All File Changes

v416_preview to v416_preview2 (2021-06-01 to 2021-06-07) v416

• LICENSE
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    e0d0dd65f53bb547c201ae1aa2bf0fa6dbbafe09 Thu Jun 3 08:25:17 2021 -0700
    changes after code review, refs #27648
• build/kent-core/LICENSE
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    d5c57763036582f8e7ee53c14ab880ac2c922c31 Wed Jun 2 06:07:20 2021 -0700
    more steps towards kent-core, refs #27614
• build/kent-core/README.md
  • lines changed 24, context: html, text, full: html, text
    d5c57763036582f8e7ee53c14ab880ac2c922c31 Wed Jun 2 06:07:20 2021 -0700
    more steps towards kent-core, refs #27614
  • lines changed 10, context: html, text, full: html, text
    e0d0dd65f53bb547c201ae1aa2bf0fa6dbbafe09 Thu Jun 3 08:25:17 2021 -0700
    changes after code review, refs #27648
• build/kent-core/makeKentCore
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    d5c57763036582f8e7ee53c14ab880ac2c922c31 Wed Jun 2 06:07:20 2021 -0700
    more steps towards kent-core, refs #27614
• build/kent-core/makeKentCore.rules
  • lines changed 31, context: html, text, full: html, text
    d5c57763036582f8e7ee53c14ab880ac2c922c31 Wed Jun 2 06:07:20 2021 -0700
    more steps towards kent-core, refs #27614
• src/hg/autoSql/LICENSE
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    2364a502e18417609bb987659315c61a2dfc1f8b Mon Jun 7 06:17:27 2021 -0700
    fixing track docs of revel track based on author feedback, refs #27142
• src/hg/htdocs/goldenPath/help/gbic.html
  • lines changed 2, context: html, text, full: html, text
    e0d0dd65f53bb547c201ae1aa2bf0fa6dbbafe09 Thu Jun 3 08:25:17 2021 -0700
    changes after code review, refs #27648
• src/hg/htdocs/goldenPath/newsarch.html
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    af7d4c9a5eb8d189dc72efc3521e6d0081d4b80a Wed Jun 2 09:59:52 2021 -0700
    Deleting Dynamic BLAT link since is an advanced feature, refs #27556
• src/hg/htdocs/license/index.html
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    e0d0dd65f53bb547c201ae1aa2bf0fa6dbbafe09 Thu Jun 3 08:25:17 2021 -0700
    changes after code review, refs #27648
• src/hg/inc/jksql.h
  • lines changed 2, context: html, text, full: html, text
    757e45a5277d0cea141c10dadb0a24f62b5734d4 Tue Jun 1 17:49:00 2021 -0700
    wnen inserting rows in hubStatus, catch and ignore duplicate entries due t new unique index on hubUrl
• src/hg/lib/hdb.c
  • lines changed 6, context: html, text, full: html, text
    b05d7e84857952421c7562e19eb37e7b679be199 Fri Jun 4 13:05:18 2021 -0700
    change dots to underbars in the track hash, fixes #27465
• src/hg/lib/hubConnect.c
  • lines changed 13, context: html, text, full: html, text
    757e45a5277d0cea141c10dadb0a24f62b5734d4 Tue Jun 1 17:49:00 2021 -0700
    wnen inserting rows in hubStatus, catch and ignore duplicate entries due t new unique index on hubUrl
• src/hg/lib/jksql.c
  • lines changed 6, context: html, text, full: html, text
    757e45a5277d0cea141c10dadb0a24f62b5734d4 Tue Jun 1 17:49:00 2021 -0700
    wnen inserting rows in hubStatus, catch and ignore duplicate entries due t new unique index on hubUrl
• src/hg/lib/trackDbCustom.c
  • lines changed 5, context: html, text, full: html, text
    b027ebc0e47be9b569aa4deca8179dcb24c00118 Thu Jun 3 13:26:35 2021 -0700
    Error out early in hub trackDb processing if a composite track has a container multiWig child, refs #15650
  • lines changed 5, context: html, text, full: html, text
    586918e76aca2adff473ae3a3116300e6a609b78 Thu Jun 3 13:26:35 2021 -0700
    Error out early in hub trackDb processing if a composite track has a container multiWig child, refs #15650
• src/hg/makeDb/doc/assemblyEquivalence/update.2021-05-11.txt
  • lines changed 309, context: html, text, full: html, text
    4a372a204622bf9a38b0cadf2a22a9fb0d09b570 Wed Jun 2 13:51:23 2021 -0700
    for Ensembl v104 update refs #27616
• src/hg/makeDb/doc/makeEnsembl.txt
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    44ac62ce8e655528d624d2b861b358981599d044 Wed Jun 2 12:08:22 2021 -0700
    Ensembl v104 update complete refs #27616
• src/hg/makeDb/revel/revelToWig-hg38.py
