All File Changes

v354_preview to v354_preview2 (2017-08-14 to 2017-08-18) v354

• src/hg/hgCollection/hgCollection.c
  • lines changed 82, context: html, text, full: html, text
    12b9c036ada723b623e3b66cd0b0c85e0328df9c Mon Aug 14 21:45:24 2017 -0700
    add AJAX store.
  • lines changed 11, context: html, text, full: html, text
    f78979b24262249568579f0f50edb0451745c2d7 Tue Aug 15 17:36:03 2017 -0700
    mostly hooked up attribute setting. Some hooks to get drag and drop to be more selective about where you can drag and drop.
  • lines changed 10, context: html, text, full: html, text
    d3a76238ad2afe6e89ba72b5b51a7bc1c12192aa Wed Aug 16 14:18:32 2017 -0700
    improve event handling
  • lines changed 1, context: html, text, full: html, text
    fe883fcf53223570d15dfbf56fcf36fb266ee4ce Thu Aug 17 16:13:27 2017 -0700
    some html text additions and an alert for Save
• src/hg/hgTables/bedList.c
  • lines changed 2, context: html, text, full: html, text
    80110c2d2f3d5cc63dab1e6100e656faecec0cd5 Tue Aug 15 11:55:57 2017 -0700
    bed names with empty string are cast to a . in custom tracks, refs #18917
• src/hg/hgVai/hgVai.c
  • lines changed 30, context: html, text, full: html, text
    bc5f960c316fcd863ff01af154b8bd67a4dc041a Mon Aug 14 15:08:45 2017 -0700
    hgVai: offer HGVS output options only when using RefSeq transcripts. refs #19968 note-8
  • lines changed 5, context: html, text, full: html, text
    1cd0b7c223ef9944459fbbdac10e3c21ab8a6edd Mon Aug 14 15:41:40 2017 -0700
    Oops, suppress HGVS output (not just options) when using non-RefSeq transcripts. refs #19968
  • lines changed 12, context: html, text, full: html, text
    3556696ddf8ee9dadf75805726fb2a4c226c7f92 Thu Aug 17 09:39:46 2017 -0700
    A little refactoring of logic that allows HGVS output only for RefSeq transcripts.
  • lines changed 1, context: html, text, full: html, text
    ea71930e7ad82f81fc98d619d39a5ac53ed55240 Thu Aug 17 10:50:50 2017 -0700
    Long-overdue renaming of hgVarAnnogrator.js to hgVai.js and removal of vestigial code. Thx Jonathan. refs #19992 note-11
• src/hg/hgVarAnnogrator/hgVarAnnogrator.c
  • lines changed 1805, context: html, text, full: html, text
    411050bf65e0240780f2657eaaee9fa92c263b59 Thu Aug 17 10:22:45 2017 -0700
    Removing abandoned experimental CGI hgVarAnnogrator. refs #19992 note-11
• src/hg/hgVarAnnogrator/makefile
  • lines changed 16, context: html, text, full: html, text
    411050bf65e0240780f2657eaaee9fa92c263b59 Thu Aug 17 10:22:45 2017 -0700
    Removing abandoned experimental CGI hgVarAnnogrator. refs #19992 note-11
• src/hg/htdocs/cite.html
  • lines changed 9, context: html, text, full: html, text
    f208591c86f7c1872b62291c183d9afa0f813e8d Tue Aug 15 09:30:22 2017 -0700
    Changing citation to be a link to PubMed search results of all NAR updates. refs #19924
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 28, context: html, text, full: html, text
    a153e7d4427d0fc937392e234c7fb9d73c68d26e Thu Aug 17 16:12:54 2017 -0700
    Announcing the CRISPR track for the criGri1 assembly, refs #19514
• src/hg/htdocs/inc/hgCollection.html
  • lines changed 2, context: html, text, full: html, text
    12b9c036ada723b623e3b66cd0b0c85e0328df9c Mon Aug 14 21:45:24 2017 -0700
    add AJAX store.
  • lines changed 8, context: html, text, full: html, text
    f78979b24262249568579f0f50edb0451745c2d7 Tue Aug 15 17:36:03 2017 -0700
    mostly hooked up attribute setting. Some hooks to get drag and drop to be more selective about where you can drag and drop.
  • lines changed 9, context: html, text, full: html, text
    fe883fcf53223570d15dfbf56fcf36fb266ee4ce Thu Aug 17 16:13:27 2017 -0700
    some html text additions and an alert for Save
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    a153e7d4427d0fc937392e234c7fb9d73c68d26e Thu Aug 17 16:12:54 2017 -0700
    Announcing the CRISPR track for the criGri1 assembly, refs #19514
• src/hg/js/hgCollection.js
  • lines changed 29, context: html, text, full: html, text
    12b9c036ada723b623e3b66cd0b0c85e0328df9c Mon Aug 14 21:45:24 2017 -0700
    add AJAX store.
  • lines changed 76, context: html, text, full: html, text
    f78979b24262249568579f0f50edb0451745c2d7 Tue Aug 15 17:36:03 2017 -0700
    mostly hooked up attribute setting. Some hooks to get drag and drop to be more selective about where you can drag and drop.
  • lines changed 46, context: html, text, full: html, text
    d3a76238ad2afe6e89ba72b5b51a7bc1c12192aa Wed Aug 16 14:18:32 2017 -0700
    improve event handling
  • lines changed 1, context: html, text, full: html, text
    fe883fcf53223570d15dfbf56fcf36fb266ee4ce Thu Aug 17 16:13:27 2017 -0700
    some html text additions and an alert for Save
• src/hg/js/hgVai.js
  • lines changed 154, context: html, text, full: html, text
