All File Changes

v372_preview2 to v372_base (2018-09-24 to 2018-10-01) v372

• src/hg/hgGateway/hgGateway.c
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    3ecfb8deb165083b0d3df5081aeb5dda2c4b6ff1 Mon Sep 24 10:53:38 2018 -0700
    Libifying JS module autocompleteCat (autocomplete with optional category labels) from hgGateway.
• src/hg/hgSuggest/hgSuggest.c
  • lines changed 162, context: html, text, full: html, text
    bffbb000a3df4b88a8117ea5f852ab3abeea6e17 Mon Sep 24 14:42:01 2018 -0700
    Added a new mode to hgSuggest: altOrPatch, to match alt haplo or fix patch sequence names. Use it in hgTracks' multi-region dialog. Make the dialog inputs activate their respective radio buttons. refs #18854
  • lines changed 26, context: html, text, full: html, text
    d86d0030a9eb8ebce064d942456b42e6f82874cf Tue Sep 25 14:11:18 2018 -0700
    In altOrPatch mode, if prefix matching yields no results, then try matching any part of sequence names. Treat '.' as a single-char wildcard so 'KI270857.1' can match chr17_KI270857v1_alt. refs #18854
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    f70c2b18fe16f73ae6faee21e006eabcf5fd9aa6 Wed Sep 26 10:05:16 2018 -0700
    Tweak to prevent symmetrical _alt and _fix mappings from causing alt results in fix searches and vice versa. refs #18854
  • lines changed 46, context: html, text, full: html, text
    e4406bcd83a67929f2c980c338eba9071818d461 Wed Sep 26 10:54:01 2018 -0700
    Add chromAlias to multi-region alt/fix autocomplete, so we can match RefSeq accessions and Assembly names. refs #18854
  • lines changed 9, context: html, text, full: html, text
    60e7358ad9239e80827ee2a9d95151ef5fc57946 Wed Sep 26 12:17:25 2018 -0700
    Add fuzzy search of chromAlias to multi-region alt/fix autocomplete, so common haplotype name components like 'cox', 'apd', 'kir' can be matched. refs #18544
  • lines changed 20, context: html, text, full: html, text
    a4234f184e880692939c7dfe967d1d3b220399e6 Wed Sep 26 12:25:10 2018 -0700
    In multi-region alt/fix autocomplete, escape search terms in the same way for chromAlias search as for {alt,fix}SeqLiftOverPsl. refs #18544
  • lines changed 14, context: html, text, full: html, text
    9c6ef86df0c2a4358634bcd9dae49093e300ff29 Wed Sep 26 15:28:10 2018 -0700
    For multi-region alt/fix autocomplete, use {alt,fix}Locations insteaf of {alt,fix}SeqLiftOverPsl because the former are more stable at this point, and the *Locations tables are used by hgTracks. refs #22144
• src/hg/hgTracks/bigWarn.c
  • lines changed 6, context: html, text, full: html, text
    61e3dea584fd29bc10d99120a480e37fea3e84da Thu Sep 27 17:11:23 2018 -0700
    make sure bigWarn statements end up in the log.
