All File Changes

v438_base to v439_preview (2022-10-10 to 2022-10-17) v439

• src/hg/cgilib/cartJson.c
  • lines changed 15, context: html, text, full: html, text
    af3a143571e5aa064eab75c34f9444b35413b562 Tue Nov 30 15:28:15 2021 -0800
    Add snippet support to trix searching. Required changing the wordPos from the first highest matching wordIndex to the wordIndex of the actual span. Have trixContextIndex create a second level index for fast retrieval of line offsets in original text file used by ixIxx. Create a simple UI for navigating hgFind search results.
  • lines changed 3, context: html, text, full: html, text
    748b06ac95ff2a3957be3845bd3594984e3cc3cf Wed Aug 17 19:21:48 2022 -0700
    Rename test cgi to official name. Always search everything, only show categories that have matches in the result list. Add /search endpoint to hubApi, add code to search help docs in hgSuggest but don't call it yet in autoComplete.js. Minor fixups so search result links work correctly. Fixing up old programs that call hgPositionsFind
• src/hg/hgGateway/hgGateway.c
  • lines changed 19, context: html, text, full: html, text
    cc1669639a750c73b05f85272a97129de52abae2 Mon Oct 10 15:40:06 2022 -0700
    Don't limit search of dbDb.description to only terms starting with GC; instead, restrict search to the part within parentheses (skipping the assembly date) and restrict searches that would match too many institutions like Broad, WUGSC, Baylor, Agencourt unless people type in more letters of those. refs #30108
• src/hg/hgGetAnn/hgGetAnn.c
  • lines changed 1, context: html, text, full: html, text
    748b06ac95ff2a3957be3845bd3594984e3cc3cf Wed Aug 17 19:21:48 2022 -0700
    Rename test cgi to official name. Always search everything, only show categories that have matches in the result list. Add /search endpoint to hubApi, add code to search help docs in hgSuggest but don't call it yet in autoComplete.js. Minor fixups so search result links work correctly. Fixing up old programs that call hgPositionsFind
• src/hg/hgPhyloPlace/hgPhyloPlace.c
  • lines changed 1, context: html, text, full: html, text
    3a59fc70bda966dd32a5d17b00dfb6688ad40e28 Fri Oct 14 09:40:30 2022 -0700
    NAR update reviewer feedback: make embedded tutorial video larger, no need to keep tiny default size.
• src/hg/hgPhyloPlace/phyloPlace.c
  • lines changed 83, context: html, text, full: html, text
    a384cc55ed66357a2e58c5d7a20f2125909b30b8 Wed Oct 12 14:32:51 2022 -0700
    Parse ranges of IDs such as EPI_SET notation (EPI_ISL_1234-5678), requested by @corneliusroemer in https://github.com/yatisht/usher/issues/276
• src/hg/hgPhyloPlace/treeToAuspiceJson.c
  • lines changed 20, context: html, text, full: html, text
    871b54b7f7262469495a2db7bc064d3322ff9fa3 Wed Oct 12 13:45:51 2022 -0700
    Auspice config: added entropy panel and filters for sample type, country, lineage/clade. HT @corneliusroemer
• src/hg/hgPhyloPlace/writeCustomTracks.c
  • lines changed 1, context: html, text, full: html, text
    7cd88510c60532d95aee9e98ba02d191990d873e Sat Oct 15 20:34:05 2022 -0700
    Fixing typo in corner case of writing alt alleles for VCF with imputed alleles, that caused segv when parsing the generated VCF. https://github.com/yatisht/usher/issues/282
• src/hg/hgSearch/hgSearch.c
  • lines changed 609, context: html, text, full: html, text
    748b06ac95ff2a3957be3845bd3594984e3cc3cf Wed Aug 17 19:21:48 2022 -0700
    Rename test cgi to official name. Always search everything, only show categories that have matches in the result list. Add /search endpoint to hubApi, add code to search help docs in hgSuggest but don't call it yet in autoComplete.js. Minor fixups so search result links work correctly. Fixing up old programs that call hgPositionsFind
• src/hg/hgSearch/makefile
  • lines changed 18, context: html, text, full: html, text
    748b06ac95ff2a3957be3845bd3594984e3cc3cf Wed Aug 17 19:21:48 2022 -0700
    Rename test cgi to official name. Always search everything, only show categories that have matches in the result list. Add /search endpoint to hubApi, add code to search help docs in hgSuggest but don't call it yet in autoComplete.js. Minor fixups so search result links work correctly. Fixing up old programs that call hgPositionsFind
• src/hg/hgSuggest/hgSuggest.c
  • lines changed 32, context: html, text, full: html, text
    748b06ac95ff2a3957be3845bd3594984e3cc3cf Wed Aug 17 19:21:48 2022 -0700
    Rename test cgi to official name. Always search everything, only show categories that have matches in the result list. Add /search endpoint to hubApi, add code to search help docs in hgSuggest but don't call it yet in autoComplete.js. Minor fixups so search result links work correctly. Fixing up old programs that call hgPositionsFind
• src/hg/hgTracks/hgTracks.c
  • lines changed 4, context: html, text, full: html, text
    af3a143571e5aa064eab75c34f9444b35413b562 Tue Nov 30 15:28:15 2021 -0800
    Add snippet support to trix searching. Required changing the wordPos from the first highest matching wordIndex to the wordIndex of the actual span. Have trixContextIndex create a second level index for fast retrieval of line offsets in original text file used by ixIxx. Create a simple UI for navigating hgFind search results.
