All File Changes

v431_base to v432_preview (2022-05-16 to 2022-05-23) v432

• src/hg/hgGateway/hgGateway.c
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    2566e43720a9ab0b37deeb281b6634cb209415d9 Mon May 16 17:49:50 2022 -0700
    Exclude genark hubs that are in dbDb from our sense of 'native assemblies' when doing a public hub search
• src/hg/hgTracks/bigRmskTrack.c
  • lines changed 2, context: html, text, full: html, text
    b24e3fe29bf4118ec0dd5804d363499a11db4311 Fri May 20 11:52:39 2022 -0700
    correctly display all items while in dense mode or original pack mode refs #29464
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    33f285063b852a8a7b9d44e36585fb77a852c677 Fri May 20 13:35:16 2022 -0700
    fix broken interpretation of the palette colors for drawing refs #29464
• src/hg/hgTracks/hgTracks.c
  • lines changed 4, context: html, text, full: html, text
    e07889d47e6f959eb8a7ea151ecf09ab6d9439d3 Tue May 17 06:32:30 2022 -0700
    adding invisible link so can find web crawlers, no redmine, making now so can analyze the data in a few months
  • lines changed 20, context: html, text, full: html, text
    0faea16954ed530c537f5aa5d0cf8e0e33441b8a Fri May 20 17:21:22 2022 -0700
    now correctly show alias names on hgTracks chromInfoPage when using chromAliasBb file refs #26360
• src/hg/hgTracks/simpleTracks.c
  • lines changed 2, context: html, text, full: html, text
    b79de32ff03612a0f5666665a45c21557c0bbf90 Thu May 19 15:04:12 2022 -0700
    Fix minor SQLINJECTION v2, param to sqlGetField should be using sqlSafef functions. refs #29274
• src/hg/hgTracks/wigTrack.c
  • lines changed 17, context: html, text, full: html, text
    ead294ac0ef6c54887676ac1fcb06172d3c71d9f Wed May 18 17:23:00 2022 -0700
    first cut at sequence logo with four bases
• src/hg/htdocs/goldenPath/help/bigWig.html
  • lines changed 25, context: html, text, full: html, text
    eb6c298ad69f65ae5d92c6e96fafa034da34286a Mon May 16 15:12:21 2022 -0700
    Adding an anchor to a new Ex4 dynseq example on bigWig.html refs #28499
  • lines changed 2, context: html, text, full: html, text
    ce69d691ca993477ded60e556750bea544ae8219 Mon May 16 15:16:53 2022 -0700
    Edit to bigWig.html refs #28499
  • lines changed 8, context: html, text, full: html, text
    7974683a1a13cb0619427249b456087c4e481f2a Tue May 17 12:02:57 2022 -0700
    Adding image to dynseq bigWig log=on at Surgar request
  • lines changed 2, context: html, text, full: html, text
    eb4adbf30d849f0a7301359e0153c0932b2660e6 Tue May 17 12:10:20 2022 -0700
    Fixing dynaseq-> dynseq typo in example custom track text
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 4, context: html, text, full: html, text
    420ef990ccc716f159f4b6f01265293abbe0d015 Tue May 17 12:08:46 2022 -0700
    Documenting logo dynaseq refs #28499
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html
  • lines changed 4, context: html, text, full: html, text
    420ef990ccc716f159f4b6f01265293abbe0d015 Tue May 17 12:08:46 2022 -0700
    Documenting logo dynaseq refs #28499
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 9, context: html, text, full: html, text
    420ef990ccc716f159f4b6f01265293abbe0d015 Tue May 17 12:08:46 2022 -0700
    Documenting logo dynaseq refs #28499
  • lines changed 2, context: html, text, full: html, text
    431855fa3001f72757a287498bdfdf278c032d1a Wed May 18 08:04:56 2022 -0700
    Adding a link to example of logo dynseq from trackDbLibrary refs #28499
• src/hg/htdocs/goldenPath/help/twoBit.html
  • lines changed 28, context: html, text, full: html, text
    02fe6028996477c06ad88319e254475bd88127fe Thu May 19 11:54:33 2022 -0700
    Adding examples on twoBit.html page about extracting squences refs MLQ #29456
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 19, context: html, text, full: html, text
