed 5, context: html, text, full: html, text
    cecef25fc1887af18396a2a28e6664198977de6f Wed Aug 9 14:08:09 2017 -0700
    Updating the 'Donech et al. 2016' link to go to the References section similar to the other links for papers. Making the Table Browser link in a new tab in the Data Access Section. Refs #19514
• src/hg/makeDb/trackDb/criGri/criGri1/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    fc7adc681e66df7b35a7fbd22827118062cb6ce4 Wed Aug 9 11:03:22 2017 -0700
    Updating the filter range to reflect the track description page, refs #19514
• src/hg/makeDb/trackDb/human/hg38/hg38Patch11.html
  • lines changed 656, context: html, text, full: html, text
    7367478384789bb7e17ccc1b3cf2bdfdcc68121d Wed Aug 9 10:03:52 2017 -0700
    finished with hg38Patch11 refs #19665
• src/hg/makeDb/trackDb/human/hg38/hg38Patch11.ra
  • lines changed 118, context: html, text, full: html, text
    7367478384789bb7e17ccc1b3cf2bdfdcc68121d Wed Aug 9 10:03:52 2017 -0700
    finished with hg38Patch11 refs #19665
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    27960bc9e588cd96eabf43f0925cefab1a75e33a Tue Aug 8 12:57:24 2017 -0700
    TrackDb stanzas and .html file pass 1 for refSeq functional elements, refs #19638
  • lines changed 2, context: html, text, full: html, text
    7367478384789bb7e17ccc1b3cf2bdfdcc68121d Wed Aug 9 10:03:52 2017 -0700
    finished with hg38Patch11 refs #19665
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    c5a15b156f54467ddbb97f161606aae66358d4d2 Mon Aug 7 10:56:01 2017 -0700
    leave staAur1 off the list for six months refs #19947
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 13, context: html, text, full: html, text
    27960bc9e588cd96eabf43f0925cefab1a75e33a Tue Aug 8 12:57:24 2017 -0700
    TrackDb stanzas and .html file pass 1 for refSeq functional elements, refs #19638
• src/hg/makeDb/trackDb/refSeqFuncElems.html
  • lines changed 45, context: html, text, full: html, text
    27960bc9e588cd96eabf43f0925cefab1a75e33a Tue Aug 8 12:57:24 2017 -0700
    TrackDb stanzas and .html file pass 1 for refSeq functional elements, refs #19638
  • lines changed 34, context: html, text, full: html, text
    9bbeab608f9e85ca550da567fcd32f4cc1713ff4 Wed Aug 9 11:07:22 2017 -0700
    Updating refSeqFuncElems html page, refs #19638
• src/hg/utils/makefile
  • lines changed 5, context: html, text, full: html, text
    e90f5a2fd5cdd909496615dacb99216c05dcfde1 Wed Aug 9 13:42:51 2017 -0700
    new util vcfToHgvs: translate genomic variants from VCF into HGVS terms using latest RefSeq transcript PSL, CDS and sequence. Tested against Personalis's "ground truth set", see PMID:28122645 and https://github.com/AngieHinrichs/hgvslib/. refs #19968
• src/hg/utils/otto/isca/buildISCA.csh
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    9e6e6f4381180bd4521989e1db844326513139d2 Wed Aug 9 09:22:42 2017 -0700
    Fixing an ISCA otto bug when alternative patch chromosomes are seen, no redmine
  • lines changed 9, context: html, text, full: html, text
    fdcec170f67061b8afe20d1514f229093e6915ce Fri Aug 11 12:09:38 2017 -0700
    Modfiying the ISCA script to be cshell compatible, no redmine
• src/hg/utils/vcfToHgvs/makefile
  • lines changed 3, context: html, text, full: html, text
    e90f5a2fd5cdd909496615dacb99216c05dcfde1 Wed Aug 9 13:42:51 2017 -0700
    new util vcfToHgvs: translate genomic variants from VCF into HGVS terms using latest RefSeq transcript PSL, CDS and sequence. Tested against Personalis's "ground truth set", see PMID:28122645 and https://github.com/AngieHinrichs/hgvslib/. refs #19968
• src/hg/utils/vcfToHgvs/tests/expected/PersonalisGroundTruth2017_agree.tab
  • lines changed 473, context: html, text, full: html, text
    e90f5a2fd5cdd909496615dacb99216c05dcfde1 Wed Aug 9 13:42:51 2017 -0700
    new util vcfToHgvs: translate genomic variants from VCF into HGVS terms using latest RefSeq transcript PSL, CDS and sequence. Tested against Personalis's "ground truth set", see PMID:28122645 and https://github.com/AngieHinrichs/hgvslib/. refs #19968
• src/hg/utils/vcfToHgvs/tests/expected/PersonalisGroundTruth2017_disagree.tab
  • lines changed 30, context: html, text, full: html, text
    e90f5a2fd5cdd909496615dacb99216c05dcfde1 Wed Aug 9 13:42:51 2017 -0700
    new util vcfToHgvs: translate genomic variants from VCF into HGVS terms using latest RefSeq transcript PSL, CDS and sequence. Tested against Personalis's "ground truth set", see PMID:28122645 and https://github.com/AngieHinrichs/hgvslib/. refs #19968