• src/hg/hgTracks/config.c
  • lines changed 22, context: html, text, full: html, text
    bffbb000a3df4b88a8117ea5f852ab3abeea6e17 Mon Sep 24 14:42:01 2018 -0700
    Added a new mode to hgSuggest: altOrPatch, to match alt haplo or fix patch sequence names. Use it in hgTracks' multi-region dialog. Make the dialog inputs activate their respective radio buttons. refs #18854
  • lines changed 5, context: html, text, full: html, text
    fca9df21f4b3dfbb1191a0fe13d1d1bb100252c3 Wed Sep 26 11:20:36 2018 -0700
    In multi-region dialog, mention fix patches if applicable, and make alt/fix input wider to accommodate long aliases and autocomplete labels. refs #18854
• src/hg/hgTracks/hgTracks.c
  • lines changed 4, context: html, text, full: html, text
    bffbb000a3df4b88a8117ea5f852ab3abeea6e17 Mon Sep 24 14:42:01 2018 -0700
    Added a new mode to hgSuggest: altOrPatch, to match alt haplo or fix patch sequence names. Use it in hgTracks' multi-region dialog. Make the dialog inputs activate their respective radio buttons. refs #18854
  • lines changed 2, context: html, text, full: html, text
    3446d0006f2c776afd02a36d351d79611383615e Tue Sep 25 13:26:29 2018 -0700
    Chop at ':', if there is one, in {alt,fix}Locations.name when matching an alt or fix sequence name. refs #18854
  • lines changed 1, context: html, text, full: html, text
    57d1068b88c6255f3530cb981bf97bb127a459f9 Wed Sep 26 11:42:17 2018 -0700
    Fixing typo in regex for ignoring stuff after the colon and position range in altLocations names. refs #18854
• src/hg/hgTracks/simpleTracks.c
  • lines changed 1, context: html, text, full: html, text
    42ac1b41b5b3b66ed8ea7828cd36f4fcd9ceb1d5 Thu Sep 27 14:38:17 2018 -0700
    fix bug in gencode knownGene bigBed support #22145
• src/hg/hgc/hgc.c
  • lines changed 13, context: html, text, full: html, text
    13827887c45cb6ba7da05276cf0c703ec7627c17 Tue Sep 25 13:29:25 2018 -0700
    Add 'show this sequence placed on its chromosome' link to fixLocations in addition to altLocations, and chop ':start-end' from item names to get just the sequence name for singleAltHaplo mode. refs #18854
• src/hg/htdocs/FAQ/FAQdownloads.html
  • lines changed 6, context: html, text, full: html, text
    2437aad3bfcbc5c48e1c83147245b99c842b7bde Wed Sep 26 09:05:06 2018 -0700
    adding link to FAQ page,refs #22122
  • lines changed 1, context: html, text, full: html, text
    25cad35eeb5338fe1c025b91b9071569ce5703b4 Thu Sep 27 14:15:59 2018 -0700
    fixing typo in FAQdownlaods.html
• src/hg/htdocs/goldenPath/help/mysql.html
  • lines changed 1, context: html, text, full: html, text
    f688b02b88b7a5ccc8954bb1e19b2c526365942d Fri Sep 28 11:44:33 2018 -0700
    Adding an anchor for the utilities section on the mysql.html help page for an MLQ, refs #22119
• src/hg/htdocs/style/HGStyle.css
  • lines changed 14, context: html, text, full: html, text
    3ecfb8deb165083b0d3df5081aeb5dda2c4b6ff1 Mon Sep 24 10:53:38 2018 -0700
    Libifying JS module autocompleteCat (autocomplete with optional category labels) from hgGateway.
• src/hg/htdocs/style/jWest.css
  • lines changed 13, context: html, text, full: html, text
    3ecfb8deb165083b0d3df5081aeb5dda2c4b6ff1 Mon Sep 24 10:53:38 2018 -0700
    Libifying JS module autocompleteCat (autocomplete with optional category labels) from hgGateway.
• src/hg/htdocs/training/index.html
  • lines changed 81, context: html, text, full: html, text
    f66bf9a373877c301fa74b003cd5d06fa836f061 Tue Sep 25 12:19:46 2018 -0700
    reason: dropping Kansas City and North Carolina workshops. updating some links and future gigs
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    7b07752c88d957fcd8dd5d282bf6dd194b15be96 Mon Oct 1 10:37:40 2018 -0700
    New version number v372
• src/hg/js/autocompleteCat.js
  • lines changed 118, context: html, text, full: html, text
    3ecfb8deb165083b0d3df5081aeb5dda2c4b6ff1 Mon Sep 24 10:53:38 2018 -0700
    Libifying JS module autocompleteCat (autocomplete with optional category labels) from hgGateway.
• src/hg/js/hgGateway.js
  • lines changed 119, context: html, text, full: html, text
    3ecfb8deb165083b0d3df5081aeb5dda2c4b6ff1 Mon Sep 24 10:53:38 2018 -0700
    Libifying JS module autocompleteCat (autocomplete with optional category labels) from hgGateway.
