All File Changes

v489_base to v490_preview (2025-10-13 to 2025-10-20) v490

• confs/hgwbeta.hg.conf
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    f20b76233a4fa3a58bdbca88cf0f6ad5d5a34fc1 Sun Oct 19 01:11:15 2025 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/cirm/gateway/htdocs/sspsygeneTimeline.html
  • lines changed 3, context: html, text, full: html, text
    26d57aa392b8bbbd106a631474cd027abf1e5fdf Tue Oct 14 14:51:31 2025 -0700
    Adding Yale link to 2025 milestone spreadsheet in mermaid code timeline page
  • lines changed 9, context: html, text, full: html, text
    31b411ea6756d18925d33cce11834319376700ee Tue Oct 14 14:59:51 2025 -0700
    Adding scripps, broad, sing links to 2025 milestone spreadsheet in mermaid code timeline page
  • lines changed 9, context: html, text, full: html, text
    9e2b362b08d98f124730f55fcff4254d97fcb158 Thu Oct 16 12:12:58 2025 -0700
    Adding UCLA, MiNND, WUSTL spreadsheet link clicks on milestone mermaid chart
• src/hg/hgGene/gtex.c
  • lines changed 1, context: html, text, full: html, text
    4d6761a82363a6853606d6b61f209214b49bb6b4 Wed Oct 15 13:57:00 2025 -0700
    fix problem with gtex and quickLift.
• src/hg/hgHubConnect/hooks/pre-create.c
  • lines changed 1, context: html, text, full: html, text
    c9f42961046e744998bbaf939cfd3e7a37fd117f Tue Oct 14 02:58:59 2025 -0700
    changing how hgcentral connection is treated when an API key is supplied, open a connection and close it right afterwards, to make sure that no sleeping CGIs clog mysql connections, refs #36498
• src/hg/hgHubConnect/hooks/pre-finish.c
  • lines changed 1, context: html, text, full: html, text
    c9f42961046e744998bbaf939cfd3e7a37fd117f Tue Oct 14 02:58:59 2025 -0700
    changing how hgcentral connection is treated when an API key is supplied, open a connection and close it right afterwards, to make sure that no sleeping CGIs clog mysql connections, refs #36498
• src/hg/hgLogin/hgLogin.c
  • lines changed 28, context: html, text, full: html, text
    ee5221ac43d6831f3cdc0ed6426eea98d12916f9 Tue Oct 14 12:33:04 2025 -0700
    New hg.conf option 'login.approvedReturn' that hgLogin uses to check the validity of the returnto argument set by hgSession to prevent credential stealing. When this setting is not present the default behavior of accepting any URL in the returnto argument is active. refs #36485
• src/hg/hgLogin/hgLogin.h
  • lines changed 1, context: html, text, full: html, text
    ee5221ac43d6831f3cdc0ed6426eea98d12916f9 Tue Oct 14 12:33:04 2025 -0700
    New hg.conf option 'login.approvedReturn' that hgLogin uses to check the validity of the returnto argument set by hgSession to prevent credential stealing. When this setting is not present the default behavior of accepting any URL in the returnto argument is active. refs #36485
• src/hg/hgMirror/makefile
  • lines changed 6, context: html, text, full: html, text
    8960c1460da7d1d2e9ff402cef4e34af70078f35 Fri Oct 17 08:48:06 2025 -0700
    removing temp file cleanup from hgMirror, slows down the build, found by Chris
• src/hg/hgTracks/decorator.c
  • lines changed 17, context: html, text, full: html, text
    e3a309047a5dbe7623f7a0f1c4a3a12163fa6290 Mon Oct 13 14:09:50 2025 -0700
