Commits for hiram

v504_base to v505_preview (2026-09-21 to 2026-10-05) v505

81a04805893ab59c954464ac449abe65da05ac7f Mon Sep 21 16:28:30 2026 -0700

• highlight NCBI "reference" assemblies in the search result and hg.conf gated with hgGateway.showRefBadge=on default is off refs #38401
  • src/hg/hgGateway/hgGateway.c - lines changed 13, context: html, text, full: html, text
  • src/hg/js/autocompleteCat.js - lines changed 16, context: html, text, full: html, text

a0dde9c4583f3f1b7e31fd079b89ef4cc9b71cfd Mon Sep 21 17:22:33 2026 -0700

• also recognize hut:/gbdb/genark as genark hubs from dbDb refs #38361
  • src/hg/lib/hdb.c - lines changed 2, context: html, text, full: html, text

a483ae438425d48eab80887eab161c20b97af775 Mon Sep 21 17:59:40 2026 -0700

• GCF_049306965.2 should also display its name GRCz12tu in the menus refs #38361
  • src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv - lines changed 1, context: html, text, full: html, text

59b419bcf74bc81e7de2f4227db3db79432e7898 Mon Sep 21 18:23:24 2026 -0700

• VGP update refs #29545
  • src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv - lines changed 5, context: html, text, full: html, text

efaa2288304bd000222111bb024c336d8c56929a Tue Sep 22 03:35:40 2026 -0700

• chainNet trackDb for danRer11 GCF_052040795.1, otto liftOver
  • src/hg/makeDb/trackDb/zebrafish/danRer11/danRer11.GCF_052040795.1.chainNet.ra - lines changed 49, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/zebrafish/danRer11/trackDb.ra - lines changed 1, context: html, text, full: html, text

a8cddaa41b8aba592873f48a24b15229c052bfbd Tue Sep 22 05:08:06 2026 -0700

• chainNet trackDb for danRer11 GCF_049306965.2, otto liftOver
  • src/hg/makeDb/trackDb/zebrafish/danRer11/danRer11.GCF_049306965.2.chainNet.ra - lines changed 49, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/zebrafish/danRer11/trackDb.ra - lines changed 1, context: html, text, full: html, text

1c0a16d8c4d5ad60b5bd5f0fe6470bdd4c5f3f58 Wed Sep 23 16:26:39 2026 -0700

• chainNet trackDb for hg38 GCA_040939475.2, otto liftOver
  • src/hg/makeDb/trackDb/human/hg38/hg38.GCA_040939475.2.chainNet.ra - lines changed 49, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 1, context: html, text, full: html, text

2289b2aaf691efca9e98d99681ae28d821012896 Wed Sep 23 16:51:58 2026 -0700

• script used by fetch.sh to load the assembly_summary files into the "genark" database refs #32596
  • src/hg/utils/otto/genArk/ncbiMirror/loadAssemblySummaries.sh - lines changed 52, context: html, text, full: html, text

b269cf8292be3c573bb92058fbd6a3df5cf385c9 Thu Sep 24 15:44:03 2026 -0700

• translation of Chenxi Zhou code from Gene Myers FASTGA PAFtoPSL.c code to kent C code refs #34360
  • src/utils/pafToPsl/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/pafToPsl/pafToPsl.c - lines changed 327, context: html, text, full: html, text

0137e8b20a8d122324fcaa984c882ade51bd41f1 Thu Sep 24 15:53:48 2026 -0700

• test for pafToPsl command refs #34360
  • src/utils/pafToPsl/tests/expected/hg38ChrMt.psl - lines changed 1, context: html, text, full: html, text
  • src/utils/pafToPsl/tests/input/hg38ChrMt.paf - lines changed 1, context: html, text, full: html, text
  • src/utils/pafToPsl/tests/makefile - lines changed 15, context: html, text, full: html, text

1e49359da6689c022a312353f97af28d161802c3 Thu Sep 24 15:54:15 2026 -0700

• add test target refs #34360
  • src/utils/pafToPsl/makefile - lines changed 3, context: html, text, full: html, text

8331ea06f434b295c7b5383bc1e64f3f4a371387 Thu Sep 24 16:01:29 2026 -0700

• adding pafToPsl to userApps output refs #34360
  • src/utils/makefile - lines changed 1, context: html, text, full: html, text

5b1a5a9767296bfeb7c1a1d08fc9c6677e7ca032 Fri Sep 25 02:32:27 2026 -0700

• chainNet trackDb for hg38 GCF_002880755.1, otto liftOver
  • src/hg/makeDb/trackDb/human/hg38/hg38.GCF_002880755.1.chainNet.ra - lines changed 49, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 1, context: html, text, full: html, text