• src/hg/js/hgTracks.js
  • lines changed 13, context: html, text, full: html, text
    bffbb000a3df4b88a8117ea5f852ab3abeea6e17 Mon Sep 24 14:42:01 2018 -0700
    Added a new mode to hgSuggest: altOrPatch, to match alt haplo or fix patch sequence names. Use it in hgTracks' multi-region dialog. Make the dialog inputs activate their respective radio buttons. refs #18854
  • lines changed 9, context: html, text, full: html, text
    31d76baa5576bc0fe479c2b9ae3d06a6df875cc1 Tue Sep 25 13:32:17 2018 -0700
    In the multi-region position pop-up, when viewing just a subregion of a large virt, add a hint about the full region size to make it clear that it's a subregion not the whole thing.
• src/hg/js/makefile
  • lines changed 1, context: html, text, full: html, text
    3ecfb8deb165083b0d3df5081aeb5dda2c4b6ff1 Mon Sep 24 10:53:38 2018 -0700
    Libifying JS module autocompleteCat (autocomplete with optional category labels) from hgGateway.
• src/hg/lib/genePred.c
  • lines changed 16, context: html, text, full: html, text
    ee6b3270d5a37e7e28c7af65aead341fa682295f Thu Sep 27 17:09:26 2018 -0700
    Fixed GTF conversion problem where final CDS exon had incorrect frame. occurred when The CDS started in the exon that contains the last codon before the stop codon. The stop code was either spliced or the only codon in the exon. This changed 44 gencode V28 transcripts, many of which were manually validated in the browser.
• src/hg/lib/mathWig.c
  • lines changed 2, context: html, text, full: html, text
    00dd647be13844229b5bacc1c4dd4ade63484af9 Wed Sep 26 15:30:53 2018 -0700
    oops... free connections in mathWig
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 1, context: html, text, full: html, text
    b8eedc7993c88486a0aecb09f70a8f22733642fc Fri Sep 28 11:31:16 2018 -0700
    make the name of ku properly adorned
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • lines changed 2, context: html, text, full: html, text
    bd71b6043279c7e75766671abb09af0ee1df6927 Wed Sep 26 10:18:25 2018 -0700
    Adding new anoGam3 assembly to the Genebank updates Ref#20743
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    69d02144099fee14c16b0d7e53b52ff4c710ae35 Wed Sep 26 13:16:23 2018 -0700
    add thaSir to hgwbeta.dbs
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    a62be5f3a3524b2cd349168700c37ed3a8bed011 Thu Sep 27 14:31:34 2018 -0700
    Added my assembly name
• src/hg/makeDb/genbank/etc/ignore.idx
  • lines changed 1, context: html, text, full: html, text
    134241d165166cbd79bb983ef4d6c23effb543b1 Sun Sep 30 08:44:57 2018 -0700
    more stuff to ignore.
• src/hg/makeDb/genbank/makefile
  • lines changed 6, context: html, text, full: html, text
    f5fa3a2cb11ba5ec0367758d4c737c6c473ecbb0 Wed Sep 26 10:56:41 2018 -0700
    take out rr related genbank commands that are no longer used.
