Commits for kent

v341_preview2 to v341_base (2016-10-31 to 2016-11-07) v341

596fceb9da320bd456bbd4cda8571d4a62cc329f Mon Oct 31 12:03:18 2016 -0700

• Relaxing some validations to accommodate newer web pages.
  • src/lib/htmlPage.c - lines changed 16, context: html, text, full: html, text

9562808bb257905689c06d196305e0b8234bf05b Mon Oct 31 12:14:08 2016 -0700

• Improving behavior when missing technically optional head section.
  • src/lib/htmlPage.c - lines changed 3, context: html, text, full: html, text

41f2f92517eff6f5b8477bdd90bfe33799eeedd0 Mon Oct 31 12:28:42 2016 -0700

• Adding DIV SCRIPT and SVG to tags checked for nesting.
  • src/lib/htmlPage.c - lines changed 2, context: html, text, full: html, text

4d0515666d53ed314b503f52a80cfb5a3744af28 Mon Oct 31 12:54:32 2016 -0700

• Fixing so that you can run htmlCheck on local files rather than just URLS.
  • src/utils/htmlCheck/htmlCheck.c - lines changed 9, context: html, text, full: html, text

ca112199cb040b7df91678144fb9ab6cc4290f77 Mon Oct 31 15:16:49 2016 -0700

• Expanding buffer for large tag values.
  • src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c - lines changed 1, context: html, text, full: html, text

3ad4f4c509134534060643ed1152f4629aab172e Wed Nov 2 14:15:58 2016 -0700

• First cut of a bamToPsl utility.
  • src/utils/bamToPsl/bamToPsl.c - lines changed 80, context: html, text, full: html, text
  • src/utils/bamToPsl/makefile - lines changed 4, context: html, text, full: html, text

07f0e0134a6eee29337add57582421937c617e9a Wed Nov 2 14:17:47 2016 -0700

• Refactoring code to convert bam to a psl from hgTracks/bamTrack.c refs #13673
  • src/lib/bamFile.c - lines changed 78, context: html, text, full: html, text

6d90b13178a35682a27514cf704f7b05794e7192 Wed Nov 2 14:18:48 2016 -0700

• Refactoring code to convert bam to a psl from hgTracks/bamTrack.c refs #13673
  • src/inc/bamFile.h - lines changed 4, context: html, text, full: html, text

a14d8dea71b926b326385cdd03a50b5db372240c Wed Nov 2 14:22:24 2016 -0700

• Updating to use htslib.
  • src/utils/bamToFastq/bamToFastq.c - lines changed 6, context: html, text, full: html, text
  • src/utils/bamToFastq/makefile - lines changed 3, context: html, text, full: html, text

12c561f936552b6604e16e209cbff155516966ca Wed Nov 2 15:16:44 2016 -0700

• Fixed year old typo!
  • src/tagStorm/tagStormQuery/tagStormQuery.c - lines changed 1, context: html, text, full: html, text

83ff9557037715521b9cb3714ec7989763b92aa7 Wed Nov 2 16:17:40 2016 -0700

• Updating cv checks for MISCE terms, and fixing a few typos in MISCE tags and removing old tag list and alphabetizing new tags list.
  • src/hg/cirm/cdw/lib/cdwValid.c - lines changed 193, context: html, text, full: html, text