All File Changes

v391_preview2 to v391_base (2019-11-18 to 2019-12-02) v391

• confs/asia.hg.conf
  • lines changed 12, context: html, text, full: html, text
    dc4a58380d23d3558f00033b6c3acce91a0402d4 Sun Nov 24 01:11:46 2019 -0800
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
  • lines changed 12, context: html, text, full: html, text
    dc4a58380d23d3558f00033b6c3acce91a0402d4 Sun Nov 24 01:11:46 2019 -0800
    Installing updated hg.conf files from UCSC servers
• confs/hgwbeta.hg.conf
  • lines changed 3, context: html, text, full: html, text
    dc4a58380d23d3558f00033b6c3acce91a0402d4 Sun Nov 24 01:11:46 2019 -0800
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 2, context: html, text, full: html, text
    dc4a58380d23d3558f00033b6c3acce91a0402d4 Sun Nov 24 01:11:46 2019 -0800
    Installing updated hg.conf files from UCSC servers
• src/hg/hgGene/hgGeneData/Human/links.ra
  • lines changed 8, context: html, text, full: html, text
    90ab34106679395529b254e024c8b0f350547195 Wed Nov 27 16:54:26 2019 -0800
    add myGene2 link from hgGene on hg38
• src/hg/hgTables/usage.c
  • lines changed 3, context: html, text, full: html, text
    97bbe123546f2ce1bdb4ee430b43098614d45eab Thu Nov 21 14:34:45 2019 -0800
    Adding a FAQ link to hgTables about the BED name column containing exon_info_0_0 refs #24517
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 15, context: html, text, full: html, text
    3d8312d50d53884f52bfff6cefde460541376566 Wed Nov 27 15:24:15 2019 -0800
    get slightly better at recognizing what people mean by specifying bigBed fields that aren't in the AS file. refs #24562
• src/hg/hgc/hgc.c
  • lines changed 26, context: html, text, full: html, text
    f0d09119e54af30308746dd1c5d4f0178f07af72 Thu Nov 21 10:45:56 2019 -0800
    When displaying ncbiRefSeq alignments, use ncbiRefSeqCds not gbCdnaInfo which may have a different version. refs #24554
• src/hg/htdocs/goldenPath/help/hgTablesHelp.html
  • lines changed 2, context: html, text, full: html, text
    0efc3b696e99ede9cd4e1df4a5c2bd12b589d7e0 Thu Nov 21 14:40:14 2019 -0800
    Adding a FAQ link to Table Browser Guide about the BED name column containing exon_info_0_0 refs #24517
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 7, context: html, text, full: html, text
    7840f74333c846da8abef1701b16feb74e8f334c Wed Nov 20 11:09:00 2019 -0800
    Adding links and allowed char set #24490
  • lines changed 1, context: html, text, full: html, text
    bb741d3e5dfe3fcc576bbe2b84080c78d1f2bc1b Wed Nov 20 11:43:03 2019 -0800
    Removed period #24490
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 3, context: html, text, full: html, text
    560b2736eecac74f65a714e84e7375ce8018730a Fri Nov 15 16:44:42 2019 -0800
    Slight change to wording to reflect that useOneFile doesn't require ordered stanzas No Rm
• src/hg/htdocs/goldenPath/help/mirrorManual.html
  • lines changed 4, context: html, text, full: html, text
    bf1863eee800c5bca944aa44e7ab3c2c954c0cd0 Mon Nov 18 10:01:00 2019 -0800
    Removing strange characters that show up on the webpage, no Redmine.
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 10, context: html, text, full: html, text
    d6a9c88aae6b16e73c626e54c5aa6082c27dbe04 Mon Nov 18 14:32:46 2019 -0800
    Expanding the filterValues section due to feedback refs #20227
  • lines changed 13, context: html, text, full: html, text
    96adb43ab302e400c7b5941131cd484de272b44d Tue Nov 19 10:14:46 2019 -0800
    Fixing the filterValues alternative name documentation which was backwards refs #20227
  • lines changed 30, context: html, text, full: html, text
    9a7dacc773d7d9c5b85291d1f3421cdfc5c341fe Fri Nov 22 08:39:26 2019 -0800
    adding my suggested changes to trackDb docs, refs ##20227
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 18, context: html, text, full: html, text
    349b1915dc2dbae9181adb5b0c270254b8e5a36f Mon Nov 25 13:02:01 2019 -0800
    Announcing the LOVD composite track change, refs #24408.
  • lines changed 39, context: html, text, full: html, text
    7ec5f6b170c7eee12739e419d7890daa4a331fcb Wed Nov 27 16:37:42 2019 -0800
    Announcing the EPD track for human and mouse, refs #23881 and #23888
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 3, context: html, text, full: html, text
    87a600aed9584d99696210fea27e0f5beb875b81 Mon Nov 18 16:30:22 2019 -0800
    refining the language
• src/hg/htdocs/indexNews.html
  • lines changed 13, context: html, text, full: html, text
    349b1915dc2dbae9181adb5b0c270254b8e5a36f Mon Nov 25 13:02:01 2019 -0800
    Announcing the LOVD composite track change, refs #24408.
