Commits for angie

v420_preview to v420_preview2 (2021-08-23 to 2021-08-30) v420

68f95eec388eb3895787fc885fa01fe7ee3447ac Thu Aug 26 11:36:26 2021 -0700

• Recently usher started prepending node_ to numeric internal node names stored in the protobuf, so node names in usher outputs are now node_<number> instead of just <number>. However, the protobuf still has numeric names, so it may be necessary to strip the prefix when looking up bigTree nodes.
  • src/hg/hgPhyloPlace/phyloPlace.c - lines changed 31, context: html, text, full: html, text
  • src/hg/hgPhyloPlace/phyloPlace.h - lines changed 8, context: html, text, full: html, text
  • src/hg/hgPhyloPlace/vcfFromFasta.c - lines changed 4, context: html, text, full: html, text

2aa99ff0ca7a50af99ba59a3e8a54d7a819e7808 Thu Aug 26 12:30:42 2021 -0700

• Yikes, I was forgetting to expand condensed nodes in the big tree when making custom track VCF for subtrees, resulting in some sequences not being found & having no alt alleles in VCF.
  • src/hg/hgPhyloPlace/phyloPlace.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgPhyloPlace/phyloPlace.h - lines changed 1, context: html, text, full: html, text
  • src/hg/hgPhyloPlace/writeCustomTracks.c - lines changed 18, context: html, text, full: html, text

eab7c9759c4a29064aab1143c2eb9d43a3050413 Thu Aug 26 12:44:56 2021 -0700

• Fixing typo: there is no webEndText, only webEnd.
  • src/hg/hgBlat/hgBlat.c - lines changed 1, context: html, text, full: html, text

755406e622ce53a7ec5be4c5210f783084d9dd0e Fri Aug 27 12:39:45 2021 -0700

• Fix valgrind warning (although the value from a bad read of [ix+1] wouldn't have been used).
  • src/hg/lib/variantProjector.c - lines changed 4, context: html, text, full: html, text

b1470d6f462f975727df99a576b1b7ec72d05491 Fri Aug 27 12:44:36 2021 -0700

• Fix valgrind warning -- I didn't realize safencpy adds a null byte.
  • src/hg/hgPhyloPlace/treeToAuspiceJson.c - lines changed 1, context: html, text, full: html, text

baef96f3db3202daa9e254b029cbdac78a8f409e Fri Aug 27 12:46:08 2021 -0700

• Fix incorrect-freeing error introduced yesterday in 2aa99ff0.
  • src/hg/hgPhyloPlace/writeCustomTracks.c - lines changed 5, context: html, text, full: html, text

20ceda8601cb6eb3713512f9e945a61be9950e68 Fri Aug 27 12:49:23 2021 -0700

• Fix unhelpful error messages
  • src/hg/hgPhyloPlace/phyloPlace.c - lines changed 4, context: html, text, full: html, text