Commits for hiram

ccff28e568396045db4f31d9fa577412b017e837 Wed Nov 19 14:28:51 2025 -0800

now getting the /gbdb/*/liftOver/ files on the RR push list refs #35575
- src/hg/utils/otto/genArk/liftOverNew.sh - lines changed 85, context: html, text, full: html, text
- src/hg/utils/otto/genArk/whatIsNew.sh - lines changed 9, context: html, text, full: html, text

83b077f17c6a2b4a297e48c035b64ac6ecc86b44 Wed Nov 19 14:48:53 2025 -0800

NCBI assembly name change refs #29545
- src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv - lines changed 1, context: html, text, full: html, text

4637fe065c495e4e12805521872e51dc45880fff Wed Nov 19 15:02:30 2025 -0800

adding several per user request refs #29545
- src/hg/makeDb/doc/bacteriaAsmHub/bacteria.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

9fd202b891f2e2d5be9cfa807e5d5ba15e7fc02d Fri Nov 21 15:59:50 2025 -0800

protect the hs1 assembly on the outlinks with db=hs1 instead of genome=hs1 refs #36540
- src/hg/hgHubConnect/hgHubConnect.c - lines changed 8, context: html, text, full: html, text

af3fb358fdeee7bf9080bdee719eb0cc1d4b4c72 Sat Nov 22 15:32:57 2025 -0800

allow input to be a bigBed file refs #36672
- src/hg/utils/twoBitMask/twoBitMask.c - lines changed 30, context: html, text, full: html, text

986f3f122a40cb28b2ac4cc6c51048784a7ea872 Sat Nov 22 15:39:03 2025 -0800

add test for bigBed input refs #36672
- src/hg/utils/twoBitMask/makefile - lines changed 3, context: html, text, full: html, text
- src/hg/utils/twoBitMask/tests/input/testMask1.bb - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)

b6f7fd1e76673d2fd96e46ede11a11f421e15675 Sat Nov 22 17:13:04 2025 -0800

now correctly managing GenArk GCA and GCF assembly names refs #34370
- src/hg/ratStuff/mafAddIRows/mafAddIRows.c - lines changed 32, context: html, text, full: html, text

c31d6f7174025d44270f64f086b06df10b4196a6 Sat Nov 22 17:14:37 2025 -0800

now correctly managing GenArk GCA and GCF assembly names refs #34370
- src/hg/ratStuff/mafSplit/mafSplit.c - lines changed 26, context: html, text, full: html, text