    Initial pass at reducing glyphs to a simple line when zoomed out, refs #35498
• src/hg/hgTracks/hgTracks.c
  • lines changed 2, context: html, text, full: html, text
    0331318608a7b0d0fae33908a6229f7bae06341a Tue Oct 14 01:58:39 2025 -0700
    change after code review, refs #36507
• src/hg/hgTracks/hgTracks.h
  • lines changed 14, context: html, text, full: html, text
    e3a309047a5dbe7623f7a0f1c4a3a12163fa6290 Mon Oct 13 14:09:50 2025 -0700
    Initial pass at reducing glyphs to a simple line when zoomed out, refs #35498
• src/hg/hgTracks/simpleTracks.c
  • lines changed 16, context: html, text, full: html, text
    e3a309047a5dbe7623f7a0f1c4a3a12163fa6290 Mon Oct 13 14:09:50 2025 -0700
    Initial pass at reducing glyphs to a simple line when zoomed out, refs #35498
• src/hg/htdocs/FAQ/FAQdownloads.html
  • lines changed 1, context: html, text, full: html, text
    630599d177b0203c123dd5e98af7a0f4102d9a05 Wed Oct 15 14:00:39 2025 -0700
    Fixing a typo feedback from CR refs #36506
• src/hg/htdocs/goldenPath/help/hubBasics.html
  • lines changed 25, context: html, text, full: html, text
    e2628a7934646bf31d8fedb840e03177790d8bf1 Tue Oct 14 08:35:25 2025 -0700
    changes based on input from Max + Lou, refs #29810
• src/hg/htdocs/goldenPath/help/posters.html
  • lines changed 12, context: html, text, full: html, text
    19c304618e4e6bb7734e8a290bee78df0956bd8c Tue Oct 14 23:44:29 2025 -0700
    Adding ASHG 2025 poster, refs #36182
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 31, context: html, text, full: html, text
    a82f9ce1e938c6bcc22065a62b93a90beb187072 Thu Oct 16 13:16:27 2025 -0700
    Releasing and announcing the SpliceAI Wildtype tracks, refs #35100
• src/hg/htdocs/images/newsArchImages/spliceAIWildtype.png
  • lines changed 0, context: html, text, full: html, text
    a82f9ce1e938c6bcc22065a62b93a90beb187072 Thu Oct 16 13:16:27 2025 -0700
    Releasing and announcing the SpliceAI Wildtype tracks, refs #35100
• src/hg/htdocs/inc/hgMyData.html
  • lines changed 4, context: html, text, full: html, text
    e6ad1f3c830ac6c46b539afb4c75d463ee323457 Fri Oct 17 11:10:05 2025 -0700
    Making changes from code review, refs #36505
• src/hg/htdocs/indexMeetings.html
  • lines changed 4, context: html, text, full: html, text
    5e5eaea033858ccd8425ecd38eb6c74bd85869a5 Wed Oct 15 13:18:56 2025 -0700
    Adding poster gallery link to the home page, refs #36182
  • lines changed 9, context: html, text, full: html, text
    d764b452ec02e93caa39423c0efe4038a28d2810 Wed Oct 15 17:34:05 2025 -0700
    Updating the home page meetings based on Bob's upcoming workshops, refs #36525
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    a82f9ce1e938c6bcc22065a62b93a90beb187072 Thu Oct 16 13:16:27 2025 -0700
    Releasing and announcing the SpliceAI Wildtype tracks, refs #35100
• src/hg/htdocs/staff.html
  • lines changed 15, context: html, text, full: html, text
    948d2a6216189ca69a2be92ee7f0b3f730c556da Fri Oct 17 12:17:59 2025 -0700
    Adding MarkD and updating our SAB members and text, refs #36420
• src/hg/inc/hdb.h
  • lines changed 3, context: html, text, full: html, text
    85e8f7400bfa53d4189f56729b3a12718f734125 Mon Oct 13 14:20:01 2025 -0700
    closing all hgcentral mysql connections before botDelay sleeping, refs #36498
