All File Changes

v418_preview2 to v418_base (2021-07-19 to 2021-07-26) v418

• confs/asia.hg.conf
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    5f9198826b275122e0b7e5a3cf52765ce569f6b2 Sun Jul 25 01:12:01 2021 -0700
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
  • lines changed 4, context: html, text, full: html, text
    5f9198826b275122e0b7e5a3cf52765ce569f6b2 Sun Jul 25 01:12:01 2021 -0700
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
  • lines changed 4, context: html, text, full: html, text
    5f9198826b275122e0b7e5a3cf52765ce569f6b2 Sun Jul 25 01:12:01 2021 -0700
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 4, context: html, text, full: html, text
    5f9198826b275122e0b7e5a3cf52765ce569f6b2 Sun Jul 25 01:12:01 2021 -0700
    Installing updated hg.conf files from UCSC servers
• src/browserbox/root/updateBrowser.sh
  • lines changed 5, context: html, text, full: html, text
    b6cbd59bc90b14b3a643ba42783040e769d238bb Wed Jul 21 10:44:57 2021 -0700
    Add gtexGenev8 to list of tables always downloaded by hgMirror and gbib, since it is a default track on hg38, refs #27854
• src/hg/cirm/cdw/cdwMakeEnrichments/cdwMakeEnrichments.c
  • lines changed 2, context: html, text, full: html, text
    9425049c9533a3349399b237409cec3152d17054 Wed Jul 21 19:39:26 2021 -0700
    Adding pdf to ignore list in cirm cdwMakeEnrichments.
• src/hg/hgMirror/hgMirror
  • lines changed 1, context: html, text, full: html, text
    b6cbd59bc90b14b3a643ba42783040e769d238bb Wed Jul 21 10:44:57 2021 -0700
    Add gtexGenev8 to list of tables always downloaded by hgMirror and gbib, since it is a default track on hg38, refs #27854
• src/hg/hgPhyloPlace/phyloPlace.c
  • lines changed 5, context: html, text, full: html, text
    1df4153e6bb5046352a48f924a8881bc4f6965d0 Tue Jul 20 10:37:04 2021 -0700
    Typo fix
• src/hg/hgTables/identifiers.c
  • lines changed 3, context: html, text, full: html, text
    a7bc95c406cb78692debf5b702d7954578b6728a Mon Jul 19 12:26:42 2021 -0700
    allow alias tables to be used with knownGene even though it's a bigBed
• src/hg/hgTracks/hgTracks.c
  • lines changed 21, context: html, text, full: html, text
    d9b708e09efd7a685da75ba1ffbb28a6174fb4d4 Fri Jul 23 15:42:06 2021 -0700
    fix up hgFind search so second pass generates a search page even if there are 0 or 1 results from the non-short circuit search
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 5, context: html, text, full: html, text
    5eb72f8f6fae1f8c4d2bdcd49b4652a5d5a0ac47 Mon Jul 19 16:40:26 2021 -0700
    Changing wording and adding title to dbSNP collapse #27518
  • lines changed 29, context: html, text, full: html, text
    72aab260adeca9c17571ae509c84bad9bbe7e9ce Tue Jul 20 12:09:35 2021 -0700
    Announcing GENCODE refs #27785
• src/hg/htdocs/goldenPath/pubs.html
  • lines changed 9, context: html, text, full: html, text
    dbff481964acf0347d7b6396a88cc6f89f3307e5 Thu Jul 22 14:15:07 2021 -0700
    Adding Matt's paper
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    72aab260adeca9c17571ae509c84bad9bbe7e9ce Tue Jul 20 12:09:35 2021 -0700
    Announcing GENCODE refs #27785
• src/hg/htdocs/staff.html
  • lines changed 1, context: html, text, full: html, text
    6d292447c25d0c9ed178279dd4f935ccc85438ce Mon Jul 19 14:57:57 2021 -0700
    Aligning Job Description
• src/hg/htdocs/training/index.html
  • lines changed 11, context: html, text, full: html, text
    c23e7eda945b9cae907282f4ad3be0cbcc6b449d Tue Jul 20 11:47:51 2021 -0700
    adding a few future appearances
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    7687d17e509506ec79dbca9f188f67bb4ff986db Mon Jul 26 10:16:50 2021 -0700
    New version number v418
• src/hg/js/hgTracks.js
  • lines changed 3, context: html, text, full: html, text
    09a54c525e1702d50b28a5635bdf736bf47cdf00 Sun Jul 25 23:05:15 2021 -0700
    fixing zoom keys again, refs #27892
• src/hg/lib/cartRewrite.c
  • lines changed 2, context: html, text, full: html, text
    7d14dd6a213e58f525cba35f579cd4ab941f6081 Mon Jul 19 14:23:50 2021 -0700
    add snp151 and and snp151Common to rewrite rules
• src/hg/lib/hgFind.c
  • lines changed 1, context: html, text, full: html, text
    d9b708e09efd7a685da75ba1ffbb28a6174fb4d4 Fri Jul 23 15:42:06 2021 -0700
    fix up hgFind search so second pass generates a search page even if there are 0 or 1 results from the non-short circuit search
• src/hg/lib/jksql.c
  • lines changed 1, context: html, text, full: html, text
    9061d3e02c215bb77e57e42e5cd22f8fd86da047 Tue Jul 20 14:02:11 2021 -0700
    New debugging fprintf from b79f8a6f8 was breaking various 'make test' diffs; show the message only when JKSQL_TRACE is set.
