All File Changes

v395_preview2 to v395_base (2020-03-02 to 2020-03-09) v395

• src/hg/genePredHisto/genePredHisto.c
  • lines changed 10, context: html, text, full: html, text
    2f4731c424be7ac8fb235f755f0a6d368dd0dcc8 Mon Mar 2 10:47:40 2020 -0800
    correct one line header message in usage() no redmine
• src/hg/genePredSingleCover/genePredSingleCover.c
  • lines changed 7, context: html, text, full: html, text
    6224a15a5899c275ac785a49c67860284dff3de9 Mon Mar 2 10:49:54 2020 -0800
    correct one line header message in usage() no redmine
• src/hg/genePredToMafFrames/genePredToMafFrames.c
  • lines changed 7, context: html, text, full: html, text
    d45f20285f046c893863653230b6e8548a4a49d7 Mon Mar 2 10:52:00 2020 -0800
    correct one line header message in usage() no redmine
• src/hg/htdocs/training/index.html
  • lines changed 31, context: html, text, full: html, text
    2a1f2bfa33b099b35864714aa7e654dec9500505 Tue Mar 3 22:28:59 2020 -0800
    dropping completed nijmegen workshop. moving slovenia gig into next-four group.
  • lines changed 1, context: html, text, full: html, text
    b7fb69088b7169e0e25479a021d080ea25123815 Sun Mar 8 13:13:35 2020 -0700
    marking acmg as cancelled
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    1b5577e8f23436a133037ad7db987ad9894b508f Mon Mar 9 09:59:12 2020 -0700
    New version number v395
• src/hg/lib/cart.c
  • lines changed 1, context: html, text, full: html, text
    d0773d1845bd3c754d79d26d790b44893cbc8bf6 Fri Mar 6 13:54:11 2020 -0800
    Added another check for cartDidContentType, thanks Jonathan. refs #25064
• src/hg/lib/cartTrackDb.c
  • lines changed 2, context: html, text, full: html, text
    37dde06377a1daa9d86150ed431b89c49c699e10 Tue Mar 3 14:45:09 2020 -0800
    fix a problem introduced by f87fbb58. Track hub tracks are in a group called after the hub name (eg hub_#). Refs #25050
• src/hg/makeDb/doc/bosTau9/clinvarLift.txt
  • lines changed 10, context: html, text, full: html, text
    47b810a94fe726a72700c7e778faee4a6b5e1460 Wed Mar 4 03:30:07 2020 -0800
    adding makedocs, refs #24825
• src/hg/makeDb/doc/danRer11/clinVarLift.txt
  • lines changed 0, context: html, text, full: html, text
    47b810a94fe726a72700c7e778faee4a6b5e1460 Wed Mar 4 03:30:07 2020 -0800
    adding makedocs, refs #24825
  • lines changed 10, context: html, text, full: html, text
    4088c518a64a2ff611abd8872458d3d164cd0629 Wed Mar 4 04:52:14 2020 -0800
    more makedocs for clinvarLift, refs #24825
• src/hg/makeDb/doc/hg19.txt
  • lines changed 32, context: html, text, full: html, text
    71b469a98a76ff8be8ab09ff421471f0e4d71351 Tue Mar 3 14:48:45 2020 -0800
    Quick run up of gnomAD structural variants track for hg19, refs #24179
• src/hg/makeDb/doc/mm10.txt
  • lines changed 12, context: html, text, full: html, text
    47b810a94fe726a72700c7e778faee4a6b5e1460 Wed Mar 4 03:30:07 2020 -0800
    adding makedocs, refs #24825
• src/hg/makeDb/doc/panTro6/clinvarLift.txt
  • lines changed 10, context: html, text, full: html, text
    4088c518a64a2ff611abd8872458d3d164cd0629 Wed Mar 4 04:52:14 2020 -0800
    more makedocs for clinvarLift, refs #24825
• src/hg/makeDb/doc/rheMac10/clinvarLift.txt
  • lines changed 10, context: html, text, full: html, text
    4088c518a64a2ff611abd8872458d3d164cd0629 Wed Mar 4 04:52:14 2020 -0800
    more makedocs for clinvarLift, refs #24825
• src/hg/makeDb/doc/susScr11/clinvarLift.txt
  • lines changed 11, context: html, text, full: html, text
    47b810a94fe726a72700c7e778faee4a6b5e1460 Wed Mar 4 03:30:07 2020 -0800
    adding makedocs, refs #24825
• src/hg/makeDb/doc/wuhCor1/comparePair