  • lines changed 2, context: html, text, full: html, text
    c9f42961046e744998bbaf939cfd3e7a37fd117f Tue Oct 14 02:58:59 2025 -0700
    changing how hgcentral connection is treated when an API key is supplied, open a connection and close it right afterwards, to make sure that no sleeping CGIs clog mysql connections, refs #36498
• src/hg/inc/hubSpaceKeys.h
  • lines changed 2, context: html, text, full: html, text
    c9f42961046e744998bbaf939cfd3e7a37fd117f Tue Oct 14 02:58:59 2025 -0700
    changing how hgcentral connection is treated when an API key is supplied, open a connection and close it right afterwards, to make sure that no sleeping CGIs clog mysql connections, refs #36498
• src/hg/js/autocomplete.js
  • lines changed 2, context: html, text, full: html, text
    6ce78cec462ba1ba659db7d90cf833f4a0d1e1b9 Fri Oct 17 14:02:38 2025 -0700
    When the 'suggestTrack' input is missing that the hgTracks search box uses to call to hgSuggest, don't error out, refs #36537
• src/hg/lib/botDelay.c
  • lines changed 1, context: html, text, full: html, text
    85e8f7400bfa53d4189f56729b3a12718f734125 Mon Oct 13 14:20:01 2025 -0700
    closing all hgcentral mysql connections before botDelay sleeping, refs #36498
  • lines changed 9, context: html, text, full: html, text
    c9f42961046e744998bbaf939cfd3e7a37fd117f Tue Oct 14 02:58:59 2025 -0700
    changing how hgcentral connection is treated when an API key is supplied, open a connection and close it right afterwards, to make sure that no sleeping CGIs clog mysql connections, refs #36498
• src/hg/lib/cart.c
  • lines changed 7, context: html, text, full: html, text
    c9f42961046e744998bbaf939cfd3e7a37fd117f Tue Oct 14 02:58:59 2025 -0700
    changing how hgcentral connection is treated when an API key is supplied, open a connection and close it right afterwards, to make sure that no sleeping CGIs clog mysql connections, refs #36498
  • lines changed 1, context: html, text, full: html, text
    fdd4eaea8cdd5dd4e2d895ae3249957859eb278b Tue Oct 14 03:12:17 2025 -0700
    change after code review, refs #36477
  • lines changed 8, context: html, text, full: html, text
    80f55de280d3cc483b772c1d02dd88b6bc1cf173 Thu Oct 16 03:01:55 2025 -0700
    adding an apache logfile line when apiKey is recognized, refs #36428
• src/hg/lib/hdb.c
  • lines changed 6, context: html, text, full: html, text
    85e8f7400bfa53d4189f56729b3a12718f734125 Mon Oct 13 14:20:01 2025 -0700
    closing all hgcentral mysql connections before botDelay sleeping, refs #36498
  • lines changed 6, context: html, text, full: html, text
    c9f42961046e744998bbaf939cfd3e7a37fd117f Tue Oct 14 02:58:59 2025 -0700
    changing how hgcentral connection is treated when an API key is supplied, open a connection and close it right afterwards, to make sure that no sleeping CGIs clog mysql connections, refs #36498
• src/hg/lib/hubSpaceKeys.c
  • lines changed 11, context: html, text, full: html, text
    c9f42961046e744998bbaf939cfd3e7a37fd117f Tue Oct 14 02:58:59 2025 -0700
    changing how hgcentral connection is treated when an API key is supplied, open a connection and close it right afterwards, to make sure that no sleeping CGIs clog mysql connections, refs #36498