    ea71930e7ad82f81fc98d619d39a5ac53ed55240 Thu Aug 17 10:50:50 2017 -0700
    Long-overdue renaming of hgVarAnnogrator.js to hgVai.js and removal of vestigial code. Thx Jonathan. refs #19992 note-11
• src/hg/js/hgVarAnnogrator.js
  • lines changed 4, context: html, text, full: html, text
    bc5f960c316fcd863ff01af154b8bd67a4dc041a Mon Aug 14 15:08:45 2017 -0700
    hgVai: offer HGVS output options only when using RefSeq transcripts. refs #19968 note-8
  • lines changed 618, context: html, text, full: html, text
    ea71930e7ad82f81fc98d619d39a5ac53ed55240 Thu Aug 17 10:50:50 2017 -0700
    Long-overdue renaming of hgVarAnnogrator.js to hgVai.js and removal of vestigial code. Thx Jonathan. refs #19992 note-11
• src/hg/js/makefile
  • lines changed 1, context: html, text, full: html, text
    ea71930e7ad82f81fc98d619d39a5ac53ed55240 Thu Aug 17 10:50:50 2017 -0700
    Long-overdue renaming of hgVarAnnogrator.js to hgVai.js and removal of vestigial code. Thx Jonathan. refs #19992 note-11
• src/hg/lib/annoFormatVep.c
  • lines changed 58, context: html, text, full: html, text
    499eb9facae2cd13591dad0256751b9742aa1bea Thu Aug 17 09:52:36 2017 -0700
    Added asColumnMustFindIx. Use it in hgVai in places where columns are expected to never go away, instead of risking that they do go away and we access row[-1]. Thx Jonathan. refs #19992 note-13
• src/hg/lib/hgHgvs.c
  • lines changed 18, context: html, text, full: html, text
    3712ae6f8f6f212bae33ecc5499feeea598d83e4 Mon Aug 14 11:52:33 2017 -0700
    HGVS pos/search: support parentheses around p. terms. Also watch out for start>end in hgvsValidateGene. refs #19968 note-6
• src/hg/makeDb/doc/hg38/hg38.txt
  • lines changed 1, context: html, text, full: html, text
    38e376b357a695a19737cb26ca1fd9dcf7e92841 Wed Aug 16 16:04:04 2017 -0700
    Updating doc for blockquote bug, refs #18762
• src/hg/makeDb/trackDb/criGri/criGri1/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    15d95ce7c232ce7b8ab873116d9c8e19162121b8 Wed Aug 16 11:15:25 2017 -0700
    Adding the beta release tag, refs #19514
  • lines changed 1, context: html, text, full: html, text
    716eeca2abf2d2cdf22f27f12bf5166d659a9a17 Wed Aug 16 16:25:48 2017 -0700
    Adding the public release tag to test on beta-public, refs #19514
• src/hg/makeDb/trackDb/human/hg38/barCharts.ra
  • lines changed 22, context: html, text, full: html, text
    3b08b1fc9793befaa527cf35739e03ea76fe29d0 Tue Aug 15 13:14:14 2017 -0700
    Development track for the Pollen lab, no redmine
• src/hg/makeDb/trackDb/human/hg38/nowakowskiGeneExp.html
  • lines changed 40, context: html, text, full: html, text
    3b08b1fc9793befaa527cf35739e03ea76fe29d0 Tue Aug 15 13:14:14 2017 -0700
    Development track for the Pollen lab, no redmine
• src/hg/utils/automation/cosmicToBed
  • lines changed 46, context: html, text, full: html, text
    a61d5c42044519e3e5e74ae9fc90d08cff0c72f7 Mon Aug 14 12:12:27 2017 -0700
    Updating the COSMIC script, refs #19932
• src/hg/utils/automation/parseRefSeqFuncElems
  • lines changed 113, context: html, text, full: html, text
    dfcf50cdb099036f7dcacaefff7985544026cec9 Mon Aug 14 12:19:38 2017 -0700
    Python script to convert refSeq files into a more browser friendly format, refs #19638
• src/hg/utils/vcfToHgvs/tests/expected/PersonalisGroundTruth2017_agree.tab
  • lines changed 2, context: html, text, full: html, text
    5964a18a24a5531f2d14eb1be5c30bca115edc44 Fri Aug 18 07:41:09 2017 -0700
    RefSeq transcript updates caused diff failure... need a stable PSL+CDS+sequence test set.
• src/hg/utils/vcfToHgvs/tests/expected/PersonalisGroundTruth2017_disagree.tab
  • lines changed 4, context: html, text, full: html, text
    5964a18a24a5531f2d14eb1be5c30bca115edc44 Fri Aug 18 07:41:09 2017 -0700
    RefSeq transcript updates caused diff failure... need a stable PSL+CDS+sequence test set.
• src/inc/asParse.h
  • lines changed 4, context: html, text, full: html, text
    499eb9facae2cd13591dad0256751b9742aa1bea Thu Aug 17 09:52:36 2017 -0700
    Added asColumnMustFindIx. Use it in hgVai in places where columns are expected to never go away, instead of risking that they do go away and we access row[-1]. Thx Jonathan. refs #19992 note-13
• src/lib/asParse.c
  • lines changed 10, context: html, text, full: html, text
    499eb9facae2cd13591dad0256751b9742aa1bea Thu Aug 17 09:52:36 2017 -0700
    Added asColumnMustFindIx. Use it in hgVai in places where columns are expected to never go away, instead of risking that they do go away and we access row[-1]. Thx Jonathan. refs #19992 note-13
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    b83df06505f16ee1622ca286860f9e9798b0e466 Fri Aug 18 18:02:02 2017 -0700
    v354 preview2

• lines changed: 3294
• files changed: 39