6dcfa7d1962d9e9dbfa5cbe651b6e301101287ef Fri Sep 25 12:51:58 2026 -0700

• beginning to get a miniMap2 process in place refs #34360
  • src/hg/utils/automation/AsmHub.pm - lines changed 37, context: html, text, full: html, text
  • src/hg/utils/automation/AssemblyDivergence.pm - lines changed 194, context: html, text, full: html, text
  • src/hg/utils/automation/HgAutomate.pm - lines changed 18, context: html, text, full: html, text
  • src/hg/utils/automation/doMiniMap2.pl - lines changed 785, context: html, text, full: html, text
  • src/hg/utils/automation/mashDistance.pl - lines changed 131, context: html, text, full: html, text

75f0d8f409975fddfd9c01378b4404d19393ec6b Fri Sep 25 12:53:35 2026 -0700

• beginning to get a miniMap2 process in place refs #34360
  • src/hg/utils/automation/mashDistance.pl - lines changed 2, context: html, text, full: html, text

59e735bf19713b82dd5898fbd7b0e34cb5e980af Fri Sep 25 12:58:50 2026 -0700

• OK to place these new functions for miniMap2 and mashDistance into scripts directory #34360
  • src/hg/utils/automation/makefile - lines changed 3, context: html, text, full: html, text

1c0824920cd06057c2e7c02d9cb7ecc153a99d5e Fri Sep 25 14:00:59 2026 -0700

• please no ssh from cluster nodes back to hgwdev to run hgsql commands refs #34360
  • src/hg/utils/automation/AssemblyDivergence.pm - lines changed 93, context: html, text, full: html, text
  • src/hg/utils/automation/HgAutomate.pm - lines changed 18, context: html, text, full: html, text
  • src/hg/utils/automation/doMiniMap2.pl - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/automation/mashDistance.pl - lines changed 46, context: html, text, full: html, text

4a6fab6dc819469ff2a299cd310ee19994d7e03a Fri Sep 25 15:08:49 2026 -0700

• allow a T2T name column refs #38110
  • src/hg/utils/automation/aliasTextToBed.pl - lines changed 1, context: html, text, full: html, text

13324df7d810e3cd1d64d93e8f83de7f7611e473 Fri Sep 25 18:55:52 2026 -0700

• claude found and error in the code and added a test for the bug refs #34360
  • src/utils/pafToPsl/pafToPsl.c - lines changed 11, context: html, text, full: html, text
  • src/utils/pafToPsl/tests/expected/indelEdges.psl - lines changed 4, context: html, text, full: html, text
  • src/utils/pafToPsl/tests/input/indelEdges.paf - lines changed 4, context: html, text, full: html, text

d6c5f9d4c46a1be9fc24bc548052232560710faf Fri Sep 25 18:58:33 2026 -0700

• claude found and error in the code and added a test for the bug refs #34360
  • src/utils/pafToPsl/tests/makefile - lines changed 12, context: html, text, full: html, text

8046b546777ffbd1c1745e081bd419901b7d2efd Sun Sep 27 09:08:33 2026 -0700

• continuing VGP update refs #39545
  • src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv - lines changed 4, context: html, text, full: html, text

e964722613c1b0f9ab40c3a6870ba6d8060f523f Sun Sep 27 09:25:53 2026 -0700

• VGP update refs #29545
  • src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv - lines changed 2, context: html, text, full: html, text

be5cbe094825357e026912debc79944cc15bacde Sun Sep 27 12:58:52 2026 -0700

• claude review fixing bugs better safety on database assembly mash sketch archive refs #34360
  • src/hg/utils/automation/AssemblyDivergence.pm - lines changed 19, context: html, text, full: html, text

e8b649b163d747c026dde4606542fcc024a6943a Sun Sep 27 13:14:54 2026 -0700

• add the mash sketch operation to the GenArk build refs #34360
  • src/hg/utils/automation/doAssemblyHub.pl - lines changed 44, context: html, text, full: html, text

5696aa327678ae46e826978431f0655af289062d Sun Sep 27 22:41:38 2026 -0700

• NCBI name changing refs #29545
  • src/hg/makeDb/doc/vgpAsmHub/vgp.primary.orderList.tsv - lines changed 4, context: html, text, full: html, text

dd43de4966296736e36a57a5921f3902e665d27a Sun Sep 27 22:43:02 2026 -0700

• VGP update refs #29545
  • src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv - lines changed 1, context: html, text, full: html, text

70b908a5c6475d6c2770a3305f9319d88d0cb62e Mon Sep 28 22:31:27 2026 -0700

• readjusting output results and feature bit file locations refs #34360
  • src/hg/utils/automation/doMiniMap2.pl - lines changed 116, context: html, text, full: html, text

cb2aa0e55497911448f0a42bff3b368057847eef Tue Sep 29 11:58:39 2026 -0700

• may have the primary query on target working OK refs #34360
  • src/hg/utils/automation/doMiniMap2.pl - lines changed 216, context: html, text, full: html, text

