Commits for angie

dde2dc8383fa276b091e085197044a61be0ee6ac Mon Jan 30 10:44:42 2017 -0800

Fix for mapping HGVS to genome when both start and end are upstream of a transcript. Previously, both start and end were set to 0 so the transcript was 0-length and not mapped by pslTransMap. hgFixed fell through to display the whole transcript. Now it maps to the correct location. Example term: NM_016176.3:c.-562A>C
- src/hg/lib/hgHgvs.c - lines changed 2, context: html, text, full: html, text

722dfea3a5bfa3ac36d8234e6698495a2a7a6cac Tue Jan 31 12:36:01 2017 -0800

Both Hiram and Matt got stale hgGateway.js in their browser caches somehow -- we do still need to use the timestamped symlinks for JS files. :(
- src/hg/hgGateway/hgGateway.c - lines changed 1, context: html, text, full: html, text

fb27495fe820777de19089a029ea5df9d4704a21 Wed Feb 1 11:08:49 2017 -0800

Adding back, until the next release is on the RR, the inline script that stores some params in Drupal.settings for later use by the nice-menus superfish jquery plugin (the script was removed in a53b9958f along with code changes for CSP2). The code on the RR and in the current release candidate still depends on this, and htdocs files are pushed from tip-of-tree not release, so this needs to support old code. refs #18686 note-25
- src/hg/htdocs/inc/globalNavBar.inc - lines changed 6, context: html, text, full: html, text

3309b481df43c9044d0adb112547e75f943bd7a1 Wed Feb 1 13:04:48 2017 -0800

Increasing string buffer size for javascript that encodes DataTable state after I got an overflow error.
- src/hg/hgSession/hgSession.c - lines changed 1, context: html, text, full: html, text

1c99dc9ac1e66b1ec169f25f3e9f8d24b9165410 Wed Feb 1 15:34:52 2017 -0800

Demoting keggPathway.kgID in identifier knownGeneId because it covers only about a quarter of kgIDs, but was picked preferentially to knownToLocusLink because it appeared first. refs #18586
- src/hg/makeDb/schema/all.joiner - lines changed 2, context: html, text, full: html, text