All File Changes

v477_preview2 to v477_base (2025-01-27 to 2025-02-03) v477

• .gitignore
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    1c002ea441ef48d4580156e0e80f23a8b7dc3eec Sun Jan 19 13:05:19 2025 -0800
    CGI loaders working
• docs/gb101.md
  • lines changed 1, context: html, text, full: html, text
    8963b9aa8f25e831ffa3038020ff4229087154f2 Wed Jan 29 12:05:12 2025 -0800
    Reducing the ratio to 95% because 100% causes the image to reach the edge of the browser. Refs #30335
• src/ameme/makefile
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    4d1132fe8af3037e9bc3f4ff419151cebcc10fc1 Sun Jan 19 11:28:49 2025 -0800
    userApps working as before on hgwdev
• src/hg/encode/hgEncodeVocab/hgEncodeVocab.c
  • lines changed 5, context: html, text, full: html, text
    156dbcfc96c9a4a5eba481f8d979700b0ca1024e Mon Feb 3 06:28:18 2025 -0800
    Fixing security concern in hgEncodeVocab. fixes #287. Note that actual full cleanup by removing the unneeded encode/cv.ra from trackDb files has not been done yet., and making the code tolerate its presence or absence in the trackDb.ra files, at the start of the controlledVocabulary setting.
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 1, context: html, text, full: html, text
    ca2aed07e13e885802670598d6e39f8984869c91 Wed Jan 29 10:20:40 2025 -0800
    Feedback typo from CR, refs #35149
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 21, context: html, text, full: html, text
    36fc997c4663f577c338a94d24cd968836c655af Fri Jan 31 12:23:27 2025 -0800
    Releasing and announcing the COSMIC v101 for hg38 and hg19, refs #34904
• src/hg/htdocs/indexNews.html
  • lines changed 13, context: html, text, full: html, text
    36fc997c4663f577c338a94d24cd968836c655af Fri Jan 31 12:23:27 2025 -0800
    Releasing and announcing the COSMIC v101 for hg38 and hg19, refs #34904
• src/hg/inc/hui.h
  • lines changed 1, context: html, text, full: html, text
    156dbcfc96c9a4a5eba481f8d979700b0ca1024e Mon Feb 3 06:28:18 2025 -0800
    Fixing security concern in hgEncodeVocab. fixes #287. Note that actual full cleanup by removing the unneeded encode/cv.ra from trackDb files has not been done yet., and making the code tolerate its presence or absence in the trackDb.ra files, at the start of the controlledVocabulary setting.
• src/hg/inc/versionInfo.h
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    6bf2d8427849abe775b422f71dae6665021a0ff8 Mon Feb 3 11:20:38 2025 -0800
    New version number v477
• src/hg/lib/cv.c
  • lines changed 1, context: html, text, full: html, text
    156dbcfc96c9a4a5eba481f8d979700b0ca1024e Mon Feb 3 06:28:18 2025 -0800
    Fixing security concern in hgEncodeVocab. fixes #287. Note that actual full cleanup by removing the unneeded encode/cv.ra from trackDb files has not been done yet., and making the code tolerate its presence or absence in the trackDb.ra files, at the start of the controlledVocabulary setting.
• src/hg/lib/hui.c
  • lines changed 16, context: html, text, full: html, text
    156dbcfc96c9a4a5eba481f8d979700b0ca1024e Mon Feb 3 06:28:18 2025 -0800
    Fixing security concern in hgEncodeVocab. fixes #287. Note that actual full cleanup by removing the unneeded encode/cv.ra from trackDb files has not been done yet., and making the code tolerate its presence or absence in the trackDb.ra files, at the start of the controlledVocabulary setting.