1c41dff03108b4818777b9c9914e81c72555163f Tue Sep 29 12:28:41 2026 -0700

• miniMap2 now with swap option refs #34360
  • src/hg/utils/automation/AsmHub.pm - lines changed 20, context: html, text, full: html, text
  • src/hg/utils/automation/doMiniMap2.pl - lines changed 209, context: html, text, full: html, text

3c1b9cee5a4152b70e2fc10b432082ea89fecae6 Tue Sep 29 15:06:19 2026 -0700

• add trackDb construction for miniMap2 chain tracks refs #34360
  • src/hg/utils/automation/asmHubMiniMap2ChainNet.pl - lines changed 183, context: html, text, full: html, text
  • src/hg/utils/automation/asmHubMiniMap2ChainNetComposite.pl - lines changed 297, context: html, text, full: html, text
  • src/hg/utils/automation/asmHubMiniMap2ChainNetTrackDb.pl - lines changed 219, context: html, text, full: html, text
  • src/hg/utils/automation/asmHubMiniMap2ChainNetTrackDb.sh - lines changed 167, context: html, text, full: html, text
  • src/hg/utils/automation/asmHubTrackDb.sh - lines changed 21, context: html, text, full: html, text

8149f2d63d04238813b626ab194b45eeaa91e32f Tue Sep 29 15:20:22 2026 -0700

• fixup swap directory recognition refs #34360
  • src/hg/utils/automation/asmHubMiniMap2ChainNetComposite.pl - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/automation/asmHubMiniMap2ChainNetTrackDb.pl - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/automation/asmHubMiniMap2ChainNetTrackDb.sh - lines changed 9, context: html, text, full: html, text
  • src/hg/utils/automation/asmHubTrackDb.sh - lines changed 6, context: html, text, full: html, text

2727d941e00bc74cc9fe53851ccc16172965646d Tue Sep 29 22:35:07 2026 -0700

• a track name too long caused a buffer overflow, claude advice here fixes this problem, track to test is in GenArk assembly GCA_020740595.1 in the "LiftOver Ring-tailed lemur (2021-11-04) minimap2 Lift Over Chained Alignments" track refs #34360
  • src/hg/hgTracks/chainTrack.c - lines changed 13, context: html, text, full: html, text
  • src/hg/hgTracks/halSnakeTrack.c - lines changed 2, context: html, text, full: html, text

7b14110dc65b6711d7c57fa03594b71b8f93a53e Tue Sep 29 22:49:39 2026 -0700

• add Data Access section to the description pages refs #34360
  • src/hg/utils/automation/asmHubMiniMap2ChainNet.pl - lines changed 68, context: html, text, full: html, text
  • src/hg/utils/automation/asmHubMiniMap2ChainNetComposite.pl - lines changed 42, context: html, text, full: html, text

bfe895921db1a915cbd21cc0e70c09d1c159e32b Tue Sep 29 23:06:22 2026 -0700

• showing minimap2 chains to hg38 refs #34360
  • src/hg/makeDb/trackDb/human/hs1/miniMapChains.ra - lines changed 52, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/trackDb.ra - lines changed 2, context: html, text, full: html, text

ad6dd2177ad20bea9e32563ee76a1c598bccb6d5 Tue Sep 29 23:22:17 2026 -0700

• adding hg38 liftOver chain from lastz refs #34360
  • src/hg/makeDb/trackDb/human/hs1/chainLiftOverHg38.ra - lines changed 12, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/humanChainNet.trackDb.ra - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hs1/miniMapChains.ra - lines changed 2, context: html, text, full: html, text

6c02c046a1f2a5d9462db2dc26dfe46369d3c3cf Wed Sep 30 15:51:43 2026 -0700

• shown miniMap2 hs1 alignment and swapped from hs1 refs #34360
  • src/hg/makeDb/trackDb/human/hg38/miniMapChains.ra - lines changed 72, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 2, context: html, text, full: html, text

2b14cc7d4cd492874f2e2a89e05d5cd720dbe304 Thu Oct 1 15:54:21 2026 -0700

• do not use any alias names if such a name, case insensitive, is already a name in hgcentral.dbDb.name column refs #38444
  • src/hg/utils/otto/genArk/asmAlias/asmAliasUpdate.py - lines changed 59, context: html, text, full: html, text

b19feb943205afd4ef3915f13476613f2562f773 Sun Oct 4 14:35:46 2026 -0700

• continue VGP update refs #29545
  • src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/birdsAsmHub/birds.orderList.tsv - lines changed 53, context: html, text, full: html, text
  • src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv - lines changed 47, context: html, text, full: html, text
  • src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv - lines changed 18, context: html, text, full: html, text
  • src/hg/makeDb/doc/vertebrateAsmHub/vertebrate.orderList.tsv - lines changed 15, context: html, text, full: html, text