All File Changes

v455_base to v456_preview (2023-10-09 to 2023-10-16) v456

• confs/hgwdev.hg.conf
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    5662954ca65c4f6512dc6a2b0f8ea84b3bb7ba23 Sun Oct 15 01:11:18 2023 -0700
    Installing updated hg.conf files from UCSC servers
• src/browserbox/root/updateBrowser.sh
  • lines changed 3, context: html, text, full: html, text
    25c489a029f5644f7afa7ab5944df7556bf6dbdc Mon Oct 9 15:57:15 2023 -0700
    gbibs need to download the encode ccre track because it is a default, refs #32440
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 4, context: html, text, full: html, text
    09908828e61d24d8a8ea32db0a2fd19c7f8ea1e1 Mon Oct 9 10:16:21 2023 -0700
    hgFind items always pass the bigBed filters and always are in pack when we're doing squishyPack
• src/hg/hgTracks/hgTracks.c
  • lines changed 5, context: html, text, full: html, text
    09908828e61d24d8a8ea32db0a2fd19c7f8ea1e1 Mon Oct 9 10:16:21 2023 -0700
    hgFind items always pass the bigBed filters and always are in pack when we're doing squishyPack
• src/hg/hgTracks/simpleTracks.c
  • lines changed 1, context: html, text, full: html, text
    07aee31e5ce5137a0d4330443c3a7922e3d8ce06 Thu Oct 12 13:06:05 2023 -0700
    Fix for missing gene labels on gtex tracks, refs #32445
• src/hg/htdocs/FAQ/FAQblat.html
  • lines changed 1, context: html, text, full: html, text
    d5932e4051a4885f0036831cdfc5fbf1eb08a499 Tue Oct 10 17:16:27 2023 -0700
    Fixing broken blog links, refs #32439
• src/hg/htdocs/FAQ/FAQdownloads.html
  • lines changed 6, context: html, text, full: html, text
    d5932e4051a4885f0036831cdfc5fbf1eb08a499 Tue Oct 10 17:16:27 2023 -0700
    Fixing broken blog links, refs #32439
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 1, context: html, text, full: html, text
    d5932e4051a4885f0036831cdfc5fbf1eb08a499 Tue Oct 10 17:16:27 2023 -0700
    Fixing broken blog links, refs #32439
• src/hg/htdocs/FAQ/FAQtracks.html
  • lines changed 2, context: html, text, full: html, text
    d5932e4051a4885f0036831cdfc5fbf1eb08a499 Tue Oct 10 17:16:27 2023 -0700
    Fixing broken blog links, refs #32439
• src/hg/htdocs/goldenPath/help/api.html
  • lines changed 2, context: html, text, full: html, text
    d5932e4051a4885f0036831cdfc5fbf1eb08a499 Tue Oct 10 17:16:27 2023 -0700
    Fixing broken blog links, refs #32439
• src/hg/htdocs/goldenPath/help/decorator.html
  • lines changed 8, context: html, text, full: html, text
    a8d0399f4520cc0198fe9e521be178a6ec2f670d Mon Oct 9 10:26:37 2023 -0700
    FIxing typos and making some edits, refs #30237
• src/hg/htdocs/goldenPath/help/gbib.html
  • lines changed 1, context: html, text, full: html, text
    d5932e4051a4885f0036831cdfc5fbf1eb08a499 Tue Oct 10 17:16:27 2023 -0700
    Fixing broken blog links, refs #32439
• src/hg/htdocs/goldenPath/help/hgSessionHelp.html
  • lines changed 2, context: html, text, full: html, text
    d5932e4051a4885f0036831cdfc5fbf1eb08a499 Tue Oct 10 17:16:27 2023 -0700
    Fixing broken blog links, refs #32439
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 1, context: html, text, full: html, text
    d5932e4051a4885f0036831cdfc5fbf1eb08a499 Tue Oct 10 17:16:27 2023 -0700
    Fixing broken blog links, refs #32439
• src/hg/htdocs/goldenPath/help/sessions.html
  • lines changed 3, context: html, text, full: html, text
    d5932e4051a4885f0036831cdfc5fbf1eb08a499 Tue Oct 10 17:16:27 2023 -0700
    Fixing broken blog links, refs #32439