• src/hg/liftOver/makefile
  • lines changed 28, context: html, text, full: html, text
    07639647efe6cfe6dbc643b8fae13c3dd153c528 Fri Jan 17 19:07:18 2025 -0800
    work on docker utils build
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 4, context: html, text, full: html, text
    e17110f14580a0246f745059d56b474d68ee0b84 Fri Jan 31 16:25:08 2025 -0800
    adding a couple per user request refs #29545
  • lines changed 1, context: html, text, full: html, text
    84391fdaa9862e725044a75732fabb41376d5ed1 Fri Jan 31 16:47:07 2025 -0800
    add one per user request refs #29545
  • lines changed 2, context: html, text, full: html, text
    54e8b53101ae6e6c2f9d686f6292343d277a130b Sat Feb 1 19:42:45 2025 -0800
    adding a couple per user request
  • lines changed 1, context: html, text, full: html, text
    a913e02395d928f3ee5fa591c309b0e0938df192 Sun Feb 2 10:34:58 2025 -0800
    adding a couple per user request refs #29545
  • lines changed 1, context: html, text, full: html, text
    ba9d5aafd83e09d48df9868ac0034154a7f6f212 Sun Feb 2 15:03:50 2025 -0800
    adding one per user request refs #29545
• src/hg/makeDb/doc/fungiAsmHub/fungi.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    9eafbb671776acf18b20ed23ec14b51e49a2a5d2 Fri Jan 31 16:49:25 2025 -0800
    add one per user request refs #29545
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    e17110f14580a0246f745059d56b474d68ee0b84 Fri Jan 31 16:25:08 2025 -0800
    adding a couple per user request refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.clade.txt
  • lines changed 1, context: html, text, full: html, text
    84391fdaa9862e725044a75732fabb41376d5ed1 Fri Jan 31 16:47:07 2025 -0800
    add one per user request refs #29545
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    84391fdaa9862e725044a75732fabb41376d5ed1 Fri Jan 31 16:47:07 2025 -0800
    add one per user request refs #29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    e17110f14580a0246f745059d56b474d68ee0b84 Fri Jan 31 16:25:08 2025 -0800
    adding a couple per user request refs #29545
  • lines changed 1, context: html, text, full: html, text
    5fe502b1541a5af8d22f10ee4879c2489468fc55 Sat Feb 1 19:42:27 2025 -0800
    asmHubs/master.run.list
  • lines changed 1, context: html, text, full: html, text
    ba9d5aafd83e09d48df9868ac0034154a7f6f212 Sun Feb 2 15:03:50 2025 -0800
    adding one per user request refs #29545
• src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    e17110f14580a0246f745059d56b474d68ee0b84 Fri Jan 31 16:25:08 2025 -0800
    adding a couple per user request refs #29545
  • lines changed 1, context: html, text, full: html, text
    5fe502b1541a5af8d22f10ee4879c2489468fc55 Sat Feb 1 19:42:27 2025 -0800
    asmHubs/master.run.list
• src/hg/makeDb/doc/repeatMasker.txt
  • lines changed 647, context: html, text, full: html, text
    d94b7ab22f12dfc6b2168b0af5c7a71d1195a7bf Wed Jan 29 15:38:56 2025 -0800
    new repeat masker installed no redmine
• src/hg/makeDb/doc/viralAsmHub/viral.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    a913e02395d928f3ee5fa591c309b0e0938df192 Sun Feb 2 10:34:58 2025 -0800
    adding a couple per user request refs #29545
• src/hg/makeDb/hgGcPercent/makefile
  • lines changed 23, context: html, text, full: html, text
    07639647efe6cfe6dbc643b8fae13c3dd153c528 Fri Jan 17 19:07:18 2025 -0800
    work on docker utils build
• src/hg/makeDb/hgGoldGapGl/makefile
  • lines changed 28, context: html, text, full: html, text
    07639647efe6cfe6dbc643b8fae13c3dd153c528 Fri Jan 17 19:07:18 2025 -0800
    work on docker utils build
  • lines changed 3, context: html, text, full: html, text