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    748b06ac95ff2a3957be3845bd3594984e3cc3cf Wed Aug 17 19:21:48 2022 -0700
    Rename test cgi to official name. Always search everything, only show categories that have matches in the result list. Add /search endpoint to hubApi, add code to search help docs in hgSuggest but don't call it yet in autoComplete.js. Minor fixups so search result links work correctly. Fixing up old programs that call hgPositionsFind
• src/hg/htdocs/addHtml
  • lines changed 92, context: html, text, full: html, text
    af3a143571e5aa064eab75c34f9444b35413b562 Tue Nov 30 15:28:15 2021 -0800
    Add snippet support to trix searching. Required changing the wordPos from the first highest matching wordIndex to the wordIndex of the actual span. Have trixContextIndex create a second level index for fast retrieval of line offsets in original text file used by ixIxx. Create a simple UI for navigating hgFind search results.
  • lines changed 92, context: html, text, full: html, text
    748b06ac95ff2a3957be3845bd3594984e3cc3cf Wed Aug 17 19:21:48 2022 -0700
    Rename test cgi to official name. Always search everything, only show categories that have matches in the result list. Add /search endpoint to hubApi, add code to search help docs in hgSuggest but don't call it yet in autoComplete.js. Minor fixups so search result links work correctly. Fixing up old programs that call hgPositionsFind
• src/hg/htdocs/contacts.html
  • lines changed 3, context: html, text, full: html, text
    ce21c29874f6e61dcc2f10ce240cca29ebca63f9 Tue Oct 11 16:45:26 2022 -0700
    Updating links to survey monkey to be emails instead. No RM.
• src/hg/htdocs/inc/hgSearch.html
  • lines changed 177, context: html, text, full: html, text
    748b06ac95ff2a3957be3845bd3594984e3cc3cf Wed Aug 17 19:21:48 2022 -0700
    Rename test cgi to official name. Always search everything, only show categories that have matches in the result list. Add /search endpoint to hubApi, add code to search help docs in hgSuggest but don't call it yet in autoComplete.js. Minor fixups so search result links work correctly. Fixing up old programs that call hgPositionsFind
• src/hg/htdocs/inc/searchExample.html
  • lines changed 76, context: html, text, full: html, text
    af3a143571e5aa064eab75c34f9444b35413b562 Tue Nov 30 15:28:15 2021 -0800
    Add snippet support to trix searching. Required changing the wordPos from the first highest matching wordIndex to the wordIndex of the actual span. Have trixContextIndex create a second level index for fast retrieval of line offsets in original text file used by ixIxx. Create a simple UI for navigating hgFind search results.
  • lines changed 76, context: html, text, full: html, text
    748b06ac95ff2a3957be3845bd3594984e3cc3cf Wed Aug 17 19:21:48 2022 -0700
    Rename test cgi to official name. Always search everything, only show categories that have matches in the result list. Add /search endpoint to hubApi, add code to search help docs in hgSuggest but don't call it yet in autoComplete.js. Minor fixups so search result links work correctly. Fixing up old programs that call hgPositionsFind
• src/hg/htdocs/training/index.html
  • lines changed 5, context: html, text, full: html, text
    ce21c29874f6e61dcc2f10ce240cca29ebca63f9 Tue Oct 11 16:45:26 2022 -0700
    Updating links to survey monkey to be emails instead. No RM.
• src/hg/hubApi/dataApi.h
  • lines changed 9, context: html, text, full: html, text
    748b06ac95ff2a3957be3845bd3594984e3cc3cf Wed Aug 17 19:21:48 2022 -0700
    Rename test cgi to official name. Always search everything, only show categories that have matches in the result list. Add /search endpoint to hubApi, add code to search help docs in hgSuggest but don't call it yet in autoComplete.js. Minor fixups so search result links work correctly. Fixing up old programs that call hgPositionsFind
• src/hg/hubApi/hubApi.c
  • lines changed 2, context: html, text, full: html, text
    748b06ac95ff2a3957be3845bd3594984e3cc3cf Wed Aug 17 19:21:48 2022 -0700
    Rename test cgi to official name. Always search everything, only show categories that have matches in the result list. Add /search endpoint to hubApi, add code to search help docs in hgSuggest but don't call it yet in autoComplete.js. Minor fixups so search result links work correctly. Fixing up old programs that call hgPositionsFind
• src/hg/hubApi/makefile
  • lines changed 1, context: html, text, full: html, text
    748b06ac95ff2a3957be3845bd3594984e3cc3cf Wed Aug 17 19:21:48 2022 -0700
    Rename test cgi to official name. Always search everything, only show categories that have matches in the result list. Add /search endpoint to hubApi, add code to search help docs in hgSuggest but don't call it yet in autoComplete.js. Minor fixups so search result links work correctly. Fixing up old programs that call hgPositionsFind
• src/hg/hubApi/search.c
  • lines changed 154, context: html, text, full: html, text
    748b06ac95ff2a3957be3845bd3594984e3cc3cf Wed Aug 17 19:21:48 2022 -0700
    Rename test cgi to official name. Always search everything, only show categories that have matches in the result list. Add /search endpoint to hubApi, add code to search help docs in hgSuggest but don't call it yet in autoComplete.js. Minor fixups so search result links work correctly. Fixing up old programs that call hgPositionsFind
  • lines changed 1, context: html, text, full: html, text
    8ba8a055a41e48f2e0f06803754544dd0089f4ec Thu Oct 13 12:48:20 2022 -0700
    explicitly return NULL if categories were asked for in hubApi but no search results for that category
• src/hg/inc/bigBedFind.h
  • lines changed 7, context: html, text, full: html, text
    af3a143571e5aa064eab75c34f9444b35413b562 Tue Nov 30 15:28:15 2021 -0800
    Add snippet support to trix searching. Required changing the wordPos from the first highest matching wordIndex to the wordIndex of the actual span. Have trixContextIndex create a second level index for fast retrieval of line offsets in original text file used by ixIxx. Create a simple UI for navigating hgFind search results.