  • lines changed 9, context: html, text, full: html, text
    7ec5f6b170c7eee12739e419d7890daa4a331fcb Wed Nov 27 16:37:42 2019 -0800
    Announcing the EPD track for human and mouse, refs #23881 and #23888
• src/hg/htdocs/training/index.html
  • lines changed 18, context: html, text, full: html, text
    81776c54da198f1b08b6a310637d0ad42a70969d Mon Nov 18 12:10:33 2019 -0800
    dropping completed ghana workshop. moving NIEHS into top four
  • lines changed 19, context: html, text, full: html, text
    399b4f78dab80928687e13cde5519d2cd08dcada Fri Nov 29 13:22:48 2019 -0800
    removed completed rotterdam workshop. moved Duke into next-four group
  • lines changed 7, context: html, text, full: html, text
    4585d60e349aeab07c82ae6d4346c6905c55674c Fri Nov 29 14:29:31 2019 -0800
    added barcolona course. split long-term workshops into two rows
• src/hg/inc/bigDbSnp.h
  • lines changed 2, context: html, text, full: html, text
    726a4c9c82592c662ae6b8c715e67b783c95beb3 Mon Nov 18 13:45:42 2019 -0800
    Instead of dropping rs IDs that have incomplete frequency data, add two new ucscNotes: freqIncomplete and freqNotMapped. refs #23283
• src/hg/inc/hui.h
  • lines changed 3, context: html, text, full: html, text
    3d8312d50d53884f52bfff6cefde460541376566 Wed Nov 27 15:24:15 2019 -0800
    get slightly better at recognizing what people mean by specifying bigBed fields that aren't in the AS file. refs #24562
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    cce8d6c511e3b139fc8437ff53c438ea57350108 Mon Dec 2 10:12:20 2019 -0800
    New version number v391
• src/hg/lib/bigDbSnp.c
  • lines changed 5, context: html, text, full: html, text
    726a4c9c82592c662ae6b8c715e67b783c95beb3 Mon Nov 18 13:45:42 2019 -0800
    Instead of dropping rs IDs that have incomplete frequency data, add two new ucscNotes: freqIncomplete and freqNotMapped. refs #23283
• src/hg/lib/hui.c
  • lines changed 1, context: html, text, full: html, text
    1bad8b54aabb3a9e40df9eb92fdda92d1a6af379 Wed Nov 27 10:24:53 2019 -0800
    add showCfg trackDb variable to automatically open hgTrackUi view configurations
  • lines changed 3, context: html, text, full: html, text
    ffbd8443f24124c3023126cccebd1d09efae07de Wed Nov 27 10:36:22 2019 -0800
    a little clean-up for safety's sake
  • lines changed 18, context: html, text, full: html, text
    3d8312d50d53884f52bfff6cefde460541376566 Wed Nov 27 15:24:15 2019 -0800
    get slightly better at recognizing what people mean by specifying bigBed fields that aren't in the AS file. refs #24562
• src/hg/makeDb/doc/bigDbSnp.txt
  • lines changed 64, context: html, text, full: html, text
    726a4c9c82592c662ae6b8c715e67b783c95beb3 Mon Nov 18 13:45:42 2019 -0800
    Instead of dropping rs IDs that have incomplete frequency data, add two new ucscNotes: freqIncomplete and freqNotMapped. refs #23283
  • lines changed 104, context: html, text, full: html, text
    6974f14d41a28ed1198110de47946370cfc2bb73 Fri Nov 22 10:29:44 2019 -0800
    dbSnp153: When different freq alleles can be expanded by different amounts, pad out the smaller range & alleles for consistency. refs #23283 One variant (rs782394990) was dropped because of that quirk, but now no variants are dropped. :) A few ucscNotes increased by 1 or 2. Some of the counts of various ucscNotes were a little out of date due to recent work on adding freq notes instead of dropping; up to date now. I was all proud of this but it's a dead end. One b153 variant, rs782394990, errored out because its freq alleles couldn't be expanded by the same amount. The insertions of pure A's could be expanded to a larger range than an ins that included a T in addition to A's. So I siezed upon the problem of independently trimmed and expanded SPDIs resulting in inconsistent dels, and set about trimming by list instead of trimming each SPDI separately. I would restrict the expansion to the minimum range by which any allele could be shifted. That would fix the problem of independent del's for rs782394990. However, there was a problem. A variant that includes both an ins and a del that could be expanded to the same range, e.g. rs201454468 with alleles ref=T, alt="", alt=TT, cannot be trimmed as a list because it already has "". T/"" is already minimal. However, T/TT is not already minimal and needs to be minimized before expansion. So no expansion was performed, and we ended up with inconsistent alleles between different sources because one was expanded (it had only the del) and the other wasn't. No good. I think that's why, although I was trimming listwise already, I did another trim just before trying to expand. Is there even a point in trimming listwise? So... back to individual trimming of each SPDI. And individual expansion. But what do we do about the 1 in 680M case of rs782394990? I think we should detect inconsistent dels -- and then pad out all dels and inses to the maximal range. So for the allele that could be shifted 2 bases less than the others because it included a T, just pad its del and ins with genomic bases. OK, now it works. Squash branch into master...