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
  • lines changed 19, context: html, text, full: html, text
    676da6b57134c0641578e9277776fb40101424c9 Sat Sep 29 14:46:42 2018 -0700
    switch loading gencode from GTFs to GFF3 so as not to need to debug yet another issue with GTF stop codon outside of CDS
• src/hg/makeDb/schema/1
  • lines changed 0, context: html, text, full: html, text
    a62be5f3a3524b2cd349168700c37ed3a8bed011 Thu Sep 27 14:31:34 2018 -0700
    Added my assembly name
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    742e724d9b639d921ffdd27c82c9e99d4543303e Thu Sep 27 14:36:17 2018 -0700
    Deleting weird empty files
• src/hg/makeDb/schema/2
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    a62be5f3a3524b2cd349168700c37ed3a8bed011 Thu Sep 27 14:31:34 2018 -0700
    Added my assembly name
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    742e724d9b639d921ffdd27c82c9e99d4543303e Thu Sep 27 14:36:17 2018 -0700
    Deleting weird empty files
• src/hg/makeDb/schema/all.joiner
  • lines changed 1, context: html, text, full: html, text
    8f26a8fbb9cd9cc2426f7653cbfc71e22e51a8cf Thu Sep 27 11:32:53 2018 -0700
    add thaSier to xenoRefGene rules refs #16028
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    e7b2488189efa44f73eec241d5661ed37e91dd4d Mon Oct 1 10:18:01 2018 -0700
    correct ensGene settings for anoGam3 refs #20743
• src/hg/makeDb/schema/temp
  • lines changed 0, context: html, text, full: html, text
    a62be5f3a3524b2cd349168700c37ed3a8bed011 Thu Sep 27 14:31:34 2018 -0700
    Added my assembly name
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    742e724d9b639d921ffdd27c82c9e99d4543303e Thu Sep 27 14:36:17 2018 -0700
    Deleting weird empty files
• src/hg/makeDb/trackDb/anopheles/anoGam3/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    090193ad75fbfbe34dd2041fa1c1723901b0f5ce Tue Sep 18 15:38:15 2018 -0700
    Hiding the gap track for new assembly, has very few gaps
  • lines changed 39, context: html, text, full: html, text
    b4d5fbacf40644f3e40289f2f56f5c83c3eb3ab8 Tue Sep 25 09:48:00 2018 -0700
    add specific search rules for Ensembl gene tables refs #20743
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    a549389058102515918d7a75f529f269303bf315 Tue Sep 25 11:10:46 2018 -0700
    turning on crispr10K track refs #20743
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    163802da5a84f494214da595ab22848eb33f92fe Wed Sep 26 17:05:38 2018 -0700
    Updating the include statement to correctly point to the trackDb file in the /human directory. no Redmine.
• src/hg/makeDb/trackDb/reptiles/thaSir1/trackDb.ra
  • lines changed 5, context: html, text, full: html, text
    8cb264df800029a6689fc51814bc72a01c9ada0d Wed Sep 26 13:17:24 2018 -0700
    editing track display for thaSir1
• src/hg/makeDb/trackDb/sheep/oviAri4/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    a62be5f3a3524b2cd349168700c37ed3a8bed011 Thu Sep 27 14:31:34 2018 -0700
    Added my assembly name
• src/hg/utils/gtfToGenePred/tests/expected/splitStop.gp
  • lines changed 1, context: html, text, full: html, text
    ee6b3270d5a37e7e28c7af65aead341fa682295f Thu Sep 27 17:09:26 2018 -0700
    Fixed GTF conversion problem where final CDS exon had incorrect frame. occurred when The CDS started in the exon that contains the last codon before the stop codon. The stop code was either spliced or the only codon in the exon. This changed 44 gencode V28 transcripts, many of which were manually validated in the browser.
• src/hg/utils/gtfToGenePred/tests/input/splitStop.gtf
  • lines changed 26, context: html, text, full: html, text
    ee6b3270d5a37e7e28c7af65aead341fa682295f Thu Sep 27 17:09:26 2018 -0700
    Fixed GTF conversion problem where final CDS exon had incorrect frame. occurred when The CDS started in the exon that contains the last codon before the stop codon. The stop code was either spliced or the only codon in the exon. This changed 44 gencode V28 transcripts, many of which were manually validated in the browser.
• src/inc/srcVersion.h
  • lines changed 1, context: html, text, full: html, text
    7b07752c88d957fcd8dd5d282bf6dd194b15be96 Mon Oct 1 10:37:40 2018 -0700
    New version number v372
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    5fbaaba7a05ecde7a492447725f2ebca8e7f2b64 Mon Oct 1 10:33:11 2018 -0700
    v372 final build, refs #22107

• lines changed: 849
• files changed: 55