• src/hg/lib/hui.c
  • lines changed 1, context: html, text, full: html, text
    4eb85cbf0be0f899ae31e9c1751e49e7e9f12b01 Mon Oct 13 15:38:31 2025 -0700
    Remove stray br tag (yet again) from code that creates select tags with options, refs #36484
• src/hg/makeDb/doc/asmHubs/lastzRuns.txt
  • lines changed 81, context: html, text, full: html, text
    46d71c2759ca70678b56df2774636f689e8e2d1a Fri Oct 17 14:18:09 2025 -0700
    mm10 to rabbit(GCA_013371645.1) lastz/chain/net run for user, refs #36348
• src/hg/makeDb/doc/asmHubs/quickLiftCatchUp.sh
  • lines changed 3, context: html, text, full: html, text
    d20e29ad88a98f2ee349187337549aa047dc8343 Fri Oct 17 12:41:00 2025 -0700
    more efficient featureBits measure and show featureBits result in output refs #35575
• src/hg/makeDb/doc/hg19.txt
  • lines changed 7, context: html, text, full: html, text
    ad92b87bb799c20abccadf1f923972c1a9b6a6e7 Fri Oct 17 06:39:16 2025 -0700
    adding gnomad mpc track, ref #36531
• src/hg/makeDb/doc/hg38/LCR.txt
  • lines changed 99, context: html, text, full: html, text
    d46ff5f42bf47817b32ec4d2559074865b7f1a07 Wed Oct 15 11:38:50 2025 -0700
    checking these files from Heng Li refs #36494
• src/hg/makeDb/doc/hs1/LCR.txt
  • lines changed 88, context: html, text, full: html, text
    ebabdfea4d994cf7e35f5d46f8b60c61f9dd203d Wed Oct 15 09:23:08 2025 -0700
    checking these files from Heng Li refs #36494
  • lines changed 99, context: html, text, full: html, text
    cd2ba925d41f6ed1749ac3e6a3f799b329fe9879 Wed Oct 15 09:32:10 2025 -0700
    checking these files from Heng Li refs #36494
• src/hg/makeDb/gnomad/gnomadMpcToBed.py
  • lines changed 85, context: html, text, full: html, text
    ad92b87bb799c20abccadf1f923972c1a9b6a6e7 Fri Oct 17 06:39:16 2025 -0700
    adding gnomad mpc track, ref #36531
• src/hg/makeDb/gnomad/mpc.as
  • lines changed 23, context: html, text, full: html, text
    ad92b87bb799c20abccadf1f923972c1a9b6a6e7 Fri Oct 17 06:39:16 2025 -0700
    adding gnomad mpc track, ref #36531
• src/hg/makeDb/trackDb/evaSnp.alpha.ra
  • lines changed 156, context: html, text, full: html, text
    7e0aebd06b2394517d4700aaba6e79ec522a4734 Mon Oct 20 15:46:55 2025 -0700
    Staging evaSnp8 and one change from ENCODE 4 cCREs I also had stages, refs #36512 #34923
• src/hg/makeDb/trackDb/evaSnpContainer.html
  • lines changed 4, context: html, text, full: html, text
    7e0aebd06b2394517d4700aaba6e79ec522a4734 Mon Oct 20 15:46:55 2025 -0700
    Staging evaSnp8 and one change from ENCODE 4 cCREs I also had stages, refs #36512 #34923
• src/hg/makeDb/trackDb/human/caddSuper.html
  • lines changed 3, context: html, text, full: html, text
    f08ed4da0b23337a71fab0aa53d5be03ad668d26 Wed Oct 15 13:40:06 2025 -0700
    Bolding the interpretation of CADD scores, refs #36519
• src/hg/makeDb/trackDb/human/caddSuper1_7.html
  • lines changed 3, context: html, text, full: html, text
    f08ed4da0b23337a71fab0aa53d5be03ad668d26 Wed Oct 15 13:40:06 2025 -0700
    Bolding the interpretation of CADD scores, refs #36519
• src/hg/makeDb/trackDb/human/hg19/gnomad.html
  • lines changed 1, context: html, text, full: html, text
    bbbf04b6ba676852d67c27718a02beb7a764b76f Fri Oct 17 06:59:10 2025 -0700
    more docs for previous commit
