Commits for braney

v455_base to v456_preview (2023-10-09 to 2023-10-16) v456

09908828e61d24d8a8ea32db0a2fd19c7f8ea1e1 Mon Oct 9 10:16:21 2023 -0700

• hgFind items always pass the bigBed filters and always are in pack when we're doing squishyPack
  • src/hg/hgTracks/bigBedTrack.c - lines changed 4, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.c - lines changed 5, context: html, text, full: html, text

7cd6003587e1e514ef27f1f7c8ed2d244630c21b Fri Oct 13 14:30:34 2023 -0700

• first pass at hg19 GENCODE knownGene
  • src/hg/makeDb/trackDb/human/hg19/knownGene.alpha.ra - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 3, context: html, text, full: html, text

393037b58276445a2af3ca72e7299eb2b39d5e9d Fri Oct 13 16:37:36 2023 -0700

• move some doc files around
  • src/hg/makeDb/doc/hg38/hprcChain.txt - lines changed 307, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38/hprcPggbChain.txt - lines changed 66, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38/hprcReChain.txt - lines changed 315, context: html, text, full: html, text

2e2674507b0968331df3f081e65b08678f860ca3 Sat Oct 14 16:45:14 2023 -0700

• some cleanup of the HPRC tracks
  • src/hg/makeDb/doc/hg38/hprcChain.txt - lines changed 193, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38/hprcInDel.txt - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38/hprcRearrange.txt - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/hprcChains.html - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/hprcCoverage97.ra - lines changed 1, context: html, text, full: html, text

c38f77acf5cf110d960192b5242a76c04ff33d54 Sun Oct 15 15:21:16 2023 -0700

• added chainDupFilter which addresses a problem in axtChain where duplicated blocks are not chained
  • src/hg/utils/chainDupFilter/chainDupFilter.c - lines changed 157, context: html, text, full: html, text
  • src/hg/utils/chainDupFilter/makefile - lines changed 3, context: html, text, full: html, text

e3be616148276adf5583f752c462be025e59fe68 Sun Oct 15 15:26:29 2023 -0700

• add HPRC indels track
  • src/hg/makeDb/doc/hg38/hprcInDel.txt - lines changed 31, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/hprcArr.ra - lines changed 22, context: html, text, full: html, text
  • src/hg/utils/bigChainArrange/bigChainArrange.c - lines changed 135, context: html, text, full: html, text
  • src/hg/utils/bigChainArrange/makefile - lines changed 3, context: html, text, full: html, text