Commits for hiram

b1ece0f85392e86c466550496925f7f1cffa61be Mon Sep 8 16:06:09 2025 -0700

hgParseChromRange does not require a database or genome name refs #35976
- src/hg/hubApi/liftOver.c - lines changed 3, context: html, text, full: html, text

fe164c83850e2adba662df57142d37321d581236 Tue Sep 9 22:16:59 2025 -0700

helper script for runBuild to find a reasonable RepeatMasker species to work with
- src/hg/makeDb/doc/asmHubs/findTaxon.pl - lines changed 82, context: html, text, full: html, text

6eff6b0c070a6bcbaf607c38239f51616d83bc96 Wed Sep 10 19:45:33 2025 -0700

eliminate the rnaSeqData include statement no longer exists refs #13553
- src/hg/utils/automation/asmHubTrackDb.sh - lines changed 4, context: html, text, full: html, text

aceeb7010c33195c4544bb76d1e56bfcc6d47239 Thu Sep 11 10:47:17 2025 -0700

BRC update refs #34337
- src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv - lines changed 84, context: html, text, full: html, text

ff30bada6966beec40c9341d94268dfe0f14b9b8 Thu Sep 11 13:15:16 2025 -0700

helper script to catch up a quick lift set of files, symLinks and table entry refs #35575
- src/hg/makeDb/doc/asmHubs/quickLiftCatchUp.sh - lines changed 178, context: html, text, full: html, text

ca0c31de09f0b88ca2a5c9b5c6d897768470740e Thu Sep 11 13:19:22 2025 -0700

quickLiftChain table entry script refs #35575
- src/hg/utils/automation/addQuickLift.py - lines changed 49, context: html, text, full: html, text

ff9e2fd834147f20ca56c3fcf674932d65fef3e3 Thu Sep 11 14:24:09 2025 -0700

adding GCA_018389105.1 chambered nautilus per user request refs #29545
- src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv - lines changed 2, context: html, text, full: html, text

7c88fd330d657bfc6007f75c75545ba63e94d87d Thu Sep 11 15:17:40 2025 -0700

adding -uncurated to the version 4.2.1 operation
- src/hg/utils/automation/doRepeatMasker.pl - lines changed 6, context: html, text, full: html, text

0cef6a4b1d730f0ecb4a5c8a0c0de6ce7a2fb13a Fri Sep 12 18:53:51 2025 -0700

temporary work-around to fix the align.tsv issue for RM 4.2.1
- src/hg/utils/automation/doRepeatMasker.pl - lines changed 4, context: html, text, full: html, text

3cc8e060d62a38f811bfe8b66f3a33c1ca5049fd Sat Sep 13 09:00:04 2025 -0700

temporary work around bugs in RepeatMasker code
- src/hg/utils/automation/asmHubRepeatMasker.sh - lines changed 4, context: html, text, full: html, text
- src/hg/utils/automation/doRepeatMasker.pl - lines changed 1, context: html, text, full: html, text

45dbcb20cdbe097028c25110bff00cad6040ef3a Sat Sep 13 21:46:41 2025 -0700

BRC update with over 3000 fungi refs #34337
- src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv - lines changed 3, context: html, text, full: html, text
- src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv - lines changed 3004, context: html, text, full: html, text
- src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv - lines changed 8, context: html, text, full: html, text

1a6e991e410cd9c58c1887c6d1b1cb9536ebcc0a Sat Sep 13 21:47:18 2025 -0700

adding one per user request refs #29545
- src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 1, context: html, text, full: html, text

7e6daa6f46ec1bc05211edb7d6241970f5afffea Sat Sep 13 22:15:32 2025 -0700

BRC update bringing in about 3000 fungi refs #34337
- src/hg/makeDb/doc/brcAsmHub/brc.orderList.tsv - lines changed 3105, context: html, text, full: html, text