  • lines changed 3, context: html, text, full: html, text
    748b06ac95ff2a3957be3845bd3594984e3cc3cf Wed Aug 17 19:21:48 2022 -0700
    Rename test cgi to official name. Always search everything, only show categories that have matches in the result list. Add /search endpoint to hubApi, add code to search help docs in hgSuggest but don't call it yet in autoComplete.js. Minor fixups so search result links work correctly. Fixing up old programs that call hgPositionsFind
• src/hg/inc/cartJson.h
  • lines changed 4, context: html, text, full: html, text
    af3a143571e5aa064eab75c34f9444b35413b562 Tue Nov 30 15:28:15 2021 -0800
    Add snippet support to trix searching. Required changing the wordPos from the first highest matching wordIndex to the wordIndex of the actual span. Have trixContextIndex create a second level index for fast retrieval of line offsets in original text file used by ixIxx. Create a simple UI for navigating hgFind search results.
• src/hg/inc/hgFind.h
  • lines changed 81, context: html, text, full: html, text
    af3a143571e5aa064eab75c34f9444b35413b562 Tue Nov 30 15:28:15 2021 -0800
    Add snippet support to trix searching. Required changing the wordPos from the first highest matching wordIndex to the wordIndex of the actual span. Have trixContextIndex create a second level index for fast retrieval of line offsets in original text file used by ixIxx. Create a simple UI for navigating hgFind search results.
  • lines changed 18, context: html, text, full: html, text
    748b06ac95ff2a3957be3845bd3594984e3cc3cf Wed Aug 17 19:21:48 2022 -0700
    Rename test cgi to official name. Always search everything, only show categories that have matches in the result list. Add /search endpoint to hubApi, add code to search help docs in hgSuggest but don't call it yet in autoComplete.js. Minor fixups so search result links work correctly. Fixing up old programs that call hgPositionsFind
• src/hg/inc/hgFindSpec.h
  • lines changed 3, context: html, text, full: html, text
    af3a143571e5aa064eab75c34f9444b35413b562 Tue Nov 30 15:28:15 2021 -0800
    Add snippet support to trix searching. Required changing the wordPos from the first highest matching wordIndex to the wordIndex of the actual span. Have trixContextIndex create a second level index for fast retrieval of line offsets in original text file used by ixIxx. Create a simple UI for navigating hgFind search results.
• src/hg/inc/trackHub.h
  • lines changed 1, context: html, text, full: html, text
    af3a143571e5aa064eab75c34f9444b35413b562 Tue Nov 30 15:28:15 2021 -0800
    Add snippet support to trix searching. Required changing the wordPos from the first highest matching wordIndex to the wordIndex of the actual span. Have trixContextIndex create a second level index for fast retrieval of line offsets in original text file used by ixIxx. Create a simple UI for navigating hgFind search results.
• src/hg/js/autocomplete.js
  • lines changed 2, context: html, text, full: html, text
    748b06ac95ff2a3957be3845bd3594984e3cc3cf Wed Aug 17 19:21:48 2022 -0700
    Rename test cgi to official name. Always search everything, only show categories that have matches in the result list. Add /search endpoint to hubApi, add code to search help docs in hgSuggest but don't call it yet in autoComplete.js. Minor fixups so search result links work correctly. Fixing up old programs that call hgPositionsFind
• src/hg/js/dbDbTaxonomy.js
  • lines changed 52, context: html, text, full: html, text
    291e6e7839cc6f1410d077b50cf71da83b5fa27a Mon Oct 10 16:16:52 2022 -0700
    rebuild to get monkeypox virus included
• src/hg/js/hgGateway.js
  • lines changed 17, context: html, text, full: html, text
    af3a143571e5aa064eab75c34f9444b35413b562 Tue Nov 30 15:28:15 2021 -0800
    Add snippet support to trix searching. Required changing the wordPos from the first highest matching wordIndex to the wordIndex of the actual span. Have trixContextIndex create a second level index for fast retrieval of line offsets in original text file used by ixIxx. Create a simple UI for navigating hgFind search results.
  • lines changed 1, context: html, text, full: html, text
    748b06ac95ff2a3957be3845bd3594984e3cc3cf Wed Aug 17 19:21:48 2022 -0700
    Rename test cgi to official name. Always search everything, only show categories that have matches in the result list. Add /search endpoint to hubApi, add code to search help docs in hgSuggest but don't call it yet in autoComplete.js. Minor fixups so search result links work correctly. Fixing up old programs that call hgPositionsFind
• src/hg/js/hgSearch.js
  • lines changed 859, context: html, text, full: html, text
    748b06ac95ff2a3957be3845bd3594984e3cc3cf Wed Aug 17 19:21:48 2022 -0700
    Rename test cgi to official name. Always search everything, only show categories that have matches in the result list. Add /search endpoint to hubApi, add code to search help docs in hgSuggest but don't call it yet in autoComplete.js. Minor fixups so search result links work correctly. Fixing up old programs that call hgPositionsFind
• src/hg/js/hgTracks.js
  • lines changed 14, context: html, text, full: html, text
    af3a143571e5aa064eab75c34f9444b35413b562 Tue Nov 30 15:28:15 2021 -0800
    Add snippet support to trix searching. Required changing the wordPos from the first highest matching wordIndex to the wordIndex of the actual span. Have trixContextIndex create a second level index for fast retrieval of line offsets in original text file used by ixIxx. Create a simple UI for navigating hgFind search results.
