Commits for braney

v342_base to v343_preview (2016-12-05 to 2016-12-19) v343

eb855900d2bd4af4bc981eb2b299b0edf7d31566 Wed Dec 7 15:06:56 2016 -0800

• update trackDbHub doc to know about bigGenePred, bigPsl, bigChain, and bigMaf #17741
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v1.html - lines changed 234, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml - lines changed 73, context: html, text, full: html, text
  • src/hg/lib/bigMaf.as - lines changed 8, context: html, text, full: html, text

d86e271296446bd244d4165ca60e2368a079998c Thu Dec 8 09:25:18 2016 -0800

• fix focus problem in hgTrackUi popup for custom tracks #18500
  • src/hg/js/hgTracks.js - lines changed 5, context: html, text, full: html, text

d0e473f2ef75388b6b7d2142f11ae4b3395ef24f Fri Dec 9 10:09:45 2016 -0800

• rudimentary tests for hubCheck.
  • src/hg/utils/hubCheck/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/hubCheck/tests/expected/output1.txt - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/utils/hubCheck/tests/expected/output2.txt - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/hubCheck/tests/input/hub1.txt - lines changed 17, context: html, text, full: html, text
  • src/hg/utils/hubCheck/tests/makefile - lines changed 20, context: html, text, full: html, text
  • src/hg/utils/makefile - lines changed 1, context: html, text, full: html, text

3c7941d4fab4c4606841a343150bc61e045ea419 Fri Dec 9 12:47:16 2016 -0800

• more changes to support the new big* formats
  • src/hg/htdocs/goldenPath/help/bigMaf.html - lines changed 2, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/cram.html - lines changed 1, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v1.html - lines changed 25, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml - lines changed 21, context: html, text, full: html, text
  • src/hg/utils/hubCheck/hubCheck.c - lines changed 5, context: html, text, full: html, text

0291671251a9d06afd8d1fe62c67c6fd3eb58a94 Fri Dec 9 16:54:41 2016 -0800

• Fix missing gene labels bug #18528. pgSnp tracks in full mode were leaving the drawing machine in a non-default state
  • src/hg/hgTracks/simpleTracks.c - lines changed 2, context: html, text, full: html, text

761c35e2360dc7d1c0d15132296c0d601ccd6d4b Sat Dec 10 10:40:29 2016 -0800

• clean up test output
  • src/hg/utils/hubCheck/makefile - lines changed 1, context: html, text, full: html, text

be9e5faa96a0773d42929c54f58ded53f40b7e88 Mon Dec 12 15:59:17 2016 -0800

• some changes that make it easier for trash cleaner to squirrel away custom tracks holding BLAT results
  • src/hg/hgBlat/hgBlat.c - lines changed 23, context: html, text, full: html, text
  • src/hg/inc/trashDir.h - lines changed 3, context: html, text, full: html, text
  • src/hg/lib/trashDir.c - lines changed 21, context: html, text, full: html, text
  • src/inc/common.h - lines changed 3, context: html, text, full: html, text
  • src/lib/common.c - lines changed 9, context: html, text, full: html, text

751228a4d6d75d72ae2407231ece2651e9f8de4d Mon Dec 12 16:05:41 2016 -0800

• fix up cgi-alpha and cgi-beta targets to copy bedToBigBed into the CGI loader directory
  • src/makefile - lines changed 2, context: html, text, full: html, text

09a44b13b888eb07a70a0baef7717dac5a9caed4 Tue Dec 13 11:02:22 2016 -0800

• some more changes per Hiram to get the trash cleaner to like BLAT result custom tracks.
  • src/hg/hgBlat/hgBlat.c - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/trashDir.c - lines changed 1, context: html, text, full: html, text

9b2bccae0dced3d04c3edb7a263437407586e1ff Tue Dec 13 11:28:53 2016 -0800

• more changes for Hiram
  • src/hg/hgBlat/hgBlat.c - lines changed 3, context: html, text, full: html, text

5941524ea9c4f355fa2710761b0149b3219bc009 Tue Dec 13 14:24:15 2016 -0800

• make track hub tracks respond to URL visibility settings even if they don't have the hub_#_ prefix #18544
  • src/hg/hgTracks/hgTracks.c - lines changed 2, context: html, text, full: html, text