• src/hg/makeDb/trackDb/human/hg19/gnomadMpc.html
  • lines changed 94, context: html, text, full: html, text
    ad92b87bb799c20abccadf1f923972c1a9b6a6e7 Fri Oct 17 06:39:16 2025 -0700
    adding gnomad mpc track, ref #36531
• src/hg/makeDb/trackDb/human/hg19/trackDb.gnomad.ra
  • lines changed 15, context: html, text, full: html, text
    ad92b87bb799c20abccadf1f923972c1a9b6a6e7 Fri Oct 17 06:39:16 2025 -0700
    adding gnomad mpc track, ref #36531
• src/hg/makeDb/trackDb/human/hg38/LCR.ra
  • lines changed 87, context: html, text, full: html, text
    d6c4d299f0805e129af5485dd9c120da03c28677 Wed Oct 15 12:13:37 2025 -0700
    checking these LCR files from Heng Li refs #36494
• src/hg/makeDb/trackDb/human/hg38/LCRs.html
  • lines changed 48, context: html, text, full: html, text
    d6c4d299f0805e129af5485dd9c120da03c28677 Wed Oct 15 12:13:37 2025 -0700
    checking these LCR files from Heng Li refs #36494
• src/hg/makeDb/trackDb/human/hg38/clsLongReadRna.html
  • lines changed 12, context: html, text, full: html, text
    0fd1efc259789856500a2725dc2f8d7e4ff2e1f3 Thu Oct 16 20:56:15 2025 -0700
    added link to ArrayExpress entry for CLS long-read experiments
• src/hg/makeDb/trackDb/human/hg38/encode.cCREs.override.ra
  • lines changed 27, context: html, text, full: html, text
    2018891bde14d82a453f32ede847dbf2fdc51aa8 Mon Oct 20 15:48:09 2025 -0700
    Separating the hg38 encode cCREs into a new container which will have the new ENCODE4 data, I had to do it this way because mm10 also has this track, but that one is not moving to the new container. Refs #34923 #36529
• src/hg/makeDb/trackDb/human/hg38/gnomad.html
  • lines changed 2, context: html, text, full: html, text
    bbbf04b6ba676852d67c27718a02beb7a764b76f Fri Oct 17 06:59:10 2025 -0700
    more docs for previous commit
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    29105ad9a07d4e71224ea64df34208824fe58a5e Wed Oct 15 12:14:08 2025 -0700
    checking these LCR files from Heng Li refs #36494
  • lines changed 2, context: html, text, full: html, text
    2018891bde14d82a453f32ede847dbf2fdc51aa8 Mon Oct 20 15:48:09 2025 -0700
    Separating the hg38 encode cCREs into a new container which will have the new ENCODE4 data, I had to do it this way because mm10 also has this track, but that one is not moving to the new container. Refs #34923 #36529
• src/hg/makeDb/trackDb/human/hs1/LCR.ra
  • lines changed 67, context: html, text, full: html, text
    d6c4d299f0805e129af5485dd9c120da03c28677 Wed Oct 15 12:13:37 2025 -0700
    checking these LCR files from Heng Li refs #36494
• src/hg/makeDb/trackDb/human/hs1/LCRs.html
  • lines changed 46, context: html, text, full: html, text
    d6c4d299f0805e129af5485dd9c120da03c28677 Wed Oct 15 12:13:37 2025 -0700
    checking these LCR files from Heng Li refs #36494
• src/hg/makeDb/trackDb/human/hs1/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    29105ad9a07d4e71224ea64df34208824fe58a5e Wed Oct 15 12:14:08 2025 -0700
    checking these LCR files from Heng Li refs #36494
• src/hg/makeDb/trackDb/human/spliceAIWt.ra
  • lines changed 1, context: html, text, full: html, text
    a82f9ce1e938c6bcc22065a62b93a90beb187072 Thu Oct 16 13:16:27 2025 -0700