• src/hg/makeDb/doc/gorGor4/initialBuild.txt
  • lines changed 26, context: html, text, full: html, text
    be368356a22764aec739b020b9597b26f7e4dc88 Mon Nov 25 10:22:24 2019 -0800
    liftOvers done for gorGor4 gorGor5 gorGor6 refs #24524
• src/hg/makeDb/doc/gorGor5/initialBuild.txt
  • lines changed 17, context: html, text, full: html, text
    be368356a22764aec739b020b9597b26f7e4dc88 Mon Nov 25 10:22:24 2019 -0800
    liftOvers done for gorGor4 gorGor5 gorGor6 refs #24524
• src/hg/makeDb/doc/gorGor6/initialBuild.txt
  • lines changed 1027, context: html, text, full: html, text
    167b2c840dd247f7254cd9c900587133ba208ab0 Tue Nov 19 13:57:33 2019 -0800
    beginning gorGor6 build refs #24524
  • lines changed 234, context: html, text, full: html, text
    be368356a22764aec739b020b9597b26f7e4dc88 Mon Nov 25 10:22:24 2019 -0800
    liftOvers done for gorGor4 gorGor5 gorGor6 refs #24524
• src/hg/makeDb/doc/hg19.txt
  • lines changed 62, context: html, text, full: html, text
    f8575fe7f3223c6279b66e2abc6b3472dad916ef Thu Nov 21 15:48:59 2019 -0800
    update ncbiRefSeq tables refs #20215
  • lines changed 7, context: html, text, full: html, text
    cade13fb56eb21ed057867859814ff02ba55457b Mon Dec 2 08:51:11 2019 -0800
    adding medline info to AVADA track, refs #24156
• src/hg/makeDb/doc/hg38/lastzRuns.txt
  • lines changed 152, context: html, text, full: html, text
    3bff517ce5a5210e0c7eb6f700b82eb0236f97f4 Tue Nov 26 12:06:36 2019 -0800
    chain/net hg38 to gorGor6 done refs #24524
  • lines changed 85, context: html, text, full: html, text
    3d5b0dec29544546bf7e8be1d923433bc5d28428 Thu Nov 28 11:04:34 2019 -0800
    done with regenCho1 chainNet refs #24524
• src/hg/makeDb/doc/mm10.txt
  • lines changed 67, context: html, text, full: html, text
    9f28b1b4d9cd670829c4aac01d702d3d78563a79 Tue Nov 26 12:02:53 2019 -0800
    chain/net mm10 to gorGor6 done refs #24524
  • lines changed 67, context: html, text, full: html, text
    3d5b0dec29544546bf7e8be1d923433bc5d28428 Thu Nov 28 11:04:34 2019 -0800
    done with regenCho1 chainNet refs #24524
• src/hg/makeDb/doc/regenCho1/initialBuild.txt
  • lines changed 1070, context: html, text, full: html, text
    7eb8b7de9987604dde002fcf9c7cb4f4b38e3d3e Mon Nov 25 15:43:05 2019 -0800
    begin build of regenCho1 refs #24524
  • lines changed 197, context: html, text, full: html, text
    437c39fa3d4b82d90f8cddf3aae8ee1630881fa0 Tue Nov 26 13:47:13 2019 -0800
    running up liftOvers refs #24568
  • lines changed 81, context: html, text, full: html, text
    8ee6e38f07d899be11e5bd15b166b251cb5420b6 Thu Nov 28 10:32:53 2019 -0800
    waiting for genbank run to complete refs #24568
• src/hg/makeDb/doc/regenRn1/initialBuild.txt
  • lines changed 242, context: html, text, full: html, text
    e0811dac684e59711b3aa4d635bc378d57e0c473 Thu Nov 28 10:31:35 2019 -0800
    build finished handed off to Regeneron refs #21579
• src/hg/makeDb/doc/regenRn1/multiz7way.txt
  • lines changed 1557, context: html, text, full: html, text
    e0811dac684e59711b3aa4d635bc378d57e0c473 Thu Nov 28 10:31:35 2019 -0800
    build finished handed off to Regeneron refs #21579
• src/hg/makeDb/doc/ucscGenes/hg38.ucscGenes20.sh
  • lines changed 10, context: html, text, full: html, text
    90ab34106679395529b254e024c8b0f350547195 Wed Nov 27 16:54:26 2019 -0800
    add myGene2 link from hgGene on hg38
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    b8db48b5bb371c5212505b58abdeca12f5203fe4 Wed Nov 20 11:43:53 2019 -0800
    Added gorGor6 - gorilla refs #24524
  • lines changed 1, context: html, text, full: html, text
    f8fa40f87c68cd0f464b3584823da107602bffc5 Tue Nov 26 13:11:07 2019 -0800
