Commits for jcasper

v469_preview to v469_preview2 (2024-07-22 to 2024-07-29) v469

6425a939b8a452d5187fb3cc68c059373428face Wed Jul 24 16:03:50 2024 -0700

• RNA structure picture generation should realize when the postscript file it wants to use doesn't exist, refs #34156
  • src/hg/hgGene/rnaStructure.c - lines changed 28, context: html, text, full: html, text

839d2067c1871e5ffa53842f1b9c04806cf14f97 Thu Jul 25 11:51:10 2024 -0700

• The new straw library should recognize when it's doing a bad data retrieval. Also added a rudimentary way to retrieve available normalization options, refs #33225
  • src/hg/lib/straw/new_cStraw.cpp - lines changed 67, context: html, text, full: html, text
  • src/hg/lib/straw/new_straw.cpp - lines changed 65, context: html, text, full: html, text
  • src/hg/lib/straw/new_straw.h - lines changed 5, context: html, text, full: html, text

c524c55a797618abe0a485574cfcc13445c22e8b Thu Jul 25 11:52:12 2024 -0700

• Adding support for setting FAILONERROR to fakeCurl, refs #33225
  • src/hg/inc/fakeCurl.h - lines changed 13, context: html, text, full: html, text
  • src/hg/lib/fakeCurl.c - lines changed 29, context: html, text, full: html, text

bf996d33a7459741eea5a172a6cd891abca8e35e Thu Jul 25 11:55:13 2024 -0700

• Staging the replacement of the old straw library with the new. Hopefully this results in an easier-to-read git commit history, since the library had significant changes. refs #33225
  • src/hg/lib/straw/cStraw.cpp - lines changed 181, context: html, text, full: html, text
  • src/hg/lib/straw/straw.cpp - lines changed 986, context: html, text, full: html, text
  • src/hg/lib/straw/straw.h - lines changed 145, context: html, text, full: html, text

ae1ef6aa226d4436d4dc9e2b9b28120d802ab8a5 Thu Jul 25 11:57:53 2024 -0700

• Dropping new straw library files into place, refs #33225
  • src/hg/lib/straw/cStraw.cpp - lines changed 247, context: html, text, full: html, text
  • src/hg/lib/straw/new_cStraw.cpp - lines changed 247, context: html, text, full: html, text
  • src/hg/lib/straw/new_straw.cpp - lines changed 1755, context: html, text, full: html, text
  • src/hg/lib/straw/new_straw.h - lines changed 132, context: html, text, full: html, text
  • src/hg/lib/straw/straw.cpp - lines changed 1755, context: html, text, full: html, text
  • src/hg/lib/straw/straw.h - lines changed 132, context: html, text, full: html, text

910378643087254ec5d8fffe664b4bf92f5e7361 Thu Jul 25 11:59:44 2024 -0700

• Final fixup for the new straw library, refs #33225
  • src/hg/lib/straw/cStraw.cpp - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/straw/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/lib/straw/straw.cpp - lines changed 1, context: html, text, full: html, text

d86ddf032b97d2014a9a97b79dd9f66d9b07db13 Thu Jul 25 15:36:52 2024 -0700

• Also need to commit these for the new Hi-C setup! refs #33225
  • src/hg/lib/hic.c - lines changed 6, context: html, text, full: html, text
  • src/hg/lib/hicUi.c - lines changed 4, context: html, text, full: html, text

c6c5c0fece6dd3a4f278a923b222c8036f363b91 Thu Jul 25 15:38:16 2024 -0700

• Needed header updates for the new Hi-C version, refs #33225
  • src/hg/inc/cStraw.h - lines changed 7, context: html, text, full: html, text
  • src/hg/inc/hic.h - lines changed 2, context: html, text, full: html, text

2f5b6e9f82297419d1f3f8539cc37a3fcec6090e Sun Jul 28 01:11:25 2024 -0700

• Installing updated hg.conf files from UCSC servers
  • confs/asia.hg.conf - lines changed 17, context: html, text, full: html, text
  • confs/euro.hg.conf - lines changed 17, context: html, text, full: html, text
  • confs/hgwbeta.hg.conf - lines changed 18, context: html, text, full: html, text
  • confs/hgwdev.hg.conf - lines changed 17, context: html, text, full: html, text
  • confs/rr.hg.conf - lines changed 17, context: html, text, full: html, text

04f94965a8d453974bbe6949ef1c5d7ddd188766 Mon Jul 29 12:01:59 2024 -0700

• v469 preview2, refs #34168
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 2, context: html, text, full: html, text