    Releasing and announcing the SpliceAI Wildtype tracks, refs #35100
  • lines changed 1, context: html, text, full: html, text
    3f87a9e09a1f6d0b0416c3174b1abaeb445dbf5d Fri Oct 17 09:00:29 2025 -0700
    Changing the Wildtype SpliceAI composite track default visibility to full, refs #35100
• src/hg/makeDb/trackDb/human/spliceImpactSuper.html
  • lines changed 3, context: html, text, full: html, text
    281685b26873cd6651852667145c7050e7f5c907 Mon Oct 13 16:58:17 2025 -0700
    Code review edits, refs #36502
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    d6b429ab3e6d240e3ae97c85d1ec15b049ea237b Tue Oct 14 14:53:11 2025 -0700
    Edits to the Credits section regarding SpliceAI, refs #35100
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    10271a8f9e23612d541e7907ddb691fc81f369d3 Wed Oct 15 16:54:35 2025 -0700
    Adding a SpliceAI Wildtype section under Display Conventions and Configuration, refs #35100
• src/hg/makeDb/trackDb/human/spliceImpactSuper.ra
  • lines changed 1, context: html, text, full: html, text
    a82f9ce1e938c6bcc22065a62b93a90beb187072 Thu Oct 16 13:16:27 2025 -0700
    Releasing and announcing the SpliceAI Wildtype tracks, refs #35100
• src/hg/makeDb/trackDb/mouse/mm10/clsLongReadRna.html
  • lines changed 14, context: html, text, full: html, text
    0fd1efc259789856500a2725dc2f8d7e4ff2e1f3 Thu Oct 16 20:56:15 2025 -0700
    added link to ArrayExpress entry for CLS long-read experiments
  • lines changed 1, context: html, text, full: html, text
    70e7951984073b44aa4c0a060e17fbdaed99b355 Fri Oct 17 20:03:27 2025 -0700
    fixed doc stray character
• src/hg/makeDb/trackDb/trackDb.cCREs.alpha.ra
  • lines changed 19, context: html, text, full: html, text
    2018891bde14d82a453f32ede847dbf2fdc51aa8 Mon Oct 20 15:48:09 2025 -0700
    Separating the hg38 encode cCREs into a new container which will have the new ENCODE4 data, I had to do it this way because mm10 also has this track, but that one is not moving to the new container. Refs #34923 #36529
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    7e0aebd06b2394517d4700aaba6e79ec522a4734 Mon Oct 20 15:46:55 2025 -0700
    Staging evaSnp8 and one change from ENCODE 4 cCREs I also had stages, refs #36512 #34923
• src/hg/makeDb/trackDb/zebrafish/danRer1/bacEndPairs.html
  • lines changed 3, context: html, text, full: html, text
    3064e879357aec796980c1fd9364590320ef19d7 Mon Oct 13 14:24:10 2025 -0700
    Adding a reference to the BAC-end pairs description page per user request, refs #36339
• src/hg/makeDb/trackDb/zebrafish/danRer2/bacEndPairs.html
  • lines changed 3, context: html, text, full: html, text
    3064e879357aec796980c1fd9364590320ef19d7 Mon Oct 13 14:24:10 2025 -0700
    Adding a reference to the BAC-end pairs description page per user request, refs #36339
• src/hg/makeDb/trackDb/zebrafish/danRer3/bacEndPairs.html
  • lines changed 3, context: html, text, full: html, text
    3064e879357aec796980c1fd9364590320ef19d7 Mon Oct 13 14:24:10 2025 -0700
    Adding a reference to the BAC-end pairs description page per user request, refs #36339
• src/hg/makeDb/trackDb/zebrafish/danRer4/bacEndPairs.html
  • lines changed 3, context: html, text, full: html, text
    3064e879357aec796980c1fd9364590320ef19d7 Mon Oct 13 14:24:10 2025 -0700