    4d1132fe8af3037e9bc3f4ff419151cebcc10fc1 Sun Jan 19 11:28:49 2025 -0800
    userApps working as before on hgwdev
  • lines changed 1, context: html, text, full: html, text
    1c002ea441ef48d4580156e0e80f23a8b7dc3eec Sun Jan 19 13:05:19 2025 -0800
    CGI loaders working
• src/hg/makeDb/hgLoadBed/makefile
  • lines changed 82, context: html, text, full: html, text
    07639647efe6cfe6dbc643b8fae13c3dd153c528 Fri Jan 17 19:07:18 2025 -0800
    work on docker utils build
  • lines changed 1, context: html, text, full: html, text
    1c002ea441ef48d4580156e0e80f23a8b7dc3eec Sun Jan 19 13:05:19 2025 -0800
    CGI loaders working
• src/hg/makeDb/hgLoadMaf/makefile
  • lines changed 80, context: html, text, full: html, text
    07639647efe6cfe6dbc643b8fae13c3dd153c528 Fri Jan 17 19:07:18 2025 -0800
    work on docker utils build
  • lines changed 1, context: html, text, full: html, text
    1c002ea441ef48d4580156e0e80f23a8b7dc3eec Sun Jan 19 13:05:19 2025 -0800
    CGI loaders working
• src/hg/makeDb/hgLoadWiggle/makefile
  • lines changed 102, context: html, text, full: html, text
    07639647efe6cfe6dbc643b8fae13c3dd153c528 Fri Jan 17 19:07:18 2025 -0800
    work on docker utils build
  • lines changed 20, context: html, text, full: html, text
    4d1132fe8af3037e9bc3f4ff419151cebcc10fc1 Sun Jan 19 11:28:49 2025 -0800
    userApps working as before on hgwdev
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    3b0285d0e228ae555eb878346c42c46906e2f8db Tue Jan 28 15:50:45 2025 -0800
    Staging the COSMIC v101 for hg38 and hg19 on hgwbeta, refs #34904
  • lines changed 1, context: html, text, full: html, text
    36fc997c4663f577c338a94d24cd968836c655af Fri Jan 31 12:23:27 2025 -0800
    Releasing and announcing the COSMIC v101 for hg38 and hg19, refs #34904
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    3b0285d0e228ae555eb878346c42c46906e2f8db Tue Jan 28 15:50:45 2025 -0800
    Staging the COSMIC v101 for hg38 and hg19 on hgwbeta, refs #34904
  • lines changed 1, context: html, text, full: html, text
    36fc997c4663f577c338a94d24cd968836c655af Fri Jan 31 12:23:27 2025 -0800
    Releasing and announcing the COSMIC v101 for hg38 and hg19, refs #34904
  • lines changed 13, context: html, text, full: html, text
    2af584d7e6278e3cc84e53d7107563b1b72fe99a Fri Jan 31 12:29:49 2025 -0800
    Replacing the COSMIC stanza for hg38, refs #34904
• src/hg/pslCDnaFilter/makefile
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    07639647efe6cfe6dbc643b8fae13c3dd153c528 Fri Jan 17 19:07:18 2025 -0800
    work on docker utils build
• src/hg/pslCDnaFilter/pslCDnaFilter.c
  • lines changed 7, context: html, text, full: html, text
    07639647efe6cfe6dbc643b8fae13c3dd153c528 Fri Jan 17 19:07:18 2025 -0800
    work on docker utils build
• src/hg/utils/automation/doRepeatMasker.pl
  • lines changed 5, context: html, text, full: html, text
    909ff18f8b72ca31971508ca13eed84633e1dc1e Sun Feb 2 10:24:45 2025 -0800
    upgrading to new version of RM no redmine
• src/hg/utils/bedExtendRanges/makefile
  • lines changed 19, context: html, text, full: html, text
    07639647efe6cfe6dbc643b8fae13c3dd153c528 Fri Jan 17 19:07:18 2025 -0800
    work on docker utils build
• src/hg/utils/chainToBigChain/makefile
  • lines changed 51, context: html, text, full: html, text
    4d1132fe8af3037e9bc3f4ff419151cebcc10fc1 Sun Jan 19 11:28:49 2025 -0800
    userApps working as before on hgwdev
• src/hg/utils/gff3ToGenePred/makefile
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    07639647efe6cfe6dbc643b8fae13c3dd153c528 Fri Jan 17 19:07:18 2025 -0800