  • lines changed 2, context: html, text, full: html, text
    7a8fdcbb9b6b28ffdeee0a1da8bb83a3c68c7ed8 Fri Jun 4 06:03:33 2021 -0700
    fixing up makedocs and track docs for revel track, refs #27142
• src/hg/makeDb/revel/revelToWig.py
  • lines changed 100, context: html, text, full: html, text
    7a8fdcbb9b6b28ffdeee0a1da8bb83a3c68c7ed8 Fri Jun 4 06:03:33 2021 -0700
    fixing up makedocs and track docs for revel track, refs #27142
• src/hg/makeDb/trackDb/human/cadd.ra
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    755a7bd1ace4575efec42d1565126aee15fe6d54 Thu Jun 3 14:11:06 2021 -0700
    Squashing stale pennantIcons, no RM
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    7a8fdcbb9b6b28ffdeee0a1da8bb83a3c68c7ed8 Fri Jun 4 06:03:33 2021 -0700
    fixing up makedocs and track docs for revel track, refs #27142
  • lines changed 1, context: html, text, full: html, text
    a03a3c86f25fd240af6850261e9f13b58af3bbcb Thu Jun 3 14:11:06 2021 -0700
    Squashing stale pennantIcons, no RM Conflicts: src/hg/makeDb/trackDb/human/hg38/knownGene.ra
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    2364a502e18417609bb987659315c61a2dfc1f8b Mon Jun 7 06:17:27 2021 -0700
    fixing track docs of revel track based on author feedback, refs #27142
• src/hg/makeDb/trackDb/human/caddAlpha.ra
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    755a7bd1ace4575efec42d1565126aee15fe6d54 Thu Jun 3 14:11:06 2021 -0700
    Squashing stale pennantIcons, no RM
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    a03a3c86f25fd240af6850261e9f13b58af3bbcb Thu Jun 3 14:11:06 2021 -0700
    Squashing stale pennantIcons, no RM Conflicts: src/hg/makeDb/trackDb/human/hg38/knownGene.ra
• src/hg/makeDb/trackDb/human/hg19/trackDb.gencode.ra
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    755a7bd1ace4575efec42d1565126aee15fe6d54 Thu Jun 3 14:11:06 2021 -0700
    Squashing stale pennantIcons, no RM
  • lines changed 1, context: html, text, full: html, text
    a03a3c86f25fd240af6850261e9f13b58af3bbcb Thu Jun 3 14:11:06 2021 -0700
    Squashing stale pennantIcons, no RM Conflicts: src/hg/makeDb/trackDb/human/hg38/knownGene.ra
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
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    755a7bd1ace4575efec42d1565126aee15fe6d54 Thu Jun 3 14:11:06 2021 -0700
    Squashing stale pennantIcons, no RM
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    a03a3c86f25fd240af6850261e9f13b58af3bbcb Thu Jun 3 14:11:06 2021 -0700
    Squashing stale pennantIcons, no RM Conflicts: src/hg/makeDb/trackDb/human/hg38/knownGene.ra
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV37lift37.ra
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    755a7bd1ace4575efec42d1565126aee15fe6d54 Thu Jun 3 14:11:06 2021 -0700
    Squashing stale pennantIcons, no RM
  • lines changed 1, context: html, text, full: html, text
    a03a3c86f25fd240af6850261e9f13b58af3bbcb Thu Jun 3 14:11:06 2021 -0700
    Squashing stale pennantIcons, no RM Conflicts: src/hg/makeDb/trackDb/human/hg38/knownGene.ra
• src/hg/makeDb/trackDb/human/hg38/knownGene.ra
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    755a7bd1ace4575efec42d1565126aee15fe6d54 Thu Jun 3 14:11:06 2021 -0700
    Squashing stale pennantIcons, no RM
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    a3c3359fc19ef2eff79b4a8461251a77acb32060 Thu Jun 3 16:12:19 2021 -0700
    add some missing trackDb items that turn on some features in hgTables for the knownGene track
• src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    755a7bd1ace4575efec42d1565126aee15fe6d54 Thu Jun 3 14:11:06 2021 -0700
    Squashing stale pennantIcons, no RM
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    a03a3c86f25fd240af6850261e9f13b58af3bbcb Thu Jun 3 14:11:06 2021 -0700
    Squashing stale pennantIcons, no RM Conflicts: src/hg/makeDb/trackDb/human/hg38/knownGene.ra
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV37.ra
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    755a7bd1ace4575efec42d1565126aee15fe6d54 Thu Jun 3 14:11:06 2021 -0700
    Squashing stale pennantIcons, no RM
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    a03a3c86f25fd240af6850261e9f13b58af3bbcb Thu Jun 3 14:11:06 2021 -0700