• src/hg/makeDb/doc/wuhCor1/primers.txt
  • lines changed 13, context: html, text, full: html, text
    1d90acb00b3120e8d1347007620e6eb35a859c84 Thu Jul 22 17:26:33 2021 -0700
    Add ARTIC Primers V4 track and add V3 label to existing track, since both schemes will probably be in use for some time.
• src/hg/makeDb/genbank/src/lib/gbFtp.pm
  • lines changed 1, context: html, text, full: html, text
    98ceaaf6eb5502a19753610999bae8f0c3b20c3d Mon Jul 19 13:10:43 2021 -0700
    Fix age old typo in genbank ftp download error message
• src/hg/makeDb/trackDb/human/hg19/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    68588edf2f5306b107676aaeda2ac9d81eb28103 Tue Jul 20 14:27:55 2021 -0700
    adding pennantIcon for superTrack refs #27785
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV37lift37.ra
  • lines changed 1, context: html, text, full: html, text
    295d75a68807483d5fbb1875c41a9cc915af8c93 Tue Jul 20 12:10:39 2021 -0700
    Turning off old Gencode versions and adding pennantIcons refs #27785
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV38lift37.ra
  • lines changed 1, context: html, text, full: html, text
    295d75a68807483d5fbb1875c41a9cc915af8c93 Tue Jul 20 12:10:39 2021 -0700
    Turning off old Gencode versions and adding pennantIcons refs #27785
• src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    68588edf2f5306b107676aaeda2ac9d81eb28103 Tue Jul 20 14:27:55 2021 -0700
    adding pennantIcon for superTrack refs #27785
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV37.ra
  • lines changed 1, context: html, text, full: html, text
    295d75a68807483d5fbb1875c41a9cc915af8c93 Tue Jul 20 12:10:39 2021 -0700
    Turning off old Gencode versions and adding pennantIcons refs #27785
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV38.ra
  • lines changed 1, context: html, text, full: html, text
    295d75a68807483d5fbb1875c41a9cc915af8c93 Tue Jul 20 12:10:39 2021 -0700
    Turning off old Gencode versions and adding pennantIcons refs #27785
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.gencode.ra
  • lines changed 2, context: html, text, full: html, text
    68588edf2f5306b107676aaeda2ac9d81eb28103 Tue Jul 20 14:27:55 2021 -0700
    adding pennantIcon for superTrack refs #27785
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM26.ra
  • lines changed 1, context: html, text, full: html, text
    295d75a68807483d5fbb1875c41a9cc915af8c93 Tue Jul 20 12:10:39 2021 -0700
    Turning off old Gencode versions and adding pennantIcons refs #27785
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM27.ra
  • lines changed 1, context: html, text, full: html, text
    295d75a68807483d5fbb1875c41a9cc915af8c93 Tue Jul 20 12:10:39 2021 -0700
    Turning off old Gencode versions and adding pennantIcons refs #27785
• src/hg/makeDb/trackDb/virus/wuhCor1/articV4.html
  • lines changed 42, context: html, text, full: html, text
    1d90acb00b3120e8d1347007620e6eb35a859c84 Thu Jul 22 17:26:33 2021 -0700
    Add ARTIC Primers V4 track and add V3 label to existing track, since both schemes will probably be in use for some time.
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
  • lines changed 12, context: html, text, full: html, text
    1d90acb00b3120e8d1347007620e6eb35a859c84 Thu Jul 22 17:26:33 2021 -0700
    Add ARTIC Primers V4 track and add V3 label to existing track, since both schemes will probably be in use for some time.
• src/inc/srcVersion.h
  • lines changed 1, context: html, text, full: html, text
    7687d17e509506ec79dbca9f188f67bb4ff986db Mon Jul 26 10:16:50 2021 -0700
    New version number v418
• src/lib/net.c
  • lines changed 45, context: html, text, full: html, text
    b3433bd3690adf7488695c3d43c7d1d9b553c859 Tue Jul 20 02:24:50 2021 -0700
    Adding needed EPSV extended passive command for IPv6 FTP. fixes #27860
• src/lib/tests/fetchUrlTest.c
  • lines changed 2, context: html, text, full: html, text
    b3433bd3690adf7488695c3d43c7d1d9b553c859 Tue Jul 20 02:24:50 2021 -0700
    Adding needed EPSV extended passive command for IPv6 FTP. fixes #27860
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    9a96b4f9e42c4527d80b99dcc32bbadff1c349dc Mon Jul 26 10:15:42 2021 -0700
    v418 final build, refs #27854
• src/utils/vcfFilter/vcfFilter.c
  • lines changed 1, context: html, text, full: html, text
    068177454064e3437abd0e2950b853de33a6f8fe Tue Jul 20 14:18:23 2021 -0700
    Allow VCF with no genotypes. A test was failing before this, but it seems like the src/utils/makefile %.testAll target overlooks failures?

• lines changed: 258
• files changed: 39