    Adding a reference to the BAC-end pairs description page per user request, refs #36339
• src/hg/utils/automation/asmHubChainNetTrackDb.pl
  • lines changed 15, context: html, text, full: html, text
    8f3961a2c9707201232363ee38cbd1e74c147637 Fri Oct 17 12:09:55 2025 -0700
    there can be a quickLift file without the chainLiftOver tracks refs #35575
• src/hg/utils/automation/doSameSpeciesLiftOver.pl
  • lines changed 54, context: html, text, full: html, text
    9110d73a77da715fc6a5a708c4de6e3ecd381110 Fri Oct 17 10:23:07 2025 -0700
    fixup correct TMPDIR with new cluster environment refs #36483
• src/hg/utils/otto/genArk/pushNewOnes.sh
  • lines changed 49, context: html, text, full: html, text
    4eed15e27ec3d99dccc2872eab03a440acbbb3d6 Fri Oct 17 10:46:46 2025 -0700
    pushing the /gbdb/*/quickLift/ files refs #35575
• src/hg/utils/otto/genArk/quickLiftNew.sh
  • lines changed 41, context: html, text, full: html, text
    4eed15e27ec3d99dccc2872eab03a440acbbb3d6 Fri Oct 17 10:46:46 2025 -0700
    pushing the /gbdb/*/quickLift/ files refs #35575
• src/hg/utils/otto/genArk/whatIsNew.sh
  • lines changed 43, context: html, text, full: html, text
    4eed15e27ec3d99dccc2872eab03a440acbbb3d6 Fri Oct 17 10:46:46 2025 -0700
    pushing the /gbdb/*/quickLift/ files refs #35575
• src/inc/basicBed.h
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    d0054a39067a773d5342af78a80d964835d47a60 Thu Oct 16 13:28:21 2025 -0700
    add bedToBigBed -fixScores to correct scores that are out-of-range or invalid
• src/lib/basicBed.c
  • lines changed 27, context: html, text, full: html, text
    d0054a39067a773d5342af78a80d964835d47a60 Thu Oct 16 13:28:21 2025 -0700
    add bedToBigBed -fixScores to correct scores that are out-of-range or invalid
• src/lib/blastParse.c
  • lines changed 4, context: html, text, full: html, text
    5c04291d6636242cb62b6f770fdc93b23873f9d3 Thu Oct 16 13:29:03 2025 -0700
    fix blast alignment parsing to handle format change
• src/utils/bedToBigBed/bedToBigBed.c
  • lines changed 15, context: html, text, full: html, text
    d0054a39067a773d5342af78a80d964835d47a60 Thu Oct 16 13:28:21 2025 -0700
    add bedToBigBed -fixScores to correct scores that are out-of-range or invalid
  • lines changed 1, context: html, text, full: html, text
    2864f251af636a178b0aab97692d09ccd4bab2ea Thu Oct 16 16:15:32 2025 -0700
    fixed typo in help message
• src/utils/bedToBigBed/tests/expected/fixScores.bed
  • lines changed 9, context: html, text, full: html, text
    d0054a39067a773d5342af78a80d964835d47a60 Thu Oct 16 13:28:21 2025 -0700
    add bedToBigBed -fixScores to correct scores that are out-of-range or invalid
• src/utils/bedToBigBed/tests/input/badScores.bed
  • lines changed 9, context: html, text, full: html, text
    d0054a39067a773d5342af78a80d964835d47a60 Thu Oct 16 13:28:21 2025 -0700
    add bedToBigBed -fixScores to correct scores that are out-of-range or invalid
• src/utils/bedToBigBed/tests/makefile
  • lines changed 8, context: html, text, full: html, text
    d0054a39067a773d5342af78a80d964835d47a60 Thu Oct 16 13:28:21 2025 -0700
    add bedToBigBed -fixScores to correct scores that are out-of-range or invalid

• lines changed: 1698
• files changed: 89