• src/hg/utils/vcfToHgvs/tests/expected/stopLoss.tab
  • lines changed 46, context: html, text, full: html, text
    904b4e4ad971a5be51a26dee4809efbe9c7b6430 Thu Aug 10 13:22:26 2017 -0700
    Support XM_/XR_/XP_ accs in HGVS position search. Generate correct HGVS p.*ext terms for stop codon loss. refs #19968
• src/hg/utils/vcfToHgvs/tests/input/PersonalisGroundTruth2017_agree.vcf
  • lines changed 128, context: html, text, full: html, text
    e90f5a2fd5cdd909496615dacb99216c05dcfde1 Wed Aug 9 13:42:51 2017 -0700
    new util vcfToHgvs: translate genomic variants from VCF into HGVS terms using latest RefSeq transcript PSL, CDS and sequence. Tested against Personalis's "ground truth set", see PMID:28122645 and https://github.com/AngieHinrichs/hgvslib/. refs #19968
• src/hg/utils/vcfToHgvs/tests/input/PersonalisGroundTruth2017_disagree.vcf
  • lines changed 48, context: html, text, full: html, text
    e90f5a2fd5cdd909496615dacb99216c05dcfde1 Wed Aug 9 13:42:51 2017 -0700
    new util vcfToHgvs: translate genomic variants from VCF into HGVS terms using latest RefSeq transcript PSL, CDS and sequence. Tested against Personalis's "ground truth set", see PMID:28122645 and https://github.com/AngieHinrichs/hgvslib/. refs #19968
• src/hg/utils/vcfToHgvs/tests/input/stopLoss.vcf
  • lines changed 11, context: html, text, full: html, text
    904b4e4ad971a5be51a26dee4809efbe9c7b6430 Thu Aug 10 13:22:26 2017 -0700
    Support XM_/XR_/XP_ accs in HGVS position search. Generate correct HGVS p.*ext terms for stop codon loss. refs #19968
• src/hg/utils/vcfToHgvs/tests/makefile
  • lines changed 29, context: html, text, full: html, text
    e90f5a2fd5cdd909496615dacb99216c05dcfde1 Wed Aug 9 13:42:51 2017 -0700
    new util vcfToHgvs: translate genomic variants from VCF into HGVS terms using latest RefSeq transcript PSL, CDS and sequence. Tested against Personalis's "ground truth set", see PMID:28122645 and https://github.com/AngieHinrichs/hgvslib/. refs #19968
  • lines changed 5, context: html, text, full: html, text
    904b4e4ad971a5be51a26dee4809efbe9c7b6430 Thu Aug 10 13:22:26 2017 -0700
    Support XM_/XR_/XP_ accs in HGVS position search. Generate correct HGVS p.*ext terms for stop codon loss. refs #19968
• src/hg/utils/vcfToHgvs/vcfToHgvs.c
  • lines changed 319, context: html, text, full: html, text
    e90f5a2fd5cdd909496615dacb99216c05dcfde1 Wed Aug 9 13:42:51 2017 -0700
    new util vcfToHgvs: translate genomic variants from VCF into HGVS terms using latest RefSeq transcript PSL, CDS and sequence. Tested against Personalis's "ground truth set", see PMID:28122645 and https://github.com/AngieHinrichs/hgvslib/. refs #19968
• src/inc/common.h
  • lines changed 4, context: html, text, full: html, text
    37977956905d588f73ee5f635fae2f609cb40842 Wed Aug 9 12:52:00 2017 -0700
    Assorted little util functions in support of adding HGVS output to hgVai -- refs #19968
• src/inc/dnaseq.h
  • lines changed 7, context: html, text, full: html, text
    37977956905d588f73ee5f635fae2f609cb40842 Wed Aug 9 12:52:00 2017 -0700
    Assorted little util functions in support of adding HGVS output to hgVai -- refs #19968
• src/inc/dnautil.h
  • lines changed 7, context: html, text, full: html, text
    37977956905d588f73ee5f635fae2f609cb40842 Wed Aug 9 12:52:00 2017 -0700
    Assorted little util functions in support of adding HGVS output to hgVai -- refs #19968
• src/lib/common.c
  • lines changed 23, context: html, text, full: html, text
    37977956905d588f73ee5f635fae2f609cb40842 Wed Aug 9 12:52:00 2017 -0700
    Assorted little util functions in support of adding HGVS output to hgVai -- refs #19968
• src/lib/dnaseq.c
  • lines changed 27, context: html, text, full: html, text
    37977956905d588f73ee5f635fae2f609cb40842 Wed Aug 9 12:52:00 2017 -0700
    Assorted little util functions in support of adding HGVS output to hgVai -- refs #19968
• src/lib/dnautil.c
  • lines changed 55, context: html, text, full: html, text
    37977956905d588f73ee5f635fae2f609cb40842 Wed Aug 9 12:52:00 2017 -0700
    Assorted little util functions in support of adding HGVS output to hgVai -- refs #19968
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    9c3f29aae9c3e46a7c562f90366dbca7846528c8 Mon Aug 14 10:05:36 2017 -0700
    v354 preview1

• lines changed: 6838
• files changed: 101