    791195a390b6bf8faf3194648e27b9fb208b9365 Thu May 19 14:52:17 2022 -0700
    added explicit opening of evaSnp tracks to release announcement. Too late for most people, but I just sent the link to someone and wanted them to see the track open and obvious
• src/hg/htdocs/images/dynseq.png
  • lines changed 0, context: html, text, full: html, text
    7974683a1a13cb0619427249b456087c4e481f2a Tue May 17 12:02:57 2022 -0700
    Adding image to dynseq bigWig log=on at Surgar request
  • lines changed 0, context: html, text, full: html, text
    eb4adbf30d849f0a7301359e0153c0932b2660e6 Tue May 17 12:10:20 2022 -0700
    Fixing dynaseq-> dynseq typo in example custom track text
• src/hg/htdocs/images/rmskClassicPack.jpg
  • lines changed 0, context: html, text, full: html, text
    6d1528f371ec8c7bfe19d0fe3f5a154a1ac82603 Tue May 17 09:50:20 2022 -0700
    images for new style repeat masker description page in place of the base64 encoding no redmine
• src/hg/htdocs/images/rmskDense.jpg
  • lines changed 0, context: html, text, full: html, text
    6d1528f371ec8c7bfe19d0fe3f5a154a1ac82603 Tue May 17 09:50:20 2022 -0700
    images for new style repeat masker description page in place of the base64 encoding no redmine
• src/hg/htdocs/images/rmskDense.png
  • lines changed 0, context: html, text, full: html, text
    6da2767e61846dd7fd6873f9897b72c56622dcda Sat May 21 20:48:28 2022 -0700
    rename rmsk PNG files
• src/hg/htdocs/images/rmskDenseMode.png
  • lines changed 0, context: html, text, full: html, text
    fd43f388f50bed0f72f6d4c8d10eb13f63ead806 Sat May 21 19:37:47 2022 -0700
    restores sharp images to CHM13 repeat masker
  • lines changed 0, context: html, text, full: html, text
    6da2767e61846dd7fd6873f9897b72c56622dcda Sat May 21 20:48:28 2022 -0700
    rename rmsk PNG files
• src/hg/htdocs/images/rmskFull.jpg
  • lines changed 0, context: html, text, full: html, text
    6d1528f371ec8c7bfe19d0fe3f5a154a1ac82603 Tue May 17 09:50:20 2022 -0700
    images for new style repeat masker description page in place of the base64 encoding no redmine
• src/hg/htdocs/images/rmskFull.png
  • lines changed 0, context: html, text, full: html, text
    6da2767e61846dd7fd6873f9897b72c56622dcda Sat May 21 20:48:28 2022 -0700
    rename rmsk PNG files
• src/hg/htdocs/images/rmskFullMode.png
  • lines changed 0, context: html, text, full: html, text
    fd43f388f50bed0f72f6d4c8d10eb13f63ead806 Sat May 21 19:37:47 2022 -0700
    restores sharp images to CHM13 repeat masker
  • lines changed 0, context: html, text, full: html, text
    6da2767e61846dd7fd6873f9897b72c56622dcda Sat May 21 20:48:28 2022 -0700
    rename rmsk PNG files
• src/hg/htdocs/images/rmskLine2fragments.jpg
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    5f4b98797c27ade66a4c599dcc5f46f1cd4458fb Thu May 19 17:18:33 2022 -0700
    more images for rmsk description page refs #29464
• src/hg/htdocs/images/rmskLine2overlap.jpg
  • lines changed 0, context: html, text, full: html, text
    5f4b98797c27ade66a4c599dcc5f46f1cd4458fb Thu May 19 17:18:33 2022 -0700
    more images for rmsk description page refs #29464
• src/hg/htdocs/images/rmskLine2unaligned.jpg
  • lines changed 0, context: html, text, full: html, text
    5f4b98797c27ade66a4c599dcc5f46f1cd4458fb Thu May 19 17:18:33 2022 -0700
    more images for rmsk description page refs #29464
• src/hg/htdocs/images/rmskOrigPack.png
  • lines changed 0, context: html, text, full: html, text
    6da2767e61846dd7fd6873f9897b72c56622dcda Sat May 21 20:48:28 2022 -0700
    rename rmsk PNG files
• src/hg/htdocs/images/rmskOrigPackMode.png
  • lines changed 0, context: html, text, full: html, text
    fd43f388f50bed0f72f6d4c8d10eb13f63ead806 Sat May 21 19:37:47 2022 -0700
    restores sharp images to CHM13 repeat masker