    work on docker utils build
• src/hg/utils/gtfToGenePred/makefile
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    07639647efe6cfe6dbc643b8fae13c3dd153c528 Fri Jan 17 19:07:18 2025 -0800
    work on docker utils build
• src/hg/utils/hubCheck/makefile
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    07639647efe6cfe6dbc643b8fae13c3dd153c528 Fri Jan 17 19:07:18 2025 -0800
    work on docker utils build
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    1c002ea441ef48d4580156e0e80f23a8b7dc3eec Sun Jan 19 13:05:19 2025 -0800
    CGI loaders working
• src/hg/utils/makeTableList/makefile
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    07639647efe6cfe6dbc643b8fae13c3dd153c528 Fri Jan 17 19:07:18 2025 -0800
    work on docker utils build
• src/hg/utils/overlapSelect/makefile
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    07639647efe6cfe6dbc643b8fae13c3dd153c528 Fri Jan 17 19:07:18 2025 -0800
    work on docker utils build
  • lines changed 0, context: html, text, full: html, text
    4d1132fe8af3037e9bc3f4ff419151cebcc10fc1 Sun Jan 19 11:28:49 2025 -0800
    userApps working as before on hgwdev
• src/hg/utils/overlapSelect/overlapSelect.c
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    07639647efe6cfe6dbc643b8fae13c3dd153c528 Fri Jan 17 19:07:18 2025 -0800
    work on docker utils build
• src/hg/utils/pslLiftSubrangeBlat/makefile
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    07639647efe6cfe6dbc643b8fae13c3dd153c528 Fri Jan 17 19:07:18 2025 -0800
    work on docker utils build
• src/hg/utils/pslToBigPsl/makefile
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    07639647efe6cfe6dbc643b8fae13c3dd153c528 Fri Jan 17 19:07:18 2025 -0800
    work on docker utils build
  • lines changed 1, context: html, text, full: html, text
    1c002ea441ef48d4580156e0e80f23a8b7dc3eec Sun Jan 19 13:05:19 2025 -0800
    CGI loaders working
• src/hg/utils/pslToBigPsl/tests/makefile
  • lines changed 1, context: html, text, full: html, text
    07639647efe6cfe6dbc643b8fae13c3dd153c528 Fri Jan 17 19:07:18 2025 -0800
    work on docker utils build
• src/hg/utils/tdbQuery/makefile
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    07639647efe6cfe6dbc643b8fae13c3dd153c528 Fri Jan 17 19:07:18 2025 -0800
    work on docker utils build
• src/inc/cgiLoader.mk
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    07639647efe6cfe6dbc643b8fae13c3dd153c528 Fri Jan 17 19:07:18 2025 -0800
    work on docker utils build
  • lines changed 21, context: html, text, full: html, text
    4d1132fe8af3037e9bc3f4ff419151cebcc10fc1 Sun Jan 19 11:28:49 2025 -0800
    userApps working as before on hgwdev
  • lines changed 14, context: html, text, full: html, text
    1c002ea441ef48d4580156e0e80f23a8b7dc3eec Sun Jan 19 13:05:19 2025 -0800
    CGI loaders working
  • lines changed 1, context: html, text, full: html, text
    3542507725a5bdeceaf09f2e8376bbe5808a6a08 Sun Jan 19 13:45:13 2025 -0800
    use user cgi-bin for default make
• src/inc/cgiVars.mk
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    1c002ea441ef48d4580156e0e80f23a8b7dc3eec Sun Jan 19 13:05:19 2025 -0800
    CGI loaders working
  • lines changed 4, context: html, text, full: html, text
    3542507725a5bdeceaf09f2e8376bbe5808a6a08 Sun Jan 19 13:45:13 2025 -0800
    use user cgi-bin for default make
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    8f59e41056ede9739e9b9ea81d52443c18ad90dd Tue Jan 21 22:14:04 2025 -0800
    with specific user
• src/inc/cgi_build_rules.mk
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    1c002ea441ef48d4580156e0e80f23a8b7dc3eec Sun Jan 19 13:05:19 2025 -0800
