Commits for galt

v494_base to v495_preview (2026-02-16 to 2026-02-23) v495

d9741ac7fe00ba4e2cc38bb8baab8c8b2ae6eec6 Fri Feb 13 18:23:42 2026 -0800

• Updated the following seven utilities bigBedToBed, bigMafToMafj, bigWigToWig, bigWigToBedGraph, bigGenePredToGenePred, bigPslToPsl, bigChainToChain, added support for multiple -range parameters that uses and validates Marks desired bed and position values, in a new callback function in the library bigBedCmdSupport.c. Also added the ability to quickly check allowed chromosomes so users see and error when specifying incorrect chromsome names, and it works with all the filter options. These utils also have a new -skipChromCheck option that users can use if the want to skip the check. These have no tests. I will make tests for these soon. refs #28109, #36925
  • src/hg/utils/bigChainToChain/bigChainToChain.c - lines changed 40, context: html, text, full: html, text
  • src/hg/utils/bigGenePredToGenePred/bigGenePredToGenePred.c - lines changed 41, context: html, text, full: html, text
  • src/hg/utils/bigMafToMaf/bigMafToMaf.c - lines changed 38, context: html, text, full: html, text
  • src/hg/utils/bigPslToPsl/bigPslToPsl.c - lines changed 40, context: html, text, full: html, text
  • src/inc/bigBedCmdSupport.h - lines changed 13, context: html, text, full: html, text
  • src/lib/bigBedCmdSupport.c - lines changed 110, context: html, text, full: html, text
  • src/utils/bigBedToBed/bigBedToBed.c - lines changed 38, context: html, text, full: html, text
  • src/utils/bigWigToBedGraph/bigWigToBedGraph.c - lines changed 38, context: html, text, full: html, text
  • src/utils/bigWigToWig/bigWigToWig.c - lines changed 37, context: html, text, full: html, text

c9b7830e130a43e817566cedfb1be819cc2164c5 Thu Feb 19 17:42:22 2026 -0800

• fix oops do not want duplicate usage line. refs #28109
  • src/hg/utils/bigChainToChain/bigChainToChain.c - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/bigGenePredToGenePred/bigGenePredToGenePred.c - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/bigPslToPsl/bigPslToPsl.c - lines changed 3, context: html, text, full: html, text
  • src/utils/bigWigToBedGraph/bigWigToBedGraph.c - lines changed 1, context: html, text, full: html, text

b96a2a4fd4c75db180a03af13a1122db5ce6d512 Fri Feb 20 20:18:33 2026 -0800

• Since it was present in 4 utils but missing and needed in 3 others, I have added bigWigToWig call in wigToBigWig test, and bigChainToChain to chainToBigChain test, and genePredToBigGenePred to bigGenePredToGenePred. Now all seven utilities properly run their inverse utilities so that they recreate the original input, verifying correctness. Requested in code-review by Mark. refs #28109, #36925
  • src/hg/utils/bigGenePredToGenePred/tests/input/basicTest.gp - lines changed 40, context: html, text, full: html, text
  • src/hg/utils/bigGenePredToGenePred/tests/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/chainToBigChain/tests/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/chainToBigChain/tests/makefile.galt.save - lines changed 28, context: html, text, full: html, text
  • src/utils/wigToBigWig/tests/makefile - lines changed 17, context: html, text, full: html, text