    Added regenCho1 - Regeneron CHO refs #24568
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 16, context: html, text, full: html, text
    7f984116bae01a32ffd01c22cbe82726bac0667c Wed Nov 20 11:19:05 2019 -0800
    Added gorGor6 gorilla; refs #24524
  • lines changed 18, context: html, text, full: html, text
    cc1b0605a9857feae65b128e658a74642e876a41 Tue Nov 26 13:04:18 2019 -0800
    Added regenCho1 - Regeneron CHO refs #24568
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 2, context: html, text, full: html, text
    b8db48b5bb371c5212505b58abdeca12f5203fe4 Wed Nov 20 11:43:53 2019 -0800
    Added gorGor6 - gorilla refs #24524
  • lines changed 1, context: html, text, full: html, text
    f8fa40f87c68cd0f464b3584823da107602bffc5 Tue Nov 26 13:11:07 2019 -0800
    Added regenCho1 - Regeneron CHO refs #24568
• src/hg/makeDb/genbank/src/lib/gbGenome.c
  • lines changed 1, context: html, text, full: html, text
    7f984116bae01a32ffd01c22cbe82726bac0667c Wed Nov 20 11:19:05 2019 -0800
    Added gorGor6 gorilla; refs #24524
• src/hg/makeDb/schema/all.joiner
  • lines changed 9, context: html, text, full: html, text
    0b52e9bb80bffd47a0fe49aba39aa233e5a5999c Wed Nov 20 14:34:13 2019 -0800
    adding rules for gorGor6 refs #24524
  • lines changed 12, context: html, text, full: html, text
    96688b9c02671c5a1119ee2a75ac0130edf711e9 Tue Nov 26 13:27:04 2019 -0800
    adding rules for regenCho1 refs #24568
• src/hg/makeDb/trackDb/criGri/regenCho1/description.html
  • lines changed 64, context: html, text, full: html, text
    e9629c393df4e1ca3874bf962c9aafa55df370b7 Mon Nov 25 15:16:50 2019 -0800
    initial set of files from makeGenomeDb refs #24524
  • lines changed 3, context: html, text, full: html, text
    62db468c99403799c47bcf72af157e625e4c7db0 Tue Nov 26 13:34:00 2019 -0800
    adding Regeneron AGP and gap tracks from their AGP and correct cell line photograph refs #24568
• src/hg/makeDb/trackDb/criGri/regenCho1/gap.html
  • lines changed 31, context: html, text, full: html, text
    e9629c393df4e1ca3874bf962c9aafa55df370b7 Mon Nov 25 15:16:50 2019 -0800
    initial set of files from makeGenomeDb refs #24524
• src/hg/makeDb/trackDb/criGri/regenCho1/gold.html
  • lines changed 33, context: html, text, full: html, text
    e9629c393df4e1ca3874bf962c9aafa55df370b7 Mon Nov 25 15:16:50 2019 -0800
    initial set of files from makeGenomeDb refs #24524
• src/hg/makeDb/trackDb/criGri/regenCho1/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    e9629c393df4e1ca3874bf962c9aafa55df370b7 Mon Nov 25 15:16:50 2019 -0800
    initial set of files from makeGenomeDb refs #24524
  • lines changed 25, context: html, text, full: html, text
    62db468c99403799c47bcf72af157e625e4c7db0 Tue Nov 26 13:34:00 2019 -0800
    adding Regeneron AGP and gap tracks from their AGP and correct cell line photograph refs #24568
• src/hg/makeDb/trackDb/epdNewPromoter.html
  • lines changed 12, context: html, text, full: html, text
    261e5208364f3825a86f8a80256e841a7b8f7507 Fri Nov 22 15:46:11 2019 -0800
    Editing the track description page to have line lengths less than 100 characters and indenting the HTML list, refs #23888
  • lines changed 13, context: html, text, full: html, text
    00f7911632fbc57aef0298adb49a64e7e7f238ba Mon Nov 25 15:08:58 2019 -0800
    Making line lengths less than 100 characters, refs #23888
• src/hg/makeDb/trackDb/gorilla/gorGor6/description.html
  • lines changed 64, context: html, text, full: html, text
    9b1768c25317ad12dce0829a6f2f36bf1f179ba3 Tue Nov 19 11:18:02 2019 -0800
    initial gorGor6 files from makeGenomeDb.pl refs #24524
• src/hg/makeDb/trackDb/gorilla/gorGor6/gap.html