  • lines changed 0, context: html, text, full: html, text
    6da2767e61846dd7fd6873f9897b72c56622dcda Sat May 21 20:48:28 2022 -0700
    rename rmsk PNG files
• src/hg/htdocs/images/rmskPack.jpg
  • lines changed 0, context: html, text, full: html, text
    6d1528f371ec8c7bfe19d0fe3f5a154a1ac82603 Tue May 17 09:50:20 2022 -0700
    images for new style repeat masker description page in place of the base64 encoding no redmine
• src/hg/htdocs/images/rmskPack.png
  • lines changed 0, context: html, text, full: html, text
    6da2767e61846dd7fd6873f9897b72c56622dcda Sat May 21 20:48:28 2022 -0700
    rename rmsk PNG files
• src/hg/htdocs/images/rmskPackMode.png
  • lines changed 0, context: html, text, full: html, text
    fd43f388f50bed0f72f6d4c8d10eb13f63ead806 Sat May 21 19:37:47 2022 -0700
    restores sharp images to CHM13 repeat masker
  • lines changed 0, context: html, text, full: html, text
    6da2767e61846dd7fd6873f9897b72c56622dcda Sat May 21 20:48:28 2022 -0700
    rename rmsk PNG files
• src/hg/htdocs/images/rmskSine384.jpg
  • lines changed 0, context: html, text, full: html, text
    5f4b98797c27ade66a4c599dcc5f46f1cd4458fb Thu May 19 17:18:33 2022 -0700
    more images for rmsk description page refs #29464
• src/hg/lib/barChartUi.c
  • lines changed 1, context: html, text, full: html, text
    ec19d3999dc5f2d7539c02e1e8e6719fec942038 Wed May 18 11:29:47 2022 -0700
    barChart stats files weren't checking the alternate GBDB file path, refs #29425
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 1, context: html, text, full: html, text
    b0838670c54b6a17b3971c11e41e84bacc89b6f7 Wed May 18 12:35:25 2022 -0700
    adding GCA_000297895.2_ASM29789v2 Pacific oyster per user request no redmine
• src/hg/makeDb/doc/asmHubs/verifyOnDownload.sh
  • lines changed 6, context: html, text, full: html, text
    bfb5934c86c6e897da243f2b9277987dc8392ce3 Wed May 18 14:01:59 2022 -0700
    the new repeat masker track has lowered the minimum amount of tracks for a valid hub no redmine
• src/hg/makeDb/doc/chm13v2.0userData/build.txt
  • lines changed 1, context: html, text, full: html, text
    6da2767e61846dd7fd6873f9897b72c56622dcda Sat May 21 20:48:28 2022 -0700
    rename rmsk PNG files
• src/hg/makeDb/doc/chm13v2.0userData/html/t2tRepeatMasker-dense-mode.png
  • lines changed 0, context: html, text, full: html, text
    fd43f388f50bed0f72f6d4c8d10eb13f63ead806 Sat May 21 19:37:47 2022 -0700
    restores sharp images to CHM13 repeat masker
• src/hg/makeDb/doc/chm13v2.0userData/html/t2tRepeatMasker-full-mode.png
  • lines changed 0, context: html, text, full: html, text
    fd43f388f50bed0f72f6d4c8d10eb13f63ead806 Sat May 21 19:37:47 2022 -0700
    restores sharp images to CHM13 repeat masker
• src/hg/makeDb/doc/chm13v2.0userData/html/t2tRepeatMasker-orig-pack-mode.png
  • lines changed 0, context: html, text, full: html, text
    fd43f388f50bed0f72f6d4c8d10eb13f63ead806 Sat May 21 19:37:47 2022 -0700
    restores sharp images to CHM13 repeat masker
• src/hg/makeDb/doc/chm13v2.0userData/html/t2tRepeatMasker-pack-mode.png
  • lines changed 0, context: html, text, full: html, text
    fd43f388f50bed0f72f6d4c8d10eb13f63ead806 Sat May 21 19:37:47 2022 -0700
    restores sharp images to CHM13 repeat masker
• src/hg/makeDb/doc/chm13v2.0userData/html/t2tRepeatMasker.html
  • lines changed 10425, context: html, text, full: html, text
    b4433df297256fc1e9d5d797aa8acc9a4ac732f5 Tue May 17 10:04:32 2022 -0700
    replace the base64 encoded png with reference to jpg images no redmine
  • lines changed 264, context: html, text, full: html, text
    ea93bef09b508ad550f5cd2f24357025ef939a31 Thu May 19 17:29:03 2022 -0700
    element drawing examples now replaced with URLs to jpg images refs #29464
  • lines changed 272, context: html, text, full: html, text