  • lines changed 1, context: html, text, full: html, text
    748b06ac95ff2a3957be3845bd3594984e3cc3cf Wed Aug 17 19:21:48 2022 -0700
    Rename test cgi to official name. Always search everything, only show categories that have matches in the result list. Add /search endpoint to hubApi, add code to search help docs in hgSuggest but don't call it yet in autoComplete.js. Minor fixups so search result links work correctly. Fixing up old programs that call hgPositionsFind
• src/hg/js/makefile
  • lines changed 1, context: html, text, full: html, text
    af3a143571e5aa064eab75c34f9444b35413b562 Tue Nov 30 15:28:15 2021 -0800
    Add snippet support to trix searching. Required changing the wordPos from the first highest matching wordIndex to the wordIndex of the actual span. Have trixContextIndex create a second level index for fast retrieval of line offsets in original text file used by ixIxx. Create a simple UI for navigating hgFind search results.
  • lines changed 1, context: html, text, full: html, text
    748b06ac95ff2a3957be3845bd3594984e3cc3cf Wed Aug 17 19:21:48 2022 -0700
    Rename test cgi to official name. Always search everything, only show categories that have matches in the result list. Add /search endpoint to hubApi, add code to search help docs in hgSuggest but don't call it yet in autoComplete.js. Minor fixups so search result links work correctly. Fixing up old programs that call hgPositionsFind
• src/hg/js/searchExample.js
  • lines changed 754, context: html, text, full: html, text
    af3a143571e5aa064eab75c34f9444b35413b562 Tue Nov 30 15:28:15 2021 -0800
    Add snippet support to trix searching. Required changing the wordPos from the first highest matching wordIndex to the wordIndex of the actual span. Have trixContextIndex create a second level index for fast retrieval of line offsets in original text file used by ixIxx. Create a simple UI for navigating hgFind search results.
  • lines changed 754, context: html, text, full: html, text
    748b06ac95ff2a3957be3845bd3594984e3cc3cf Wed Aug 17 19:21:48 2022 -0700
    Rename test cgi to official name. Always search everything, only show categories that have matches in the result list. Add /search endpoint to hubApi, add code to search help docs in hgSuggest but don't call it yet in autoComplete.js. Minor fixups so search result links work correctly. Fixing up old programs that call hgPositionsFind
• src/hg/js/utils.js
  • lines changed 9, context: html, text, full: html, text
    af3a143571e5aa064eab75c34f9444b35413b562 Tue Nov 30 15:28:15 2021 -0800
    Add snippet support to trix searching. Required changing the wordPos from the first highest matching wordIndex to the wordIndex of the actual span. Have trixContextIndex create a second level index for fast retrieval of line offsets in original text file used by ixIxx. Create a simple UI for navigating hgFind search results.
• src/hg/lib/bigBedFind.c
  • lines changed 114, context: html, text, full: html, text
    af3a143571e5aa064eab75c34f9444b35413b562 Tue Nov 30 15:28:15 2021 -0800
    Add snippet support to trix searching. Required changing the wordPos from the first highest matching wordIndex to the wordIndex of the actual span. Have trixContextIndex create a second level index for fast retrieval of line offsets in original text file used by ixIxx. Create a simple UI for navigating hgFind search results.
  • lines changed 59, context: html, text, full: html, text
    748b06ac95ff2a3957be3845bd3594984e3cc3cf Wed Aug 17 19:21:48 2022 -0700
    Rename test cgi to official name. Always search everything, only show categories that have matches in the result list. Add /search endpoint to hubApi, add code to search help docs in hgSuggest but don't call it yet in autoComplete.js. Minor fixups so search result links work correctly. Fixing up old programs that call hgPositionsFind
• src/hg/lib/hdb.c
  • lines changed 2, context: html, text, full: html, text
    af3a143571e5aa064eab75c34f9444b35413b562 Tue Nov 30 15:28:15 2021 -0800
    Add snippet support to trix searching. Required changing the wordPos from the first highest matching wordIndex to the wordIndex of the actual span. Have trixContextIndex create a second level index for fast retrieval of line offsets in original text file used by ixIxx. Create a simple UI for navigating hgFind search results.
• src/hg/lib/hgFind.c
  • lines changed 591, context: html, text, full: html, text
    af3a143571e5aa064eab75c34f9444b35413b562 Tue Nov 30 15:28:15 2021 -0800
    Add snippet support to trix searching. Required changing the wordPos from the first highest matching wordIndex to the wordIndex of the actual span. Have trixContextIndex create a second level index for fast retrieval of line offsets in original text file used by ixIxx. Create a simple UI for navigating hgFind search results.