  • lines changed 31, context: html, text, full: html, text
    9b1768c25317ad12dce0829a6f2f36bf1f179ba3 Tue Nov 19 11:18:02 2019 -0800
    initial gorGor6 files from makeGenomeDb.pl refs #24524
• src/hg/makeDb/trackDb/gorilla/gorGor6/gold.html
  • lines changed 34, context: html, text, full: html, text
    9b1768c25317ad12dce0829a6f2f36bf1f179ba3 Tue Nov 19 11:18:02 2019 -0800
    initial gorGor6 files from makeGenomeDb.pl refs #24524
• src/hg/makeDb/trackDb/gorilla/gorGor6/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    9b1768c25317ad12dce0829a6f2f36bf1f179ba3 Tue Nov 19 11:18:02 2019 -0800
    initial gorGor6 files from makeGenomeDb.pl refs #24524
  • lines changed 7, context: html, text, full: html, text
    eb2bf6fbb61f74a73398179bc40429e807c5be80 Wed Nov 20 14:31:09 2019 -0800
    added search rule for gold/assembly track and ncbiRefSeq track refs #24524
• src/hg/makeDb/trackDb/human/chainNetPrimate.ra
  • lines changed 19, context: html, text, full: html, text
    7ad022adbcd9514fad51c749ec15feb362287b26 Mon Nov 25 10:15:20 2019 -0800
    adding gorGor6 chain/net definitions refs #24524
• src/hg/makeDb/trackDb/human/dbSnp153Composite.html
  • lines changed 19, context: html, text, full: html, text
    726a4c9c82592c662ae6b8c715e67b783c95beb3 Mon Nov 18 13:45:42 2019 -0800
    Instead of dropping rs IDs that have incomplete frequency data, add two new ucscNotes: freqIncomplete and freqNotMapped. refs #23283
  • lines changed 39, context: html, text, full: html, text
    6974f14d41a28ed1198110de47946370cfc2bb73 Fri Nov 22 10:29:44 2019 -0800
    dbSnp153: When different freq alleles can be expanded by different amounts, pad out the smaller range & alleles for consistency. refs #23283 One variant (rs782394990) was dropped because of that quirk, but now no variants are dropped. :) A few ucscNotes increased by 1 or 2. Some of the counts of various ucscNotes were a little out of date due to recent work on adding freq notes instead of dropping; up to date now. I was all proud of this but it's a dead end. One b153 variant, rs782394990, errored out because its freq alleles couldn't be expanded by the same amount. The insertions of pure A's could be expanded to a larger range than an ins that included a T in addition to A's. So I siezed upon the problem of independently trimmed and expanded SPDIs resulting in inconsistent dels, and set about trimming by list instead of trimming each SPDI separately. I would restrict the expansion to the minimum range by which any allele could be shifted. That would fix the problem of independent del's for rs782394990. However, there was a problem. A variant that includes both an ins and a del that could be expanded to the same range, e.g. rs201454468 with alleles ref=T, alt="", alt=TT, cannot be trimmed as a list because it already has "". T/"" is already minimal. However, T/TT is not already minimal and needs to be minimized before expansion. So no expansion was performed, and we ended up with inconsistent alleles between different sources because one was expanded (it had only the del) and the other wasn't. No good. I think that's why, although I was trimming listwise already, I did another trim just before trying to expand. Is there even a point in trimming listwise? So... back to individual trimming of each SPDI. And individual expansion. But what do we do about the 1 in 680M case of rs782394990? I think we should detect inconsistent dels -- and then pad out all dels and inses to the maximal range. So for the allele that could be shifted 2 bases less than the others because it included a T, just pad its del and ins with genomic bases. OK, now it works. Squash branch into master...