    CGI loaders working
• src/inc/common.mk
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    07639647efe6cfe6dbc643b8fae13c3dd153c528 Fri Jan 17 19:07:18 2025 -0800
    work on docker utils build
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    4d1132fe8af3037e9bc3f4ff419151cebcc10fc1 Sun Jan 19 11:28:49 2025 -0800
    userApps working as before on hgwdev
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    8f59e41056ede9739e9b9ea81d52443c18ad90dd Tue Jan 21 22:14:04 2025 -0800
    with specific user
• src/inc/srcVersion.h
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    6bf2d8427849abe775b422f71dae6665021a0ff8 Mon Feb 3 11:20:38 2025 -0800
    New version number v477
• src/inc/userApp.mk
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    07639647efe6cfe6dbc643b8fae13c3dd153c528 Fri Jan 17 19:07:18 2025 -0800
    work on docker utils build
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    4d1132fe8af3037e9bc3f4ff419151cebcc10fc1 Sun Jan 19 11:28:49 2025 -0800
    userApps working as before on hgwdev
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    c2da02cbbc11577b49eddb96740144ec4f24e872 Tue Jan 28 18:59:29 2025 -0800
    add script to check that SEMI_STATIC userApp are linked with only the allowed shared libraries
• src/makefile
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    07639647efe6cfe6dbc643b8fae13c3dd153c528 Fri Jan 17 19:07:18 2025 -0800
    work on docker utils build
• src/utils/bedToBigBed/makefile
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    4d1132fe8af3037e9bc3f4ff419151cebcc10fc1 Sun Jan 19 11:28:49 2025 -0800
    userApps working as before on hgwdev
• src/utils/makefile
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    07639647efe6cfe6dbc643b8fae13c3dd153c528 Fri Jan 17 19:07:18 2025 -0800
    work on docker utils build
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    7478677e5ba8806f2ffde474524dccd6fc37ed72 Thu Jan 30 20:10:01 2025 -0800
    added my old tabFmt command due to popular demand
• src/utils/qa/weeklybld/buildEnv.csh
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    7485e5ac56ea6f9989d25ac08dbdca5cfab4380f Mon Feb 3 11:20:15 2025 -0800
    v477 final build, refs #35106
• src/utils/qa/weeklybld/makeUserApps.csh
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    f1e2c1529d1222a0793a30bc4997a65e6f6694c9 Wed Jan 22 07:40:55 2025 -0800
    run docker as current user
• src/utils/qa/weeklybld/userApps.dockerfile
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    8f59e41056ede9739e9b9ea81d52443c18ad90dd Tue Jan 21 22:14:04 2025 -0800
    with specific user
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    f1e2c1529d1222a0793a30bc4997a65e6f6694c9 Wed Jan 22 07:40:55 2025 -0800
    run docker as current user
• src/utils/qa/weeklybld/userAppsCheckLinking
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    c2da02cbbc11577b49eddb96740144ec4f24e872 Tue Jan 28 18:59:29 2025 -0800
    add script to check that SEMI_STATIC userApp are linked with only the allowed shared libraries
• src/utils/qa/weeklybld/userAppsCompileInDocker
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    8f59e41056ede9739e9b9ea81d52443c18ad90dd Tue Jan 21 22:14:04 2025 -0800
    with specific user
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    f1e2c1529d1222a0793a30bc4997a65e6f6694c9 Wed Jan 22 07:40:55 2025 -0800
    run docker as current user
  • lines changed 11, context: html, text, full: html, text
    c2da02cbbc11577b49eddb96740144ec4f24e872 Tue Jan 28 18:59:29 2025 -0800
    add script to check that SEMI_STATIC userApp are linked with only the allowed shared libraries