  • lines changed 373, context: html, text, full: html, text
    748b06ac95ff2a3957be3845bd3594984e3cc3cf Wed Aug 17 19:21:48 2022 -0700
    Rename test cgi to official name. Always search everything, only show categories that have matches in the result list. Add /search endpoint to hubApi, add code to search help docs in hgSuggest but don't call it yet in autoComplete.js. Minor fixups so search result links work correctly. Fixing up old programs that call hgPositionsFind
  • lines changed 4, context: html, text, full: html, text
    8ba8a055a41e48f2e0f06803754544dd0089f4ec Thu Oct 13 12:48:20 2022 -0700
    explicitly return NULL if categories were asked for in hubApi but no search results for that category
• src/hg/lib/hgFindSpecCustom.c
  • lines changed 1, context: html, text, full: html, text
    af3a143571e5aa064eab75c34f9444b35413b562 Tue Nov 30 15:28:15 2021 -0800
    Add snippet support to trix searching. Required changing the wordPos from the first highest matching wordIndex to the wordIndex of the actual span. Have trixContextIndex create a second level index for fast retrieval of line offsets in original text file used by ixIxx. Create a simple UI for navigating hgFind search results.
• src/hg/lib/tablesTables.c
  • lines changed 2, context: html, text, full: html, text
    c29257eb287f434d58772864a45eee7a2604e3de Tue Oct 11 10:42:33 2022 -0700
    Cleaning up debugging comment.
• src/hg/lib/trackHub.c
  • lines changed 2, context: html, text, full: html, text
    af3a143571e5aa064eab75c34f9444b35413b562 Tue Nov 30 15:28:15 2021 -0800
    Add snippet support to trix searching. Required changing the wordPos from the first highest matching wordIndex to the wordIndex of the actual span. Have trixContextIndex create a second level index for fast retrieval of line offsets in original text file used by ixIxx. Create a simple UI for navigating hgFind search results.
• src/hg/makeDb/doc/asmHubs/commonNames.pl
  • lines changed 36, context: html, text, full: html, text
    dd97b4a2ecd10761d802b7f63bf64f147399a609 Sun Oct 16 19:23:31 2022 -0700
    better names on viruses and add addition info to others no redmine
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 1, context: html, text, full: html, text
    60bd2913a4e064341f3327a5942b78cca019d441 Mon Oct 10 12:08:17 2022 -0700
    adding GCA_917862395.1_iHelSar1.1 Sara longwing butterfly per user request refs #29545
  • lines changed 16, context: html, text, full: html, text
    2b1824e2cb99b427ee749f5df2e4cf0e80f1f19f Sun Oct 16 20:08:30 2022 -0700
    adding 16 invertebrates per user request refs #29545
• src/hg/makeDb/doc/asmHubs/verifyOnDownload.sh
  • lines changed 9, context: html, text, full: html, text
    f3f18ba1ffec58fc4a7811f60b394e0c3d83cbe9 Sun Oct 16 20:09:17 2022 -0700
    adjuste lower limits for valid hubs in different clades refs $29545
• src/hg/makeDb/doc/hg19.txt
  • lines changed 1, context: html, text, full: html, text
    99856cacdbaa78c1e10650c00ee8cff19bc9c0da Tue Oct 11 10:37:37 2022 -0700
    update clinVarSub track
• src/hg/makeDb/doc/hg38/clinvarSubLolly.txt
  • lines changed 1, context: html, text, full: html, text
    99856cacdbaa78c1e10650c00ee8cff19bc9c0da Tue Oct 11 10:37:37 2022 -0700
    update clinVarSub track
• src/hg/makeDb/doc/hg38/grcH38P14.txt
  • lines changed 445, context: html, text, full: html, text
    fa35e265cbbfb28dc28b754cdfd4e79c05b42970 Fri Oct 14 19:49:24 2022 -0700
    Finished genome build of database that has ONLY new fix and patch chromosomes. The first part of the hg38 patch14 build.
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    60bd2913a4e064341f3327a5942b78cca019d441 Mon Oct 10 12:08:17 2022 -0700
    adding GCA_917862395.1_iHelSar1.1 Sara longwing butterfly per user request refs #29545
  • lines changed 20, context: html, text, full: html, text
    2b1824e2cb99b427ee749f5df2e4cf0e80f1f19f Sun Oct 16 20:08:30 2022 -0700
    adding 16 invertebrates per user request refs #29545
• src/hg/makeDb/doc/mpxvRivers/mask.txt
  • lines changed 16, context: html, text, full: html, text
    56f456777997dd6dc603bca06fe8fbcfc46111ce Thu Oct 13 03:01:41 2022 -0700
    adding masking tracks, no redmine yet because no docs page
• src/hg/makeDb/trackDb/buildTrix
  • lines changed 7, context: html, text, full: html, text
    af3a143571e5aa064eab75c34f9444b35413b562 Tue Nov 30 15:28:15 2021 -0800
    Add snippet support to trix searching. Required changing the wordPos from the first highest matching wordIndex to the wordIndex of the actual span. Have trixContextIndex create a second level index for fast retrieval of line offsets in original text file used by ixIxx. Create a simple UI for navigating hgFind search results.
  • lines changed 7, context: html, text, full: html, text
    1d898c9229d7e39bd62ace51dac43823a6a18212 Thu Oct 13 09:25:40 2022 -0700
    Remove testing changes to buildTrix, refs #29811
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
  • lines changed 12, context: html, text, full: html, text
    748b06ac95ff2a3957be3845bd3594984e3cc3cf Wed Aug 17 19:21:48 2022 -0700
    Rename test cgi to official name. Always search everything, only show categories that have matches in the result list. Add /search endpoint to hubApi, add code to search help docs in hgSuggest but don't call it yet in autoComplete.js. Minor fixups so search result links work correctly. Fixing up old programs that call hgPositionsFind
• src/hg/makeDb/trackDb/human/hg38/knownGene.ra
  • lines changed 1, context: html, text, full: html, text
    af3a143571e5aa064eab75c34f9444b35413b562 Tue Nov 30 15:28:15 2021 -0800
    Add snippet support to trix searching. Required changing the wordPos from the first highest matching wordIndex to the wordIndex of the actual span. Have trixContextIndex create a second level index for fast retrieval of line offsets in original text file used by ixIxx. Create a simple UI for navigating hgFind search results.