  • lines changed 30, context: html, text, full: html, text
    a9cd9c0403a2126a2d84e5e711ac07df8ee95db5 Sat Mar 7 12:20:18 2020 -0800
    scripts used to compare all the kmers refs #25090
• src/hg/makeDb/doc/wuhCor1/mkCompareJobList.pl
  • lines changed 46, context: html, text, full: html, text
    a9cd9c0403a2126a2d84e5e711ac07df8ee95db5 Sat Mar 7 12:20:18 2020 -0800
    scripts used to compare all the kmers refs #25090
• src/hg/makeDb/doc/wuhCor1/mkTestData.pl
  • lines changed 123, context: html, text, full: html, text
    829e6da5fbf3a357ca0bc1592695f567ac817d64 Sat Mar 7 12:46:45 2020 -0800
    describing the kmer phylo tree generation procedure refs #25090
• src/hg/makeDb/doc/wuhCor1/multiz.txt
  • lines changed 168, context: html, text, full: html, text
    79fe45f9415da16d9bf774a1a92f147c00ea3809 Sat Mar 7 12:12:16 2020 -0800
    begin documentation of the multiple alignment refs #25090
  • lines changed 139, context: html, text, full: html, text
    829e6da5fbf3a357ca0bc1592695f567ac817d64 Sat Mar 7 12:46:45 2020 -0800
    describing the kmer phylo tree generation procedure refs #25090
• src/hg/makeDb/doc/wuhCor1/neighbor
  • lines changed 0, context: html, text, full: html, text
    829e6da5fbf3a357ca0bc1592695f567ac817d64 Sat Mar 7 12:46:45 2020 -0800
    describing the kmer phylo tree generation procedure refs #25090
• src/hg/makeDb/doc/wuhCor1/wuhCor1.119way.nh
  • lines changed 119, context: html, text, full: html, text
    829e6da5fbf3a357ca0bc1592695f567ac817d64 Sat Mar 7 12:46:45 2020 -0800
    describing the kmer phylo tree generation procedure refs #25090
• src/hg/makeDb/gnomad/gnomadSvToUcsc.awk
  • lines changed 51, context: html, text, full: html, text
    71b469a98a76ff8be8ab09ff421471f0e4d71351 Tue Mar 3 14:48:45 2020 -0800
    Quick run up of gnomAD structural variants track for hg19, refs #24179
• src/hg/makeDb/hgLoadWiggle/fixStepToBedGraph.pl
  • lines changed 1, context: html, text, full: html, text
    a3499beb622c64ee44fc2e31a4191f89f46ae7cb Mon Mar 2 10:42:07 2020 -0800
    correct one line header message in usage() no redmine
• src/hg/makeDb/hgLoadWiggle/varStepToBedGraph.pl
  • lines changed 1, context: html, text, full: html, text
    8a13935409e81abd2840eee06e0d11618080075b Mon Mar 2 10:44:10 2020 -0800
    correct one line header message in usage() no redmine
• src/hg/makeDb/trackDb/clinvarLift.html
  • lines changed 21, context: html, text, full: html, text
    2424b8aceac9331a6ea246de0c2574fa852a3fc9 Tue Mar 3 17:27:08 2020 -0800
    Minor edits to clinVarLift html #24835
• src/hg/makeDb/trackDb/ensGene.html
  • lines changed 1, context: html, text, full: html, text
    759c1b5ef911a0331ce1d047836a2202697bb696 Fri Mar 6 13:28:45 2020 -0800
    Adding target=blank refs #25059
  • lines changed 1, context: html, text, full: html, text
    39bccead5304920ff7345c2aa5a89b0d3d8b370d Fri Mar 6 13:52:45 2020 -0800
    fixing typo #25059
• src/hg/makeDb/trackDb/human/hg19/knownGene.html
  • lines changed 1, context: html, text, full: html, text
    759c1b5ef911a0331ce1d047836a2202697bb696 Fri Mar 6 13:28:45 2020 -0800
    Adding target=blank refs #25059
• src/hg/makeDb/trackDb/human/hg19/trackDb.gnomad.ra
  • lines changed 49, context: html, text, full: html, text
    71b469a98a76ff8be8ab09ff421471f0e4d71351 Tue Mar 3 14:48:45 2020 -0800
    Quick run up of gnomAD structural variants track for hg19, refs #24179
• src/hg/makeDb/trackDb/human/hg38/knownGene.html
  • lines changed 1, context: html, text, full: html, text
    759c1b5ef911a0331ce1d047836a2202697bb696 Fri Mar 6 13:28:45 2020 -0800
    Adding target=blank refs #25059
