Commits for galt
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v496_preview to v496_preview2 (2026-03-16 to 2026-03-23) v496
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15080c151c9929733fa2af71ce5dc98533c4f913 Fri Mar 20 18:45:40 2026 -0700
- The error messages are more detailed to help users, something MarkD wanted.
It aborts by default if chromStart or chromEnd are greater than chromSize,
unless the user has specified -skipChromCheck which skips both chrom name and chrom size checks now.
Fixes issues with undetected overflowing integers issues, warns when they are too large
instead of silently failing. Expanded the all the coordinates in the utils and the lib
so that they use full range of unsigned integer space when querying and using GB for chromStart and chromEnd coordinates used by BED standard and supported by .2bit chroms. Fixed minor overflow issue with bigBed.c going past the end of the 4GB space.
I made changes to bigBedToBed.c and then used CLAUDE prompt to refactor those changes into the 6 other utilities
bigMafToMaf, bigChainToChain, bigGenePredToGenePred, bigPslToPsl, bigWigToBedGraph, bigWigToWig.
refs #28109
- src/hg/utils/bigChainToChain/bigChainToChain.c - lines changed 41, 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 40, context: html, text, full: html, text
- src/hg/utils/bigPslToPsl/bigPslToPsl.c - lines changed 41, context: html, text, full: html, text
- src/inc/bigBedCmdSupport.h - lines changed 3, context: html, text, full: html, text
- src/lib/bigBedCmdSupport.c - lines changed 141, context: html, text, full: html, text
- src/utils/bigBedToBed/bigBedToBed.c - lines changed 41, context: html, text, full: html, text
- src/utils/bigWigToBedGraph/bigWigToBedGraph.c - lines changed 41, context: html, text, full: html, text
- src/utils/bigWigToWig/bigWigToWig.c - lines changed 42, context: html, text, full: html, text
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