Commits for galt

v481_preview2 to v481_base (2025-04-21 to 2025-04-28) v481

27ef3088295431a5fdadf5def360a14151ac574f Mon Apr 21 12:12:26 2025 -0700

• last fix for Jonathans contribution for verbose, however this was not a bug that mattered much since it was in the verbose statement. I have updated the exec in /cluster/bin/x86_64/ wwith the latest compiling version.
  • src/hg/hgcentralTidy/hgcentralTidy.c - lines changed 1, context: html, text, full: html, text

e1988a798585c610e2399538a900fd57cfa83d63 Tue Apr 22 11:19:22 2025 -0700

• Fixes VCF does not work on extended case-color options in Get DNA for vcf, vcfTabix, and vcfPhasedTrio. fixes #16386
  • src/hg/hgc/hgc.c - lines changed 26, context: html, text, full: html, text
  • src/hg/hgc/hgc.h - lines changed 8, context: html, text, full: html, text
  • src/hg/hgc/vcfClick.c - lines changed 53, context: html, text, full: html, text
  • src/hg/lib/featureBits.c - lines changed 23, context: html, text, full: html, text

ce90ee5ec5f7377937451a8c8eb93a7dc33731de Tue Apr 22 13:56:24 2025 -0700

• hgcentralTidy.c cleaner - added -skipDel option and verbose=4 for seeing sql delete statements detail. dryRun skips too many details.
  • src/hg/hgcentralTidy/hgcentralTidy.c - lines changed 14, context: html, text, full: html, text

f00d46c3edc5ac3916e8e0c7bb0fbe5e4915145d Tue Apr 22 15:56:51 2025 -0700

• Fixes minor bug vcf extended color dna download. refs #16386
  • src/hg/hgc/vcfClick.c - lines changed 8, context: html, text, full: html, text

43a557569d3db3c7f5b301e1c0c87d83556d10ee Wed Apr 23 12:34:07 2025 -0700

• updating expected for hubApi tests
  • src/hg/hubApi/tests/expected/list22.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/hg/hubApi/tests/expected/list26.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/hg/hubApi/tests/expected/list27.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/hg/hubApi/tests/expected/redmine23733.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)

df0b444ffb7c4b4f6ec8e745ad0e0f22b46cd15f Thu Apr 24 02:29:22 2025 -0700

• Found hgNear as a highly executed CGI on RR, added botDelay. No rm.
  • src/hg/near/hgNear/hgNear.c - lines changed 13, context: html, text, full: html, text

74693f4a03751622a098ed60a2a38c256c66b216 Fri Apr 25 16:40:20 2025 -0700

• Fixing small off by one error specify the days range. refs #35554
  • src/hg/hgcentralTidy/hgcentralTidy.c - lines changed 5, context: html, text, full: html, text

823555550e19e556ca7f3ac9ebcc9793f0c39668 Fri Apr 25 19:56:46 2025 -0700

• Since it was confusing not to have the end included in the range, fixed binary search to specify flag if you want the beginning or the end of the range. THis allows the natural expression of day 0 instead of -1.
  • src/hg/hgcentralTidy/hgcentralTidy.c - lines changed 33, context: html, text, full: html, text