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    66df8a7b18595619b01d9b373ed1f229329ca0da Mon Mar 2 14:17:25 2020 -0800
    Hiding dbSNP151 from default view for human refs #23283
• src/hg/pslCDnaFilter/pslCDnaFilter.c
  • lines changed 3, context: html, text, full: html, text
    4f2982742c32be90ddb2c601937a7f8531ad14e1 Mon Mar 2 12:48:11 2020 -0800
    correct one line header message in usage() no redmine
• src/hg/pslCDnaFilter/usage.txt
  • lines changed 2, context: html, text, full: html, text
    4f2982742c32be90ddb2c601937a7f8531ad14e1 Mon Mar 2 12:48:11 2020 -0800
    correct one line header message in usage() no redmine
• src/hg/pslHisto/pslHisto.c
  • lines changed 10, context: html, text, full: html, text
    0186982e4dd1912d6a8bf518d5d0301901fb4e4c Mon Mar 2 12:50:21 2020 -0800
    correct one line header message in usage() no redmine
• src/hg/pslPartition/pslPartition.c
  • lines changed 5, context: html, text, full: html, text
    ae06b237971133bc7e68daa85cb34d32cdeabd6f Mon Mar 2 12:55:59 2020 -0800
    correct one line header message in usage() no redmine
• src/hg/pslSwap/pslSwap.c
  • lines changed 8, context: html, text, full: html, text
    11cd242e75d51c384ededd99808435593abf85de Mon Mar 2 13:09:15 2020 -0800
    correct one line header message in usage() refs #25071
• src/hg/pslToBed/pslToBed.c
  • lines changed 2, context: html, text, full: html, text
    183b7ea6d5861dc5aa8ae734c27b02af6c056722 Mon Mar 2 13:10:54 2020 -0800
    correct one line header message in usage() refs #25071
• src/hg/utils/automation/EnsGeneAutomate.pm
  • lines changed 10, context: html, text, full: html, text
    cf078156da3eb0042503c279d0c0bddb9786c355 Thu Mar 5 12:01:59 2020 -0800
    now running up Ensembl genes on assembly hubs refs #24963
• src/hg/utils/automation/asmHubEnsGene.pl
  • lines changed 20, context: html, text, full: html, text
    cf078156da3eb0042503c279d0c0bddb9786c355 Thu Mar 5 12:01:59 2020 -0800
    now running up Ensembl genes on assembly hubs refs #24963
• src/hg/utils/automation/asmHubTrackDb.sh
  • lines changed 12, context: html, text, full: html, text
    cf078156da3eb0042503c279d0c0bddb9786c355 Thu Mar 5 12:01:59 2020 -0800
    now running up Ensembl genes on assembly hubs refs #24963
• src/hg/utils/automation/doEnsGeneUpdate.pl
  • lines changed 88, context: html, text, full: html, text
    cf078156da3eb0042503c279d0c0bddb9786c355 Thu Mar 5 12:01:59 2020 -0800
    now running up Ensembl genes on assembly hubs refs #24963
• src/hg/utils/automation/gff3ToRefLink.pl
  • lines changed 4, context: html, text, full: html, text
    a1f736b4dc8cf37703c5bb6e85818416374e8058 Tue Mar 3 11:04:01 2020 -0800
    show inputs on startup refs #23891
• src/hg/utils/bedToPsl/bedToPsl.c
  • lines changed 4, context: html, text, full: html, text
    ef3707f0ca7e1592d542f28fdd4b254bf104d854 Mon Mar 2 10:36:00 2020 -0800
    correct one line header message in usage() no redmine
  • lines changed 1, context: html, text, full: html, text
    12454aa5329fdd7d21b31c9d187e07f81e6c082d Mon Mar 2 13:54:04 2020 -0800
    correct one line header message in usage() refs #25071
• src/hg/utils/overlapSelect/overlapSelect.c
  • lines changed 3, context: html, text, full: html, text
    0e69037441c493289ea56f19a2e26ed24c80152a Mon Mar 2 10:58:04 2020 -0800
    correct one line header message in usage() no redmine
• src/hg/utils/overlapSelect/usage.txt
  • lines changed 2, context: html, text, full: html, text
    0e69037441c493289ea56f19a2e26ed24c80152a Mon Mar 2 10:58:04 2020 -0800
    correct one line header message in usage() no redmine
• src/hg/utils/pslMap/pslMap.c