    fd43f388f50bed0f72f6d4c8d10eb13f63ead806 Sat May 21 19:37:47 2022 -0700
    restores sharp images to CHM13 repeat masker
• src/hg/makeDb/doc/chm13v2.0userData/trackDb/t2tRepeatMasker.trackDb.txt
  • lines changed 1, context: html, text, full: html, text
    e9b23f957d397c61d0447bfc6dcaeb3d5c4d9ec7 Thu May 19 15:24:37 2022 -0700
    updated incorrect path not detected by repeat masker
• src/hg/makeDb/doc/hg19.txt
  • lines changed 11, context: html, text, full: html, text
    9a7166e85eed31008c9235b2d219c5705f6613f6 Mon May 23 08:16:52 2022 -0700
    adding revel subtrack for locations where the scores differ, refs #29475
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    b0838670c54b6a17b3971c11e41e84bacc89b6f7 Wed May 18 12:35:25 2022 -0700
    adding GCA_000297895.2_ASM29789v2 Pacific oyster per user request no redmine
• src/hg/makeDb/doc/wuhCor1/pond.txt
  • lines changed 12, context: html, text, full: html, text
    0122974795a3f2b9261ad4cccda2b0245c5a7731 Mon May 23 03:48:36 2022 -0700
    updating natural selection track on wuhCor1, refs #29478
• src/hg/makeDb/hgTrackDb/hgTrackDb.c
  • lines changed 2, context: html, text, full: html, text
    87479c84a64c6528b33331467ba6f22ff769e50c Fri May 20 13:12:12 2022 -0700
    don't assume that html lines haven't already added ".html"
• src/hg/makeDb/revel/revel.as
  • lines changed 14, context: html, text, full: html, text
    9a7166e85eed31008c9235b2d219c5705f6613f6 Mon May 23 08:16:52 2022 -0700
    adding revel subtrack for locations where the scores differ, refs #29475
• src/hg/makeDb/scripts/pondToBed
  • lines changed 109, context: html, text, full: html, text
    0122974795a3f2b9261ad4cccda2b0245c5a7731 Mon May 23 03:48:36 2022 -0700
    updating natural selection track on wuhCor1, refs #29478
• src/hg/makeDb/trackDb/human/constraintSuper.html
  • lines changed 7, context: html, text, full: html, text
    4f77004a3c34cc23be70bee9e2e833c339cf943d Wed May 18 02:00:44 2022 -0700
    removing merge conflict markers from a track docs html file, my fault
• src/hg/makeDb/trackDb/human/hg38/reMap.ra
  • lines changed 1, context: html, text, full: html, text
    57af71a02b8962af5be514126a97d60f9f563776 Mon May 23 07:13:39 2022 -0700
    Adding a change to ReMap to solve the problem of parent configuration filter not working. ref #28960
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    1d071f07ea1c27fe8251862799a2f5f3f22d7d54 Wed May 18 10:23:18 2022 -0700
    add a release tag to an experimental track
  • lines changed 44, context: html, text, full: html, text
    ead294ac0ef6c54887676ac1fcb06172d3c71d9f Wed May 18 17:23:00 2022 -0700
    first cut at sequence logo with four bases
• src/hg/makeDb/trackDb/human/revel.html
  • lines changed 32, context: html, text, full: html, text
    b9e9c95d252ccc45abcc72febdd019227ee0786e Mon May 23 08:56:44 2022 -0700
    doc'ing new revel subtrack, refs #29475
• src/hg/makeDb/trackDb/human/revel.ra
  • lines changed 26, context: html, text, full: html, text
    9a7166e85eed31008c9235b2d219c5705f6613f6 Mon May 23 08:16:52 2022 -0700
    adding revel subtrack for locations where the scores differ, refs #29475
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    dcbedab26adcc6bc9a477efffcd9e0b1767574ce Wed May 18 17:36:14 2022 -0700
    add logo trackDb variable to bigWig support
  • lines changed 1, context: html, text, full: html, text
    57af71a02b8962af5be514126a97d60f9f563776 Mon May 23 07:13:39 2022 -0700
    Adding a change to ReMap to solve the problem of parent configuration filter not working. ref #28960
• src/hg/makeDb/trackDb/virus/wuhCor1/pond.ra
  • lines changed 86, context: html, text, full: html, text
    0122974795a3f2b9261ad4cccda2b0245c5a7731 Mon May 23 03:48:36 2022 -0700
    updating natural selection track on wuhCor1, refs #29478