• src/hg/makeDb/trackDb/human/hg16/encodeMlaganAlign.html
  • lines changed 1, context: html, text, full: html, text
    8f3b6d3c57e3a1b970ee63c759546a144b17eb98 Tue Nov 19 13:27:42 2019 -0800
    Updating redirected links for hg16, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg16/encodeRegulomeAmplicon.html
  • lines changed 1, context: html, text, full: html, text
    8f3b6d3c57e3a1b970ee63c759546a144b17eb98 Tue Nov 19 13:27:42 2019 -0800
    Updating redirected links for hg16, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg16/encodeRegulomeBase.html
  • lines changed 1, context: html, text, full: html, text
    8f3b6d3c57e3a1b970ee63c759546a144b17eb98 Tue Nov 19 13:27:42 2019 -0800
    Updating redirected links for hg16, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg16/encodeRegulomeProb.html
  • lines changed 1, context: html, text, full: html, text
    8f3b6d3c57e3a1b970ee63c759546a144b17eb98 Tue Nov 19 13:27:42 2019 -0800
    Updating redirected links for hg16, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg16/encodeRegulomeQuality.html
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    8f3b6d3c57e3a1b970ee63c759546a144b17eb98 Tue Nov 19 13:27:42 2019 -0800
    Updating redirected links for hg16, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg16/encodeTbaAlign.html
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    8f3b6d3c57e3a1b970ee63c759546a144b17eb98 Tue Nov 19 13:27:42 2019 -0800
    Updating redirected links for hg16, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg16/hapmapLd.html
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    8f3b6d3c57e3a1b970ee63c759546a144b17eb98 Tue Nov 19 13:27:42 2019 -0800
    Updating redirected links for hg16, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg16/mzPt1Mm3Rn3Gg2_pHMM.html
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    8f3b6d3c57e3a1b970ee63c759546a144b17eb98 Tue Nov 19 13:27:42 2019 -0800
    Updating redirected links for hg16, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/hg19/rao2014Hic.html
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    ee66025f6559f569ed7a38242fcf03c21d162c6f Tue Nov 26 10:33:08 2019 -0800
    Adding cell description to Hi-C description pages refs #24527
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    a299bfda31f1d93b04b270bd03ae19a8680bb1a8 Tue Nov 26 15:08:58 2019 -0800
    Changing citation and correcting typo refs #25427
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
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    2eeb51e4a1b9b7cf48824a9bd504eb1f9a24e092 Fri Nov 22 08:40:26 2019 -0800
    adding special genomic regions / manual comments to tdb, refs #24245
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    b2bf06d1938cc86f2bee8c36984c47ac699a911c Wed Nov 27 16:49:00 2019 -0800
    Adding the pennantIcon for the newly released EPD tracks, refs #23888 and #23881
• src/hg/makeDb/trackDb/human/hg38/hicAndMicroC.html
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    ee66025f6559f569ed7a38242fcf03c21d162c6f Tue Nov 26 10:33:08 2019 -0800
    Adding cell description to Hi-C description pages refs #24527
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    a299bfda31f1d93b04b270bd03ae19a8680bb1a8 Tue Nov 26 15:08:58 2019 -0800
    Changing citation and correcting typo refs #25427
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    b2bf06d1938cc86f2bee8c36984c47ac699a911c Wed Nov 27 16:49:00 2019 -0800
    Adding the pennantIcon for the newly released EPD tracks, refs #23888 and #23881
• src/hg/makeDb/trackDb/human/lovdComp.html
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    10530f734a3c301a58c7ea30ffe5d74559215561 Tue Nov 19 16:50:02 2019 -0800
    Making all the line lengths less than 100 characters. Also adding hyperlinks for the URLs referenced in the text. In the trackDb.ra file, the correct HTML file is specified using the 'html' trackDb option. refs #24408
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    dfbcbc98dac158890c1d7e9cce6338cd6d446fa5 Thu Nov 21 13:10:10 2019 -0800
    Creating lists of the URLs and variant types to make it easier to read, refs #24408
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    55714b9d6370aa54873fe0c58e5618c984a357dc Fri Nov 22 11:32:57 2019 -0800
    Removing databases that do not exist anymore, refs #24408
• src/hg/makeDb/trackDb/human/perlegen.html
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    8f3b6d3c57e3a1b970ee63c759546a144b17eb98 Tue Nov 19 13:27:42 2019 -0800
    Updating redirected links for hg16, uiLinks cronjob.