    Squashing stale pennantIcons, no RM Conflicts: src/hg/makeDb/trackDb/human/hg38/knownGene.ra
• src/hg/makeDb/trackDb/human/revel.html
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    e0d0dd65f53bb547c201ae1aa2bf0fa6dbbafe09 Thu Jun 3 08:25:17 2021 -0700
    changes after code review, refs #27648
  • lines changed 3, context: html, text, full: html, text
    2364a502e18417609bb987659315c61a2dfc1f8b Mon Jun 7 06:17:27 2021 -0700
    fixing track docs of revel track based on author feedback, refs #27142
• src/hg/makeDb/trackDb/human/revel.ra
  • lines changed 1, context: html, text, full: html, text
    7a8fdcbb9b6b28ffdeee0a1da8bb83a3c68c7ed8 Fri Jun 4 06:03:33 2021 -0700
    fixing up makedocs and track docs for revel track, refs #27142
  • lines changed 1, context: html, text, full: html, text
    2364a502e18417609bb987659315c61a2dfc1f8b Mon Jun 7 06:17:27 2021 -0700
    fixing track docs of revel track based on author feedback, refs #27142
• src/hg/makeDb/trackDb/loadTracks
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    5be8770a26878928217c735aa67fc78cc1361d91 Tue Jun 1 15:51:50 2021 -0700
    add cartVersion trackDb entry on alpha and user targets
• src/hg/makeDb/trackDb/makefile
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    5be8770a26878928217c735aa67fc78cc1361d91 Tue Jun 1 15:51:50 2021 -0700
    add cartVersion trackDb entry on alpha and user targets
• src/hg/makeDb/trackDb/marmoset/calJac4/trackDb.catV2.ra
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    755a7bd1ace4575efec42d1565126aee15fe6d54 Thu Jun 3 14:11:06 2021 -0700
    Squashing stale pennantIcons, no RM
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    a03a3c86f25fd240af6850261e9f13b58af3bbcb Thu Jun 3 14:11:06 2021 -0700
    Squashing stale pennantIcons, no RM Conflicts: src/hg/makeDb/trackDb/human/hg38/knownGene.ra
• src/hg/makeDb/trackDb/marmoset/calJac4/trackDb.uwIsoSeq.ra
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    755a7bd1ace4575efec42d1565126aee15fe6d54 Thu Jun 3 14:11:06 2021 -0700
    Squashing stale pennantIcons, no RM
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    a03a3c86f25fd240af6850261e9f13b58af3bbcb Thu Jun 3 14:11:06 2021 -0700
    Squashing stale pennantIcons, no RM Conflicts: src/hg/makeDb/trackDb/human/hg38/knownGene.ra
• src/hg/makeDb/trackDb/mouse/mm39/knownGene.ra
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    755a7bd1ace4575efec42d1565126aee15fe6d54 Thu Jun 3 14:11:06 2021 -0700
    Squashing stale pennantIcons, no RM
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    a03a3c86f25fd240af6850261e9f13b58af3bbcb Thu Jun 3 14:11:06 2021 -0700
    Squashing stale pennantIcons, no RM Conflicts: src/hg/makeDb/trackDb/human/hg38/knownGene.ra
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.chainNet.ra
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    755a7bd1ace4575efec42d1565126aee15fe6d54 Thu Jun 3 14:11:06 2021 -0700
    Squashing stale pennantIcons, no RM
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    a03a3c86f25fd240af6850261e9f13b58af3bbcb Thu Jun 3 14:11:06 2021 -0700
    Squashing stale pennantIcons, no RM Conflicts: src/hg/makeDb/trackDb/human/hg38/knownGene.ra
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.gencode.ra
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    755a7bd1ace4575efec42d1565126aee15fe6d54 Thu Jun 3 14:11:06 2021 -0700
    Squashing stale pennantIcons, no RM
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    a03a3c86f25fd240af6850261e9f13b58af3bbcb Thu Jun 3 14:11:06 2021 -0700
    Squashing stale pennantIcons, no RM Conflicts: src/hg/makeDb/trackDb/human/hg38/knownGene.ra
• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM26.ra
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    755a7bd1ace4575efec42d1565126aee15fe6d54 Thu Jun 3 14:11:06 2021 -0700
    Squashing stale pennantIcons, no RM
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    a03a3c86f25fd240af6850261e9f13b58af3bbcb Thu Jun 3 14:11:06 2021 -0700
    Squashing stale pennantIcons, no RM Conflicts: src/hg/makeDb/trackDb/human/hg38/knownGene.ra
