Commits for jcasper

v472_preview2 to v472_base (2024-09-30 to 2024-10-07) v472

8f29deda5ff897fbf1d208907ac7f734afc07ed2 Tue Oct 1 20:31:17 2024 -0700

• Many liftOver functions now have a preserveInput argument, which appends the input position to the name field. This makes it easier to see what got mapped where. The option is made available through a command-line argument to the liftOver utility and a checkbox in the hgLiftOver CGI, refs #28023
  • src/hg/hgLiftOver/hgLiftOver.c - lines changed 17, context: html, text, full: html, text
  • src/hg/inc/liftOver.h - lines changed 7, context: html, text, full: html, text
  • src/hg/lib/liftOver.c - lines changed 67, context: html, text, full: html, text
  • src/hg/liftOver/liftOver.c - lines changed 15, context: html, text, full: html, text
  • src/hg/liftOver/tests/expected/bed12Preserve.bed - lines changed 2, context: html, text, full: html, text
  • src/hg/liftOver/tests/expected/bed3Preserve.bed - lines changed 2, context: html, text, full: html, text
  • src/hg/liftOver/tests/expected/genePredPreserve.gp - lines changed 3, context: html, text, full: html, text
  • src/hg/liftOver/tests/expected/gffPreserve.gff - lines changed 6, context: html, text, full: html, text
  • src/hg/liftOver/tests/expected/gtfPreserve.gtf - lines changed 5, context: html, text, full: html, text
  • src/hg/liftOver/tests/expected/positionPreserve.pos - lines changed 1, context: html, text, full: html, text
  • src/hg/liftOver/tests/expected/pslPreserve.psl - lines changed 6, context: html, text, full: html, text
  • src/hg/liftOver/tests/expected/samplePreserve.sample - lines changed 2, context: html, text, full: html, text
  • src/hg/liftOver/tests/input/bed12Preserve.bed - lines changed 2, context: html, text, full: html, text
  • src/hg/liftOver/tests/input/bed3Preserve.bed - lines changed 2, context: html, text, full: html, text
  • src/hg/liftOver/tests/input/genePredPreserve.gp - lines changed 3, context: html, text, full: html, text
  • src/hg/liftOver/tests/input/gffPreserve.gff - lines changed 3, context: html, text, full: html, text
  • src/hg/liftOver/tests/input/gtfPreserve.gtf - lines changed 5, context: html, text, full: html, text
  • src/hg/liftOver/tests/input/positionPreserve.pos - lines changed 1, context: html, text, full: html, text
  • src/hg/liftOver/tests/input/pslPreserve.psl - lines changed 3, context: html, text, full: html, text
  • src/hg/liftOver/tests/input/samplePreserve.sample - lines changed 3, context: html, text, full: html, text
  • src/hg/liftOver/tests/makefile - lines changed 70, context: html, text, full: html, text

2d6c8b5aa593976bc312cb3111d9d4cd7b46938a Wed Oct 2 09:29:18 2024 -0700

• Position liftovers need to clean up temp files when they're done, refs #28023
  • src/hg/lib/liftOver.c - lines changed 5, context: html, text, full: html, text
  • src/hg/liftOver/tests/makefile - lines changed 4, context: html, text, full: html, text

641180ca8796b2ecea29edaee9c46ad617a35835 Sun Oct 6 01:11:21 2024 -0700

• Installing updated hg.conf files from UCSC servers
  • confs/asia.hg.conf - lines changed 6, context: html, text, full: html, text
  • confs/euro.hg.conf - lines changed 6, context: html, text, full: html, text
  • confs/hgwdev.hg.conf - lines changed 6, context: html, text, full: html, text
  • confs/rr.hg.conf - lines changed 6, context: html, text, full: html, text

04d6dae916262b3d2c4b15aef684cea90cf1f1e5 Mon Oct 7 15:08:00 2024 -0700

• v472 final build, refs #34490
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 3, context: html, text, full: html, text

14e458a2850b153c5abf5c8cc329accdb0047d37 Mon Oct 7 15:09:22 2024 -0700

• New version number v472
  • src/hg/inc/versionInfo.h - lines changed 1, context: html, text, full: html, text
  • src/inc/srcVersion.h - lines changed 1, context: html, text, full: html, text