Commits for braney

v397_base to v398_preview (2020-04-20 to 2020-04-27) v398

9a20f2ebc987790ac14e33d5bc9b57c9899bd4c5 Mon Apr 20 10:44:13 2020 -0700

• move a release tag to be after the track definition
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra - lines changed 2, context: html, text, full: html, text

298302978224472f8e84720e6c11272684346e6b Wed Apr 22 12:24:25 2020 -0700

• add some code to recognize ribosomal slips in codon display mode. Only works on the + stand right now for wuhCor1
  • src/hg/hgTracks/cds.c - lines changed 32, context: html, text, full: html, text
  • src/hg/hgTracks/cds.h - lines changed 12, context: html, text, full: html, text

a5378ba7d46c47d2c3d4b7dbdd0b7777ed7854ed Thu Apr 23 13:37:43 2020 -0700

• using mtime to keep track of access time was resulting in a race condition in recognizing new trackDb or hub contents. This change will require that trackDb cache be on a filesystem that updates atime (e.g. /dev/shm)
  • src/hg/lib/trackDbCache.c - lines changed 2, context: html, text, full: html, text

08b1be37724c83f2dab17f71b5494963f34180b7 Fri Apr 24 08:16:21 2020 -0700

• expand the size of a buffer in net.c to 8k instead of 2000
  • src/lib/net.c - lines changed 1, context: html, text, full: html, text

3dcfa772d1883dd243f418e7808d82b8096cb335 Fri Apr 24 08:34:25 2020 -0700

• increase the number of bases that extended DNA color choices will allow from 1 million to 5 million
  • src/hg/hgc/hgc.c - lines changed 2, context: html, text, full: html, text

433ed3d13a7fd8e09901031c223c54d5abc77178 Fri Apr 24 13:11:54 2020 -0700

• add a flag to bedToBigBed to allow exons to have 1bp overlapping
  • src/inc/basicBed.h - lines changed 3, context: html, text, full: html, text
  • src/lib/basicBed.c - lines changed 14, context: html, text, full: html, text
  • src/utils/bedToBigBed/bedToBigBed.c - lines changed 5, context: html, text, full: html, text

faeba1ede00712f52d33e8b1b5093df8723fce4d Fri Apr 24 17:47:02 2020 -0700

• new stuff from Manny
  • src/hg/makeDb/doc/wuhCor1/rnaStructRangan.txt - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/rnaStructRangan.html - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra - lines changed 2, context: html, text, full: html, text

2e5f6cee6de726f2def8e0f95d4873ac168a0faa Mon Apr 27 10:02:43 2020 -0700

• v398 preview1
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 2, context: html, text, full: html, text