  • lines changed 3, context: html, text, full: html, text
    7e8a696881983f39aaf4d358a618217cae150ed8 Mon Mar 2 12:52:44 2020 -0800
    correct one line header message in usage() no redmine
• src/hg/utils/pslMap/usage.txt
  • lines changed 7, context: html, text, full: html, text
    7e8a696881983f39aaf4d358a618217cae150ed8 Mon Mar 2 12:52:44 2020 -0800
    correct one line header message in usage() no redmine
• src/hg/utils/pslMapPostChain/pslMapPostChain.c
  • lines changed 6, context: html, text, full: html, text
    860c752347c2a0ccc99794d772babffae640dab5 Mon Mar 2 12:54:27 2020 -0800
    correct one line header message in usage() no redmine
  • lines changed 2, context: html, text, full: html, text
    075a3ad3e1b1e77472825a0e6daa83dde05dd022 Mon Mar 2 14:12:35 2020 -0800
    correct one line header in usage message no redmine
• src/hg/utils/pslRc/pslRc.c
  • lines changed 5, context: html, text, full: html, text
    d11aff78d1b8b998525b47db166bb5128bc96374 Mon Mar 2 12:57:12 2020 -0800
    correct one line header message in usage() no redmine
• src/hg/utils/vai.pl
  • lines changed 3, context: html, text, full: html, text
    cf37e57c66f855418bc05aff039ab846ad317354 Mon Mar 2 13:20:42 2020 -0800
    correct one line header message in usage() refs #25071
• src/inc/srcVersion.h
  • lines changed 1, context: html, text, full: html, text
    1b5577e8f23436a133037ad7db987ad9894b508f Mon Mar 9 09:59:12 2020 -0700
    New version number v395
• src/parasol/parasol/parasol.c
  • lines changed 1, context: html, text, full: html, text
    fe728170025b04cc26b65f933ddce4d354c5ac5f Mon Mar 2 11:02:14 2020 -0800
    correct one line header message in usage() no redmine
• src/utils/chromToUcsc/chromToUcsc
  • lines changed 9, context: html, text, full: html, text
    a1c986a99e519e259360bb99682b8b8842666bd9 Tue Mar 3 02:40:14 2020 -0800
    tiny docs change to chromToUcsc
  • lines changed 2, context: html, text, full: html, text
    beec258cf09f6fb519a05e28a2ab17ca3fef4858 Tue Mar 3 02:45:02 2020 -0800
    another tiny docs change to chromToUcsc
• src/utils/cpgIslandExt/cpg_lh.c
  • lines changed 2, context: html, text, full: html, text
    d486edad7214c55c607e4c8302ec1b0e10a1daf8 Mon Mar 2 14:13:48 2020 -0800
    correct one line header in usage message no redmine
• src/utils/doClinvarLift
  • lines changed 24, context: html, text, full: html, text
    d74dfc1624d496349de6061ed0fb1e068318291d Wed Mar 4 02:23:29 2020 -0800
    adding help message to doClinvarLift, refs #24825
• src/utils/qa/getRRtableStatus.csh
  • lines changed 27, context: html, text, full: html, text
    b54d340566cdff0bb6ab626ef3d0c5bc383038c4 Sun Mar 8 18:13:43 2020 -0700
    reconfigured to account for the missing header row in table dumpfiles
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    b172dfb35118ba2c45e509fb07cc782dca9765ac Mon Mar 9 09:57:58 2020 -0700
    v395 final build, refs #25041
• src/utils/rmFaDups/rmFaDups.c
  • lines changed 3, context: html, text, full: html, text
    b4c59514f00bdfba0db99fed67740ef8858ac583 Mon Mar 2 13:13:28 2020 -0800
    correct one line header message in usage() refs #25071
• src/utils/sizeof/sizeof.c
  • lines changed 2, context: html, text, full: html, text
    28240bc5f0c103b9bf8e90637e6c5464bca55dc7 Mon Mar 2 13:14:45 2020 -0800
    correct one line header message in usage() refs #25071
• src/utils/userApps/fetchChromSizes
  • lines changed 1, context: html, text, full: html, text
    b9215df0d1df3b3e2a655c0fa506bcfc20f243d6 Mon Mar 2 10:40:13 2020 -0800
    correct one line header message in usage() no redmine

• lines changed: 1183
• files changed: 65