• src/hg/makeDb/trackDb/human/trackDb.clinvar.ra
  • lines changed 2, context: html, text, full: html, text
    748b06ac95ff2a3957be3845bd3594984e3cc3cf Wed Aug 17 19:21:48 2022 -0700
    Rename test cgi to official name. Always search everything, only show categories that have matches in the result list. Add /search endpoint to hubApi, add code to search help docs in hgSuggest but don't call it yet in autoComplete.js. Minor fixups so search result links work correctly. Fixing up old programs that call hgPositionsFind
• src/hg/makeDb/trackDb/human/trackDb.dbVar.ra
  • lines changed 7, context: html, text, full: html, text
    748b06ac95ff2a3957be3845bd3594984e3cc3cf Wed Aug 17 19:21:48 2022 -0700
    Rename test cgi to official name. Always search everything, only show categories that have matches in the result list. Add /search endpoint to hubApi, add code to search help docs in hgSuggest but don't call it yet in autoComplete.js. Minor fixups so search result links work correctly. Fixing up old programs that call hgPositionsFind
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 6, context: html, text, full: html, text
    af3a143571e5aa064eab75c34f9444b35413b562 Tue Nov 30 15:28:15 2021 -0800
    Add snippet support to trix searching. Required changing the wordPos from the first highest matching wordIndex to the wordIndex of the actual span. Have trixContextIndex create a second level index for fast retrieval of line offsets in original text file used by ixIxx. Create a simple UI for navigating hgFind search results.
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    af3a143571e5aa064eab75c34f9444b35413b562 Tue Nov 30 15:28:15 2021 -0800
    Add snippet support to trix searching. Required changing the wordPos from the first highest matching wordIndex to the wordIndex of the actual span. Have trixContextIndex create a second level index for fast retrieval of line offsets in original text file used by ixIxx. Create a simple UI for navigating hgFind search results.
• src/hg/makeDb/trackDb/virus/mpxvRivers/mask.ra
  • lines changed 30, context: html, text, full: html, text
    56f456777997dd6dc603bca06fe8fbcfc46111ce Thu Oct 13 03:01:41 2022 -0700
    adding masking tracks, no redmine yet because no docs page
• src/hg/makeDb/trackDb/virus/mpxvRivers/strs.ra
  • lines changed 10, context: html, text, full: html, text
    56f456777997dd6dc603bca06fe8fbcfc46111ce Thu Oct 13 03:01:41 2022 -0700
    adding masking tracks, no redmine yet because no docs page
• src/hg/makeDb/trackDb/virus/mpxvRivers/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    7069dedbc90558888eac98f2c655d6a3909ea081 Mon Oct 10 11:01:38 2022 -0700
    fixing build
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    e6fcc3e64852efaf942943673b997d95fc87d79e Mon Oct 10 11:08:46 2022 -0700
    fixing build again, refs #30112
  • lines changed 3, context: html, text, full: html, text
    56f456777997dd6dc603bca06fe8fbcfc46111ce Thu Oct 13 03:01:41 2022 -0700
    adding masking tracks, no redmine yet because no docs page
• src/hg/makeDb/trackDb/virus/wuhCor1/recomb.html
  • lines changed 17, context: html, text, full: html, text
    20061ad1f79429da23c658f3a18702b989b4ba6c Fri Oct 14 12:18:18 2022 -0700
    Made edits to recomb.html and long label, refs #30075
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    20061ad1f79429da23c658f3a18702b989b4ba6c Fri Oct 14 12:18:18 2022 -0700
    Made edits to recomb.html and long label, refs #30075
• src/hg/makefile
  • lines changed 1, context: html, text, full: html, text
    af3a143571e5aa064eab75c34f9444b35413b562 Tue Nov 30 15:28:15 2021 -0800
    Add snippet support to trix searching. Required changing the wordPos from the first highest matching wordIndex to the wordIndex of the actual span. Have trixContextIndex create a second level index for fast retrieval of line offsets in original text file used by ixIxx. Create a simple UI for navigating hgFind search results.
  • lines changed 1, context: html, text, full: html, text
    748b06ac95ff2a3957be3845bd3594984e3cc3cf Wed Aug 17 19:21:48 2022 -0700
    Rename test cgi to official name. Always search everything, only show categories that have matches in the result list. Add /search endpoint to hubApi, add code to search help docs in hgSuggest but don't call it yet in autoComplete.js. Minor fixups so search result links work correctly. Fixing up old programs that call hgPositionsFind
• src/hg/qa/testSearch.c
  • lines changed 1, context: html, text, full: html, text
    748b06ac95ff2a3957be3845bd3594984e3cc3cf Wed Aug 17 19:21:48 2022 -0700
    Rename test cgi to official name. Always search everything, only show categories that have matches in the result list. Add /search endpoint to hubApi, add code to search help docs in hgSuggest but don't call it yet in autoComplete.js. Minor fixups so search result links work correctly. Fixing up old programs that call hgPositionsFind
• src/hg/searchExample/makefile
  • lines changed 18, context: html, text, full: html, text
    af3a143571e5aa064eab75c34f9444b35413b562 Tue Nov 30 15:28:15 2021 -0800
    Add snippet support to trix searching. Required changing the wordPos from the first highest matching wordIndex to the wordIndex of the actual span. Have trixContextIndex create a second level index for fast retrieval of line offsets in original text file used by ixIxx. Create a simple UI for navigating hgFind search results.
