Commits for angie

v322_preview to v322_preview2 (2015-08-31 to 2015-09-07) v322

• If querying in a region, restrict wiggle values to the part of the region
  that overlaps the primary item, don't just use the bounds of the db rows
  that overlap start/end of region.
  fixes #15952
  
  • src/lib/annoGrateWig.c - lines changed 25, context: html, text, full: html, text
  • src/lib/annoGrator.c - lines changed 1, context: html, text, full: html, text
• Discard large-bin items that fall on or after nextChunkStart because they
  will break the (chrom, chromStart) sorting order if they are also to the
  right of small-bin items on or after nextChunkStart -- and they will appear
  again in the next chunk of rows.
  
  Also a couple other fixes for problems found while debugging:
  - there was a spot where I forgot to restart merging after calling
  resetMergeState (when moving on to the next chrom in a genome-wide query)
  - in mergeRow, don't resetMergeState until both big and small queues are empty
  
  refs #15953
  
  • src/hg/lib/annoStreamDb.c - lines changed 41, context: html, text, full: html, text
• Set verbose level to 0 so we don't get informational messages cluttering up stderr.
  
  • src/utils/bigWigMerge/tests/makefile - lines changed 4, context: html, text, full: html, text
• Added 'top' target for faster development of top-level .js files
  (i.e. skip all of the new subdirs).
  
  • src/hg/js/install.mk - lines changed 7, context: html, text, full: html, text
  • src/hg/js/makefile - lines changed 4, context: html, text, full: html, text
• Look for trackDbSetting "trackHandler" in lookupTrackHandler instead of looking it up at the end of lookupTrackHandlerClosestToHome after modifying tdb. That was losing child trackHandler settings.
  
  • src/hg/hgTracks/simpleTracks.c - lines changed 30, context: html, text, full: html, text
• Add trackHandler settings for snp144* tracks.
  
  • src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 4, context: html, text, full: html, text
• Check whether local file "extTools.ra" exists before calling printExtMenuData and showing the keyboard shortcuts for it.
  
  • src/hg/hgTracks/extTools.c - lines changed 8, context: html, text, full: html, text
  • src/hg/hgTracks/extTools.h - lines changed 3, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.c - lines changed 9, context: html, text, full: html, text