Commits for hiram

v476_base to v477_preview (2025-01-13 to 2025-01-21) v477

3844728d1f5262afe91c7dfdd7187cb46f8fa568 Mon Jan 13 14:05:12 2025 -0800

• eliminate the duplication of the -lm library refs #35048
  • src/hg/affyGnf/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/lib/straw/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/agpCondense/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/bedExtendRanges/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/bedMergeExpData/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/bedMergeOverlappingBlocks/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/bedRandom/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/blatServersCheck/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/cageSingleTrack/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/checkUrlsInTable/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/coloredExonToBed/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/findCutters/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/fiveCToBed/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/geoMirrorNode/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/gff3ToGenePred/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/gff3ToPsl/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/gffToBed/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/gtfToGenePred/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/hubCheck/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/liftUpBedFromTable/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/makeTableList/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/makeTrackIndex/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/mdbQuery/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/mutationClassifier/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/overlapSelect/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/pslLiftSubrangeBlat/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/randFrag/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/refSeqGet/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/repeatSelect/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/rgdGeneXref2/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/sqlPerf/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/wigAsciiAverageOverBed/makefile - lines changed 1, context: html, text, full: html, text
  • src/parasol/dataSim/makefile - lines changed 1, context: html, text, full: html, text
  • src/parasol/gensub2/makefile - lines changed 1, context: html, text, full: html, text
  • src/parasol/para/makefile - lines changed 1, context: html, text, full: html, text
  • src/parasol/paraHub/makefile - lines changed 1, context: html, text, full: html, text
  • src/parasol/paraHubStop/makefile - lines changed 1, context: html, text, full: html, text
  • src/parasol/paraNode/makefile - lines changed 1, context: html, text, full: html, text
  • src/parasol/paraNodeStart/makefile - lines changed 1, context: html, text, full: html, text
  • src/parasol/paraNodeStatus/makefile - lines changed 1, context: html, text, full: html, text
  • src/parasol/paraNodeStop/makefile - lines changed 1, context: html, text, full: html, text
  • src/parasol/paraTestJob/makefile - lines changed 1, context: html, text, full: html, text
  • src/parasol/parasol/makefile - lines changed 1, context: html, text, full: html, text
  • src/tracks/makefile - lines changed 1, context: html, text, full: html, text

4888af47a6dceb9a40e20276c1acf861edf02479 Tue Jan 14 07:02:55 2025 -0800

• more useful to have the mail subject say assembly request rather than asr request refs #32596
  • src/hg/gar/asr.cgi.pl - lines changed 2, context: html, text, full: html, text

160145e7459ad9c3252fa47ddff8c1db634688a0 Tue Jan 14 07:07:44 2025 -0800

• eliminate duplicate declaration of $fh no redmine
  • src/hg/utils/automation/doCpgIslands.pl - lines changed 1, context: html, text, full: html, text

d46e25fbafa02b136e9cdbb6eafcbf01583d2a8a Tue Jan 14 10:51:47 2025 -0800

• dramatically faster than the perl equivalent no redmine
  • src/hg/utils/automation/kmerPrint.py - lines changed 61, context: html, text, full: html, text

a20a64637b2a8bddd07aa4071beb839daa464230 Tue Jan 14 10:53:07 2025 -0800

• using the faster python kmerPrint.py no redmine
  • src/hg/utils/automation/doTandemDup.pl - lines changed 1, context: html, text, full: html, text

a3a313b3fa4aa9c77d0b9827f8721ef57990bebd Tue Jan 14 12:24:02 2025 -0800

• no using kmerPrint.py in place of kmerPrint.pl no redmine
  • src/hg/utils/automation/makefile - lines changed 3, context: html, text, full: html, text

47a1923ca3817900bbd90d07d9a073719a0a7f32 Tue Jan 14 14:35:05 2025 -0800

• adding a couple per user request refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv - lines changed 1, context: html, text, full: html, text

0bb1aded8773d1762002ee556834f582252e0711 Tue Jan 14 16:08:12 2025 -0800

• legacy reached a new low with a virus no redmine
  • src/hg/makeDb/doc/asmHubs/verifyOnDownload.sh - lines changed 1, context: html, text, full: html, text

d2353c8c3ff43dc95f0fb2a13e5d0592c7521a25 Mon Jan 20 09:28:40 2025 -0800

• adding a couple per user request refs #29545
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 2, context: html, text, full: html, text