• src/hg/makeDb/trackDb/human/trackDb.ra
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    726a4c9c82592c662ae6b8c715e67b783c95beb3 Mon Nov 18 13:45:42 2019 -0800
    Instead of dropping rs IDs that have incomplete frequency data, add two new ucscNotes: freqIncomplete and freqNotMapped. refs #23283
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    c0401cde5d3035571adf6898d572a60f756d0af2 Mon Nov 18 15:36:10 2019 -0800
    dbSnp153: Use new FilterLabel setting to replace the long definition of numeric maxFuncImpact column with a label that is more congruent with dropdown choices. refs #23283
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    10530f734a3c301a58c7ea30ffe5d74559215561 Tue Nov 19 16:50:02 2019 -0800
    Making all the line lengths less than 100 characters. Also adding hyperlinks for the URLs referenced in the text. In the trackDb.ra file, the correct HTML file is specified using the 'html' trackDb option. refs #24408
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    edc8f59828de1e36a4583e1bd6c35dbd1ec692e6 Fri Nov 22 15:16:02 2019 -0800
    Staging the LOVD track on the hgwbeta. Turning off Table Browser usage like on the RR, refs #24408
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    631b128d1dec1926bddca573b3e5b6c6ce9cb41f Fri Nov 22 15:57:57 2019 -0800
    Releasing the LOVD composite changes to the RR, refs #24408
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    4e0719d608c56995a991d31ce5c03ac9db7010ca Wed Nov 27 10:06:58 2019 -0800
    Make dbSnp153BadCoords gray. refs #23283
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    1bad8b54aabb3a9e40df9eb92fdda92d1a6af379 Wed Nov 27 10:24:53 2019 -0800
    add showCfg trackDb variable to automatically open hgTrackUi view configurations
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    cade13fb56eb21ed057867859814ff02ba55457b Mon Dec 2 08:51:11 2019 -0800
    adding medline info to AVADA track, refs #24156
• src/hg/makeDb/trackDb/makefile
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    9b1768c25317ad12dce0829a6f2f36bf1f179ba3 Tue Nov 19 11:18:02 2019 -0800
    initial gorGor6 files from makeGenomeDb.pl refs #24524
• src/hg/makeDb/trackDb/mouse/mm10/encode3RenEnhancerGene.html
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    3bd1cb49a4ecf0b49c662453d5c301b9b75a9ccd Mon Nov 18 16:11:07 2019 -0800
    Making the line length less than 100 characters, refs #23881
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    6982375a8f7edf6b89491e57eb55460bd80cb0d3 Mon Nov 25 15:12:05 2019 -0800
    Making line lengths less than 100 characters, refs #23881
• src/hg/makeDb/trackDb/mouse/mm10/encode3RenEnhancerGene.ra
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    51be79bf56a48c61d34f8d14ee0fda86651d1667 Tue Nov 26 14:49:41 2019 -0800
    Minor change to labels, thanks Max. refs #23881
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    b2bf06d1938cc86f2bee8c36984c47ac699a911c Wed Nov 27 16:49:00 2019 -0800
    Adding the pennantIcon for the newly released EPD tracks, refs #23888 and #23881
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.euarchontoglireChainNet.ra
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    7ad022adbcd9514fad51c749ec15feb362287b26 Mon Nov 25 10:15:20 2019 -0800
    adding gorGor6 chain/net definitions refs #24524
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
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    b2bf06d1938cc86f2bee8c36984c47ac699a911c Wed Nov 27 16:49:00 2019 -0800
    Adding the pennantIcon for the newly released EPD tracks, refs #23888 and #23881
• src/hg/makeDb/trackDb/refSeqComposite.ra
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    966c6acca66b653cfbccc2575db57f250c37dd15 Thu Nov 21 12:29:02 2019 -0800
    Adding baseColorDefault genomicCodons to NCBI gene tracks refs #24553
• src/hg/makeDb/trackDb/tagTypes.tab
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    c0401cde5d3035571adf6898d572a60f756d0af2 Mon Nov 18 15:36:10 2019 -0800
    dbSnp153: Use new FilterLabel setting to replace the long definition of numeric maxFuncImpact column with a label that is more congruent with dropdown choices. refs #23283
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    1bad8b54aabb3a9e40df9eb92fdda92d1a6af379 Wed Nov 27 10:24:53 2019 -0800
    add showCfg trackDb variable to automatically open hgTrackUi view configurations
• src/hg/makeDb/trackDb/trackDb.chainNet.mammal.ra
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    60ba163cfec41900cbd7db7c31981fa7bac6e1e5 Wed Nov 27 12:06:52 2019 -0800
    adding regenCho1 chainNet refs #24568
• src/hg/makeDb/trackDb/trackDb.chainNet.primates.ra
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    7ad022adbcd9514fad51c749ec15feb362287b26 Mon Nov 25 10:15:20 2019 -0800
    adding gorGor6 chain/net definitions refs #24524
• src/hg/snp/dbSnpJsonToTab/dbSnpJsonToTab.c
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    726a4c9c82592c662ae6b8c715e67b783c95beb3 Mon Nov 18 13:45:42 2019 -0800
    Instead of dropping rs IDs that have incomplete frequency data, add two new ucscNotes: freqIncomplete and freqNotMapped. refs #23283
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    6974f14d41a28ed1198110de47946370cfc2bb73 Fri Nov 22 10:29:44 2019 -0800
    dbSnp153: When different freq alleles can be expanded by different amounts, pad out the smaller range & alleles for consistency. refs #23283 One variant (rs782394990) was dropped because of that quirk, but now no variants are dropped. :) A few ucscNotes increased by 1 or 2. Some of the counts of various ucscNotes were a little out of date due to recent work on adding freq notes instead of dropping; up to date now. I was all proud of this but it's a dead end. One b153 variant, rs782394990, errored out because its freq alleles couldn't be expanded by the same amount. The insertions of pure A's could be expanded to a larger range than an ins that included a T in addition to A's. So I siezed upon the problem of independently trimmed and expanded SPDIs resulting in inconsistent dels, and set about trimming by list instead of trimming each SPDI separately. I would restrict the expansion to the minimum range by which any allele could be shifted. That would fix the problem of independent del's for rs782394990. However, there was a problem. A variant that includes both an ins and a del that could be expanded to the same range, e.g. rs201454468 with alleles ref=T, alt="", alt=TT, cannot be trimmed as a list because it already has "". T/"" is already minimal. However, T/TT is not already minimal and needs to be minimized before expansion. So no expansion was performed, and we ended up with inconsistent alleles between different sources because one was expanded (it had only the del) and the other wasn't. No good. I think that's why, although I was trimming listwise already, I did another trim just before trying to expand. Is there even a point in trimming listwise? So... back to individual trimming of each SPDI. And individual expansion. But what do we do about the 1 in 680M case of rs782394990? I think we should detect inconsistent dels -- and then pad out all dels and inses to the maximal range. So for the allele that could be shifted 2 bases less than the others because it included a T, just pad its del and ins with genomic bases. OK, now it works. Squash branch into master...