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    ed2c9e2f464996fffa38546987be244ada38c07a Fri Jan 31 19:42:06 2025 -0800
    echo the docker run command when building userApps
• src/utils/qa/weeklybld/userAppsCreateDockerImage
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    8f59e41056ede9739e9b9ea81d52443c18ad90dd Tue Jan 21 22:14:04 2025 -0800
    with specific user
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    f1e2c1529d1222a0793a30bc4997a65e6f6694c9 Wed Jan 22 07:40:55 2025 -0800
    run docker as current user
• src/utils/tabFmt/makefile
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    7478677e5ba8806f2ffde474524dccd6fc37ed72 Thu Jan 30 20:10:01 2025 -0800
    added my old tabFmt command due to popular demand
• src/utils/tabFmt/tabFmt.c
  • lines changed 274, context: html, text, full: html, text
    7478677e5ba8806f2ffde474524dccd6fc37ed72 Thu Jan 30 20:10:01 2025 -0800
    added my old tabFmt command due to popular demand
• src/utils/tabFmt/tests/expected/defaultTest.txt
  • lines changed 8, context: html, text, full: html, text
    7478677e5ba8806f2ffde474524dccd6fc37ed72 Thu Jan 30 20:10:01 2025 -0800
    added my old tabFmt command due to popular demand
• src/utils/tabFmt/tests/expected/numRightPassNoTabTest.txt
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    7478677e5ba8806f2ffde474524dccd6fc37ed72 Thu Jan 30 20:10:01 2025 -0800
    added my old tabFmt command due to popular demand
• src/utils/tabFmt/tests/expected/numRightTest.txt
  • lines changed 8, context: html, text, full: html, text
    7478677e5ba8806f2ffde474524dccd6fc37ed72 Thu Jan 30 20:10:01 2025 -0800
    added my old tabFmt command due to popular demand
• src/utils/tabFmt/tests/expected/passNoTabTest.txt
  • lines changed 13, context: html, text, full: html, text
    7478677e5ba8806f2ffde474524dccd6fc37ed72 Thu Jan 30 20:10:01 2025 -0800
    added my old tabFmt command due to popular demand
• src/utils/tabFmt/tests/expected/rightTest.txt
  • lines changed 8, context: html, text, full: html, text
    7478677e5ba8806f2ffde474524dccd6fc37ed72 Thu Jan 30 20:10:01 2025 -0800
    added my old tabFmt command due to popular demand
• src/utils/tabFmt/tests/expected/specialTest.txt
  • lines changed 3, context: html, text, full: html, text
    7478677e5ba8806f2ffde474524dccd6fc37ed72 Thu Jan 30 20:10:01 2025 -0800
    added my old tabFmt command due to popular demand
• src/utils/tabFmt/tests/input/basic.tab
  • lines changed 8, context: html, text, full: html, text
    7478677e5ba8806f2ffde474524dccd6fc37ed72 Thu Jan 30 20:10:01 2025 -0800
    added my old tabFmt command due to popular demand
• src/utils/tabFmt/tests/input/numRightPassNoTab.tab
  • lines changed 15, context: html, text, full: html, text
    7478677e5ba8806f2ffde474524dccd6fc37ed72 Thu Jan 30 20:10:01 2025 -0800
    added my old tabFmt command due to popular demand
• src/utils/tabFmt/tests/input/special.tab
  • lines changed 3, context: html, text, full: html, text
    7478677e5ba8806f2ffde474524dccd6fc37ed72 Thu Jan 30 20:10:01 2025 -0800
    added my old tabFmt command due to popular demand
• src/utils/tabFmt/tests/input/statsLabels.tab
  • lines changed 13, context: html, text, full: html, text
    7478677e5ba8806f2ffde474524dccd6fc37ed72 Thu Jan 30 20:10:01 2025 -0800
    added my old tabFmt command due to popular demand
• src/utils/tabFmt/tests/makefile
  • lines changed 39, context: html, text, full: html, text
    7478677e5ba8806f2ffde474524dccd6fc37ed72 Thu Jan 30 20:10:01 2025 -0800
    added my old tabFmt command due to popular demand

• lines changed: 2414
• files changed: 104