• src/hg/makeDb/trackDb/refSeqComposite.ra
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    755a7bd1ace4575efec42d1565126aee15fe6d54 Thu Jun 3 14:11:06 2021 -0700
    Squashing stale pennantIcons, no RM
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    a03a3c86f25fd240af6850261e9f13b58af3bbcb Thu Jun 3 14:11:06 2021 -0700
    Squashing stale pennantIcons, no RM Conflicts: src/hg/makeDb/trackDb/human/hg38/knownGene.ra
• src/hg/makeDb/trackDb/relatedTracks.ra
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    8ef8d5ab68481f9310f06d7423c2e6d0363261b7 Wed Jun 2 01:36:38 2021 -0700
    fixing revel docs, refs #27142
• src/hg/makeDb/trackDb/tagTypes.tab
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    a00acd77fef9eeb8c41af5a1c4e056cc866822d0 Thu Jun 3 16:27:44 2021 -0700
    oops... bigGenePred changes for hgTables tweaks
• src/hg/makeDb/trackDb/virus/wuhCor1/ConservedAAs.html
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    f8316db93ddbd7026417356ff53e87e35c97fa56 Mon Jun 7 02:42:46 2021 -0700
    adding mutCons track for wuhCor1, no redmine yet, waiting for feedback from Irwin
• src/hg/makeDb/trackDb/virus/wuhCor1/SNVconservation.html
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    f8316db93ddbd7026417356ff53e87e35c97fa56 Mon Jun 7 02:42:46 2021 -0700
    adding mutCons track for wuhCor1, no redmine yet, waiting for feedback from Irwin
• src/hg/makeDb/trackDb/virus/wuhCor1/Starr_Bloom.html
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    f8316db93ddbd7026417356ff53e87e35c97fa56 Mon Jun 7 02:42:46 2021 -0700
    adding mutCons track for wuhCor1, no redmine yet, waiting for feedback from Irwin
• src/hg/makeDb/trackDb/virus/wuhCor1/Starr_Bloom_antibody.html
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    f8316db93ddbd7026417356ff53e87e35c97fa56 Mon Jun 7 02:42:46 2021 -0700
    adding mutCons track for wuhCor1, no redmine yet, waiting for feedback from Irwin
• src/hg/makeDb/trackDb/virus/wuhCor1/SynConsCodons.html
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    f8316db93ddbd7026417356ff53e87e35c97fa56 Mon Jun 7 02:42:46 2021 -0700
    adding mutCons track for wuhCor1, no redmine yet, waiting for feedback from Irwin
• src/hg/makeDb/trackDb/virus/wuhCor1/mutCons.ra
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    f8316db93ddbd7026417356ff53e87e35c97fa56 Mon Jun 7 02:42:46 2021 -0700
    adding mutCons track for wuhCor1, no redmine yet, waiting for feedback from Irwin
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
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    755a7bd1ace4575efec42d1565126aee15fe6d54 Thu Jun 3 14:11:06 2021 -0700
    Squashing stale pennantIcons, no RM
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    a03a3c86f25fd240af6850261e9f13b58af3bbcb Thu Jun 3 14:11:06 2021 -0700
    Squashing stale pennantIcons, no RM Conflicts: src/hg/makeDb/trackDb/human/hg38/knownGene.ra
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    f8316db93ddbd7026417356ff53e87e35c97fa56 Mon Jun 7 02:42:46 2021 -0700
    adding mutCons track for wuhCor1, no redmine yet, waiting for feedback from Irwin
• src/hg/utils/automation/EnsGeneAutomate.pm
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    44ac62ce8e655528d624d2b861b358981599d044 Wed Jun 2 12:08:22 2021 -0700
    Ensembl v104 update complete refs #27616
• src/hg/utils/hubCheck/hubCheck.c
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    4061b6e207c4cbf9d7162c4b8aa2d8d1329c7e92 Thu Jun 3 11:00:39 2021 -0700
    hubCheck now complains about multiWigs that are children of composites, refs #15650
• src/hg/utils/makefile
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    424b815648ae4f70f28c17d140ba635a5b14a9f9 Fri Jun 4 05:01:14 2021 -0700
    finishup up the move of four tools into the hg directory, refs #27498
• src/hg/utils/pslLiftSubrangeBlat/tests/makefile
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    424b815648ae4f70f28c17d140ba635a5b14a9f9 Fri Jun 4 05:01:14 2021 -0700
    finishup up the move of four tools into the hg directory, refs #27498
• src/inc/common.mk
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    7d1c9114915734afc25cb3da5a611bcf387c0bc3 Thu Jun 3 12:07:51 2021 -0700