• src/hg/utils/archiveTracks.sh
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    5538246d3229013664d13136606cc7a3c2fa779a Wed Nov 20 08:26:47 2019 -0800
    Adding a script that assists with some common track archiving operations, refs #21825
• src/hg/utils/hubCheck/tests/expected/manyErrors.output.txt
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    6a2716efadd8b37d455f38339a897d187fc811fe Tue Nov 19 13:21:16 2019 -0800
    Adding a test hub with many common trackDb configuration errors to source tree, after discussion with Max and Braney
• src/hg/utils/hubCheck/tests/input/araTha1.trackDb.txt
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    6a2716efadd8b37d455f38339a897d187fc811fe Tue Nov 19 13:21:16 2019 -0800
    Adding a test hub with many common trackDb configuration errors to source tree, after discussion with Max and Braney
• src/hg/utils/hubCheck/tests/input/manyErrorsGenomes.txt
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    6a2716efadd8b37d455f38339a897d187fc811fe Tue Nov 19 13:21:16 2019 -0800
    Adding a test hub with many common trackDb configuration errors to source tree, after discussion with Max and Braney
• src/hg/utils/hubCheck/tests/input/manyErrorsHub.txt
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    6a2716efadd8b37d455f38339a897d187fc811fe Tue Nov 19 13:21:16 2019 -0800
    Adding a test hub with many common trackDb configuration errors to source tree, after discussion with Max and Braney
• src/hg/utils/hubCheck/tests/input/ricCom1.trackDb.txt
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    6a2716efadd8b37d455f38339a897d187fc811fe Tue Nov 19 13:21:16 2019 -0800
    Adding a test hub with many common trackDb configuration errors to source tree, after discussion with Max and Braney
• src/hg/utils/hubCheck/tests/makefile
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    6a2716efadd8b37d455f38339a897d187fc811fe Tue Nov 19 13:21:16 2019 -0800
    Adding a test hub with many common trackDb configuration errors to source tree, after discussion with Max and Braney
• src/inc/srcVersion.h
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    cce8d6c511e3b139fc8437ff53c438ea57350108 Mon Dec 2 10:12:20 2019 -0800
    New version number v391
• src/product/installer/browserSetup.sh
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    4135384610a351357fc0c99af2e1dddd77139bde Wed Nov 27 10:42:55 2019 -0800
    Adding the knownGeneToTag tables for the minimal tables downloaded for a database, refs #24540
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    a7afb0ad8dd1393590625f077324ba0f3e04cb79 Wed Nov 27 12:41:48 2019 -0800
    Fixing a typo. The correct spelling of missing table is 'knownToTag' not 'knownGeneToTag', refs #24573
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    02424e8a450eb2268a4b402b50862bac68bacb07 Wed Nov 27 14:48:32 2019 -0800
    Adding another missing table that a was discovered during the testing of the build patch ticket, refs #24573
• src/utils/bedAppendPaperInfo
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    cade13fb56eb21ed057867859814ff02ba55457b Mon Dec 2 08:51:11 2019 -0800
    adding medline info to AVADA track, refs #24156
• src/utils/chromToUcsc/tests/makefile
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    a5d6fcc334aadcbf49830278704ee6729bc5fd10 Tue Nov 26 06:59:15 2019 -0800
    changes after code review, refs #24511
• src/utils/makefile
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    cade13fb56eb21ed057867859814ff02ba55457b Mon Dec 2 08:51:11 2019 -0800
    adding medline info to AVADA track, refs #24156
• src/utils/qa/weeklybld/buildEnv.csh
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    63548c51addb5be86098c14a754d47cfb9422d6b Mon Dec 2 10:05:10 2019 -0800
    v391 final build, refs #24481

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