  • lines changed 18, context: html, text, full: html, text
    748b06ac95ff2a3957be3845bd3594984e3cc3cf Wed Aug 17 19:21:48 2022 -0700
    Rename test cgi to official name. Always search everything, only show categories that have matches in the result list. Add /search endpoint to hubApi, add code to search help docs in hgSuggest but don't call it yet in autoComplete.js. Minor fixups so search result links work correctly. Fixing up old programs that call hgPositionsFind
• src/hg/searchExample/searchExample.c
  • lines changed 710, context: html, text, full: html, text
    af3a143571e5aa064eab75c34f9444b35413b562 Tue Nov 30 15:28:15 2021 -0800
    Add snippet support to trix searching. Required changing the wordPos from the first highest matching wordIndex to the wordIndex of the actual span. Have trixContextIndex create a second level index for fast retrieval of line offsets in original text file used by ixIxx. Create a simple UI for navigating hgFind search results.
  • lines changed 710, context: html, text, full: html, text
    748b06ac95ff2a3957be3845bd3594984e3cc3cf Wed Aug 17 19:21:48 2022 -0700
    Rename test cgi to official name. Always search everything, only show categories that have matches in the result list. Add /search endpoint to hubApi, add code to search help docs in hgSuggest but don't call it yet in autoComplete.js. Minor fixups so search result links work correctly. Fixing up old programs that call hgPositionsFind
• src/hg/utils/automation/asmHubTrackDb.sh
  • lines changed 4, context: html, text, full: html, text
    3eae75c8bc0186c7ea7a6b70a77c132e913dc474 Tue Oct 11 14:37:49 2022 -0700
    reset default name to display on RefSeq gene track and XenoRefMrna no redmine
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    4a57b140a286234b72b802aae6b9be52bf79ca5c Wed Oct 12 08:29:35 2022 -0700
    reset default name on Gene models track no redmine
• src/hg/utils/automation/doTandemDup.pl
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    68a21741ea6388775442314e7e71e98c7a15adad Sat Oct 15 22:29:42 2022 -0700
    rail para job ram size to 32g to avoid crashes due to out of memory no redmine
• src/hg/utils/otto/sarscov2phylo/fixNcbiFastaNames.pl
  • lines changed 1, context: html, text, full: html, text
    de878cd5e29e32002ebc64b66d7cf6989091f8ce Mon Oct 10 15:46:16 2022 -0700
    Another regex tweak for fluff that ends up in GenBank names. Oh, those crazy [Hh]umans.
• src/hg/utils/otto/sarscov2phylo/includeRecombinants.tsv
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    9be0c7e4b3f76f5dcf979c2469e05b9ee20b2fab Mon Oct 10 15:47:00 2022 -0700
    Adding recent recombinants that required explicit inclusion.
• src/hg/utils/otto/sarscov2phylo/makeNewMaskedVcf.sh
  • lines changed 1, context: html, text, full: html, text
    b81e6071edc73b0d973b29689c9d2dd6c84b8e8d Mon Oct 10 15:48:55 2022 -0700
    Tighten -maxDiff since it is still a lot less stringent than the --max-path-length filtering applied after placement.
• src/hg/utils/otto/sarscov2phylo/makePangolinAssignmentRelease.sh
  • lines changed 64, context: html, text, full: html, text
    068a98d10ad734d52ac41951bd10dc4222952e67 Mon Oct 10 16:02:25 2022 -0700
    Helper script for pango releases: put pip-compatible tarfiles in a staging directory for eventual hgdownload accessibility.
• src/hg/utils/otto/sarscov2phylo/maskDelta.sh
  • lines changed 7, context: html, text, full: html, text
    f35cefd3435d1513f3e130db211faa845068913a Mon Oct 10 15:43:36 2022 -0700
    Move node for BA.2.75-masking back a few levels; add more sites, especially BA.2-level reversions.
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
  • lines changed 218, context: html, text, full: html, text
    ca41ef450e78c43619fcb96bfc6d8002fac95e32 Mon Oct 3 15:27:50 2022 -0700
    Resolved more Ns to expected alleles. Added another bunch of new lineages for pango-designation v1.15.
  • lines changed 5, context: html, text, full: html, text
    541895c46dffc490e977491ac9361b49a8e9437f Mon Oct 10 15:42:43 2022 -0700
    Add BA.5.1.29, BF.7.1, BA.5.3.5, and correct paths for XBC and XBC.1.
  • lines changed 26, context: html, text, full: html, text
    74b9ff8522c8be268456f80f8c8dbe8af73f447c Wed Oct 12 14:39:49 2022 -0700
    Added two lineages that I should have added before v1.15 data release: BV.2 and BE.4.1.1. Added a bunch of recently designated lineages. Added BA.2.75.4_no9532 to fix problem with split BA.2.75.4. Added XA for easier comparison of two-letter lineages present in pango-designation vs. this file.
• src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
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    009620a961ec07ce597829ebac077d1920fae8f1 Mon Oct 10 15:47:58 2022 -0700
    Loosen filtering parameters so we don't lop off XAW.
• src/inc/trix.h
  • lines changed 42, context: html, text, full: html, text
    af3a143571e5aa064eab75c34f9444b35413b562 Tue Nov 30 15:28:15 2021 -0800
    Add snippet support to trix searching. Required changing the wordPos from the first highest matching wordIndex to the wordIndex of the actual span. Have trixContextIndex create a second level index for fast retrieval of line offsets in original text file used by ixIxx. Create a simple UI for navigating hgFind search results.