    use our local static copy of freetype on dev for the moment. Using the distributed one is slightly changing the images, which needs to be examined more closely
• src/makefile
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    14bd3b4e737b599508510c1192885d3ba044b12a Wed Jun 2 06:04:23 2021 -0700
    ignoring jkOwnLib, refs #27614
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    ea0720bc6efa1e0d09989ae7c1febc3af1c07e68 Wed Jun 2 06:23:21 2021 -0700
    make utils should work now in kent-core, refs #27614
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    e8f235db71e7f70fa7aa9588525650dc5b1c7977 Fri Jun 4 03:07:44 2021 -0700
    fixing my makefile bug, refs #27614
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    9a67d40fbebefe0bb2b2fba60d65b4215a7478ba Fri Jun 4 03:12:41 2021 -0700
    actually fixing the makefile bug, refs #27614
• src/utils/bedToBigBed/bedToBigBed.c
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    8d827f0ba59bf5b3e1ddad20a067172873ae3957 Wed Jun 2 15:40:41 2021 -0700
    Count zero width items in the summary levels
• src/utils/bedToBigBed/tests/input/tabSep.as
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    d336a27e7f63d6b9228461464ef00acf64939ad8 Sun Jun 6 20:18:19 2021 -0700
    Added test case for -tab. Though there was a bug, not sure now, but another test is a good thing
• src/utils/bedToBigBed/tests/input/tabSep.bed
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    d336a27e7f63d6b9228461464ef00acf64939ad8 Sun Jun 6 20:18:19 2021 -0700
    Added test case for -tab. Though there was a bug, not sure now, but another test is a good thing
• src/utils/bedToBigBed/tests/makefile
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    d336a27e7f63d6b9228461464ef00acf64939ad8 Sun Jun 6 20:18:19 2021 -0700
    Added test case for -tab. Though there was a bug, not sure now, but another test is a good thing
• src/utils/chromToUcsc/chromToUcsc
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    8cbd73320598db4c37c75666e518622f82fbc326 Sun Jun 6 20:53:15 2021 -0700
    added option for chromToUcsc to skip unmapped chromosomes rather than error
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    d7e3477e89a22c7a00c5ac85528d2d21477695f8 Sun Jun 6 22:06:34 2021 -0700
    allow mate chrom name of "*"
• src/utils/chromToUcsc/tests/expected/mm10.bad-names.bed
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    8cbd73320598db4c37c75666e518622f82fbc326 Sun Jun 6 20:53:15 2021 -0700
    added option for chromToUcsc to skip unmapped chromosomes rather than error
• src/utils/chromToUcsc/tests/expected/mm10.bad-names.err
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    8cbd73320598db4c37c75666e518622f82fbc326 Sun Jun 6 20:53:15 2021 -0700
    added option for chromToUcsc to skip unmapped chromosomes rather than error
• src/utils/chromToUcsc/tests/in/mm10.bad-names.bed
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    8cbd73320598db4c37c75666e518622f82fbc326 Sun Jun 6 20:53:15 2021 -0700
    added option for chromToUcsc to skip unmapped chromosomes rather than error
• src/utils/chromToUcsc/tests/makefile
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    8cbd73320598db4c37c75666e518622f82fbc326 Sun Jun 6 20:53:15 2021 -0700
    added option for chromToUcsc to skip unmapped chromosomes rather than error
• src/utils/qa/weeklybld/NOTES-for-manually-updating-BLAT-FOOTER.txt
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    585200184be9957f52b64807b8c7b1dc501b90c7 Wed Jun 2 13:21:37 2021 -0700
    Added gfPcr since we had added isPcr recently. Also added notes for manually updating blat/FOOTER.txt
• src/utils/qa/weeklybld/buildEnv.csh
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    1f1f4ba4ced1572436c71a87da3908ad1c9f3c2b Mon Jun 7 10:08:52 2021 -0700
    v416 preview2, refs #27655
• src/utils/qa/weeklybld/makeUserApps.csh
  • lines changed 5, context: html, text, full: html, text
    585200184be9957f52b64807b8c7b1dc501b90c7 Wed Jun 2 13:21:37 2021 -0700
    Added gfPcr since we had added isPcr recently. Also added notes for manually updating blat/FOOTER.txt

• lines changed: 1290
• files changed: 91