• src/hg/ratStuff/mafCounts/mafCounts.c
  • lines changed 136, context: html, text, full: html, text
    0eb7bb9aa4577cfa8dbce54d835fd39ced613785 Wed May 18 11:03:21 2022 -0700
    first cut of mafCounts, a utility to help build a sequence logo track from a MAF file
• src/hg/ratStuff/mafCounts/makefile
  • lines changed 3, context: html, text, full: html, text
    0eb7bb9aa4577cfa8dbce54d835fd39ced613785 Wed May 18 11:03:21 2022 -0700
    first cut of mafCounts, a utility to help build a sequence logo track from a MAF file
• src/hg/utils/automation/aliasBedToCt.pl
  • lines changed 14, context: html, text, full: html, text
    0aa6ca4913057168625becbe9dde31c55116272e Tue May 17 16:21:57 2022 -0700
    better use of sizesIsBb for alias.bb test generation no redmine
• src/hg/utils/automation/aliasTextToBed.pl
  • lines changed 1, context: html, text, full: html, text
    1386b5f91d8d635cd76b984482e460dd05464237 Tue May 17 17:06:35 2022 -0700
    correctly sorting bed file output no redmine
• src/hg/utils/automation/asmHubRepeatMasker.sh
  • lines changed 33, context: html, text, full: html, text
    7c934496e3650521dc129b65658326d542cbd20b Tue May 17 12:52:51 2022 -0700
    trying out new rmsk format bigBed joined display no redmine
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    f1b5eb49959cc16f05675a7f5e254bc787b99409 Wed May 18 09:08:32 2022 -0700
    better recognition of the align file presence no redmine
• src/hg/utils/automation/asmHubRmskJoinAlign.pl
  • lines changed 571, context: html, text, full: html, text
    7c934496e3650521dc129b65658326d542cbd20b Tue May 17 12:52:51 2022 -0700
    trying out new rmsk format bigBed joined display no redmine
  • lines changed 264, context: html, text, full: html, text
    a8b96119d44c0455a215ea0000c001bc4a7b9074 Thu May 19 17:34:51 2022 -0700
    element drawing examples now replaced with URLs to jpg images refs #29464
• src/hg/utils/automation/asmHubTrackDb.sh
  • lines changed 29, context: html, text, full: html, text
    7c934496e3650521dc129b65658326d542cbd20b Tue May 17 12:52:51 2022 -0700
    trying out new rmsk format bigBed joined display no redmine
  • lines changed 8, context: html, text, full: html, text
    463d8ccfcc27e9ea403fbf2ed74c344bfbf3897c Wed May 18 13:10:50 2022 -0700
    correct if statements to separate the two types of RM tracks no redmine
  • lines changed 11, context: html, text, full: html, text
    1268543255ec6202fedc7d12bf2054d031f2fb89 Thu May 19 15:44:49 2022 -0700
    the new rmsk track can be done without the align file refs #29464
• src/hg/utils/automation/doAssemblyHub.pl
  • lines changed 3, context: html, text, full: html, text
    7c934496e3650521dc129b65658326d542cbd20b Tue May 17 12:52:51 2022 -0700
    trying out new rmsk format bigBed joined display no redmine
  • lines changed 1, context: html, text, full: html, text
    0aa6ca4913057168625becbe9dde31c55116272e Tue May 17 16:21:57 2022 -0700
    better use of sizesIsBb for alias.bb test generation no redmine
• src/hg/utils/automation/doRepeatMasker.pl
  • lines changed 26, context: html, text, full: html, text
    7c934496e3650521dc129b65658326d542cbd20b Tue May 17 12:52:51 2022 -0700
    trying out new rmsk format bigBed joined display no redmine
• src/hg/utils/otto/decipher/decipherWrapper.sh
  • lines changed 1, context: html, text, full: html, text
    f594c0e37b16d1fabcd9a58211de4a04356ccfde Tue May 17 12:25:33 2022 -0700
    Removing Chris from recipient, decipher had been off for a long time and was recently re-enabled. No RM
• src/utils/qa/weeklybld/buildEnv.csh
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    49a467bc5b71254e0fd2b53ef4b5b6c02cff3261 Mon May 23 10:13:37 2022 -0700
    v432 preview1, refs #29479

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• files changed: 82