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    748b06ac95ff2a3957be3845bd3594984e3cc3cf Wed Aug 17 19:21:48 2022 -0700
    Rename test cgi to official name. Always search everything, only show categories that have matches in the result list. Add /search endpoint to hubApi, add code to search help docs in hgSuggest but don't call it yet in autoComplete.js. Minor fixups so search result links work correctly. Fixing up old programs that call hgPositionsFind
• src/index/ixIxx/ixIxx.c
  • lines changed 48, context: html, text, full: html, text
    af3a143571e5aa064eab75c34f9444b35413b562 Tue Nov 30 15:28:15 2021 -0800
    Add snippet support to trix searching. Required changing the wordPos from the first highest matching wordIndex to the wordIndex of the actual span. Have trixContextIndex create a second level index for fast retrieval of line offsets in original text file used by ixIxx. Create a simple UI for navigating hgFind search results.
• src/index/trixContextIndex/trixContextIndex.c
  • lines changed 112, context: html, text, full: html, text
    af3a143571e5aa064eab75c34f9444b35413b562 Tue Nov 30 15:28:15 2021 -0800
    Add snippet support to trix searching. Required changing the wordPos from the first highest matching wordIndex to the wordIndex of the actual span. Have trixContextIndex create a second level index for fast retrieval of line offsets in original text file used by ixIxx. Create a simple UI for navigating hgFind search results.
• src/index/trixSearch/trixSearch.c
  • lines changed 22, context: html, text, full: html, text
    af3a143571e5aa064eab75c34f9444b35413b562 Tue Nov 30 15:28:15 2021 -0800
    Add snippet support to trix searching. Required changing the wordPos from the first highest matching wordIndex to the wordIndex of the actual span. Have trixContextIndex create a second level index for fast retrieval of line offsets in original text file used by ixIxx. Create a simple UI for navigating hgFind search results.
• src/lib/trix.c
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    af3a143571e5aa064eab75c34f9444b35413b562 Tue Nov 30 15:28:15 2021 -0800
    Add snippet support to trix searching. Required changing the wordPos from the first highest matching wordIndex to the wordIndex of the actual span. Have trixContextIndex create a second level index for fast retrieval of line offsets in original text file used by ixIxx. Create a simple UI for navigating hgFind search results.
  • lines changed 10, context: html, text, full: html, text
    748b06ac95ff2a3957be3845bd3594984e3cc3cf Wed Aug 17 19:21:48 2022 -0700
    Rename test cgi to official name. Always search everything, only show categories that have matches in the result list. Add /search endpoint to hubApi, add code to search help docs in hgSuggest but don't call it yet in autoComplete.js. Minor fixups so search result links work correctly. Fixing up old programs that call hgPositionsFind
• src/makefile
  • lines changed 1, context: html, text, full: html, text
    af3a143571e5aa064eab75c34f9444b35413b562 Tue Nov 30 15:28:15 2021 -0800
    Add snippet support to trix searching. Required changing the wordPos from the first highest matching wordIndex to the wordIndex of the actual span. Have trixContextIndex create a second level index for fast retrieval of line offsets in original text file used by ixIxx. Create a simple UI for navigating hgFind search results.
• src/utils/pslMap/pslMap.c
  • lines changed 22, context: html, text, full: html, text
    fc825ca18eeb99e3807a73d23fd26b614807fa0f Tue Oct 11 19:26:06 2022 -0700
    add row number of output psl to pslMap mapInfo file to make it easy to sync up the two files
• src/utils/pslMap/tests/expected/mrnaMapOver.mapinfo
  • lines changed 2, context: html, text, full: html, text
    fc825ca18eeb99e3807a73d23fd26b614807fa0f Tue Oct 11 19:26:06 2022 -0700
    add row number of output psl to pslMap mapInfo file to make it easy to sync up the two files
• src/utils/pslMap/tests/expected/mrnaMapOverSwap.mapinfo
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    fc825ca18eeb99e3807a73d23fd26b614807fa0f Tue Oct 11 19:26:06 2022 -0700
    add row number of output psl to pslMap mapInfo file to make it easy to sync up the two files
• src/utils/pslMap/tests/expected/testMapFileWithInQName.mapinfo
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    fc825ca18eeb99e3807a73d23fd26b614807fa0f Tue Oct 11 19:26:06 2022 -0700
    add row number of output psl to pslMap mapInfo file to make it easy to sync up the two files
• src/utils/pslMap/tests/makefile
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    fc825ca18eeb99e3807a73d23fd26b614807fa0f Tue Oct 11 19:26:06 2022 -0700
    add row number of output psl to pslMap mapInfo file to make it easy to sync up the two files
• src/utils/pslMap/usage.txt
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    fc825ca18eeb99e3807a73d23fd26b614807fa0f Tue Oct 11 19:26:06 2022 -0700
    add row number of output psl to pslMap mapInfo file to make it easy to sync up the two files
• src/utils/qa/checkSyncAndMetaDataAll.py
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    633b46775a52967bb8eb5a28548e1c3187f4171f Sun Oct 16 14:48:02 2022 -0700
    Editing the script to ignore hs1 and mpxvRivers (curated hubs) for checkSync, cronjob no RM
• src/utils/qa/weeklybld/buildEnv.csh
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    58539a117f710be181124206a533532da1a1bf12 Mon Oct 17 10:35:23 2022 -0700
    v439 preview1, refs #30145

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• files changed: 113