Commits for braney

v411_base to v412_preview (2021-03-01 to 2021-03-08) v412

f1065efe3aadb9b2f83c1a3a0a48afd9a47d9153 Mon Mar 1 15:57:17 2021 -0800

• implement wiggleWindow that forces a track into density coverage mode when the window exceeds a specified width
  • src/hg/hgTracks/hgTracks.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.h - lines changed 2, context: html, text, full: html, text
  • src/hg/hgTracks/simpleTracks.c - lines changed 18, context: html, text, full: html, text

067683ca6588c8a088ce2ffed87eacaecac4757a Tue Mar 2 14:15:43 2021 -0800

• add wiggleWindow to CADD inserts and deletes
  • src/hg/makeDb/trackDb/human/caddAlpha.ra - lines changed 6, context: html, text, full: html, text

fac00bb05cae24df45a5382901f0d433cfb9f79c Tue Mar 2 14:17:18 2021 -0800

• oops, forgot to add this
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 1, context: html, text, full: html, text

2126da777ab1677598eeb020127005477ee51ac9 Tue Mar 2 14:49:29 2021 -0800

• when counting overlaps for density coverage, make zero width elements cover a single base.
  • src/hg/hgTracks/simpleTracks.c - lines changed 2, context: html, text, full: html, text

d4c1526c6c8d7a2b709fbeaa336bfc01c4a76ed5 Tue Mar 2 14:53:56 2021 -0800

• add density coverage option to bigBeds
  • src/hg/lib/hui.c - lines changed 1, context: html, text, full: html, text

d248ea47e2ffed0b22206642ad3477c1213ec5cc Wed Mar 3 14:15:32 2021 -0800

• add -countBlocks option. Support bigBeds.
  • src/hg/featureBits/featureBits.c - lines changed 101, context: html, text, full: html, text

e1487d60d004ee8de24e6e1e7dfd12919104e19d Thu Mar 4 09:37:02 2021 -0800

• allow use of blat custom track in DNA extra color/case options #23045
  • src/hg/hgc/hgc.c - lines changed 15, context: html, text, full: html, text
  • src/hg/lib/customFactory.c - lines changed 2, context: html, text, full: html, text

a0d381e86081dc1e4d53c8a519a30db607d30c7f Thu Mar 4 13:40:57 2021 -0800

• oops, hadn't checked this in.
  • src/hg/makeDb/trackDb/human/hg38/knownGeneOld12.html - lines changed 25, context: html, text, full: html, text

14a7e9de4b1e9c2cc6fd6c1b4912c147afd05064 Fri Mar 5 10:56:27 2021 -0800

• fix up usage message to make it clearer that bigBeds are allowed and that the tool does a bitwise AND
  • src/hg/featureBits/featureBits.c - lines changed 4, context: html, text, full: html, text