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v2.html
  • lines changed 1, context: html, text, full: html, text
    d5932e4051a4885f0036831cdfc5fbf1eb08a499 Tue Oct 10 17:16:27 2023 -0700
    Fixing broken blog links, refs #32439
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v3.html
  • lines changed 1, context: html, text, full: html, text
    d5932e4051a4885f0036831cdfc5fbf1eb08a499 Tue Oct 10 17:16:27 2023 -0700
    Fixing broken blog links, refs #32439
• src/hg/htdocs/goldenPath/help/twoBit.html
  • lines changed 1, context: html, text, full: html, text
    d5932e4051a4885f0036831cdfc5fbf1eb08a499 Tue Oct 10 17:16:27 2023 -0700
    Fixing broken blog links, refs #32439
• src/hg/htdocs/goldenPath/help/wiggle.html
  • lines changed 1, context: html, text, full: html, text
    d5932e4051a4885f0036831cdfc5fbf1eb08a499 Tue Oct 10 17:16:27 2023 -0700
    Fixing broken blog links, refs #32439
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 19, context: html, text, full: html, text
    d5932e4051a4885f0036831cdfc5fbf1eb08a499 Tue Oct 10 17:16:27 2023 -0700
    Fixing broken blog links, refs #32439
• src/hg/htdocs/gtex.html
  • lines changed 1, context: html, text, full: html, text
    d5932e4051a4885f0036831cdfc5fbf1eb08a499 Tue Oct 10 17:16:27 2023 -0700
    Fixing broken blog links, refs #32439
• src/hg/htdocs/images/glyphsEx.png
  • lines changed 0, context: html, text, full: html, text
    a22d6c20b600fc2457e0a16bbf749cef590c3f10 Mon Oct 9 15:52:20 2023 -0700
    Adding image to display glyph options, refs #30237
• src/hg/htdocs/inc/dataApi.html
  • lines changed 1, context: html, text, full: html, text
    d5932e4051a4885f0036831cdfc5fbf1eb08a499 Tue Oct 10 17:16:27 2023 -0700
    Fixing broken blog links, refs #32439
• src/hg/htdocs/training/index.html
  • lines changed 3, context: html, text, full: html, text
    78ff54fabbaa25355a0076ba43217afd006f601d Tue Oct 10 10:22:51 2023 -0700
    Removing training sessions in your area line, refs #32300
• src/hg/inc/hdb.h
  • lines changed 3, context: html, text, full: html, text
    5f7b28612df1ff4e29c31020b33f8fee9c097b11 Tue Oct 10 12:35:00 2023 -0700
    Check for refseq historical old table existence before querying them for hgvs terms, refs #26016
  • lines changed 3, context: html, text, full: html, text
    c9ddf4ca037d9b61b462b77da54bc2f5b14726be Wed Oct 11 12:05:59 2023 -0700
    Revert historical refSeq track changes This reverts the following commits 5f7b28612df1ff4e29c31020b33f8fee9c097b11 346fa22af4717e4d8bdaa6a22a873ac4324c357b d2346420237f134dff79722739380d022c5ec48d fbcacfcd4a8baadb31fca8b07c8f831580c31c82 db4660fe604ccb1b21aa3b5dfe3421cf8ac662eb bbca1ee6f90a46e7a139434849dbf32bd206b522
• src/hg/lib/hdb.c
  • lines changed 11, context: html, text, full: html, text
    5f7b28612df1ff4e29c31020b33f8fee9c097b11 Tue Oct 10 12:35:00 2023 -0700
    Check for refseq historical old table existence before querying them for hgvs terms, refs #26016
  • lines changed 11, context: html, text, full: html, text
    c9ddf4ca037d9b61b462b77da54bc2f5b14726be Wed Oct 11 12:05:59 2023 -0700
    Revert historical refSeq track changes This reverts the following commits 5f7b28612df1ff4e29c31020b33f8fee9c097b11 346fa22af4717e4d8bdaa6a22a873ac4324c357b d2346420237f134dff79722739380d022c5ec48d fbcacfcd4a8baadb31fca8b07c8f831580c31c82 db4660fe604ccb1b21aa3b5dfe3421cf8ac662eb bbca1ee6f90a46e7a139434849dbf32bd206b522
• src/hg/lib/hgHgvs.c
  • lines changed 6, context: html, text, full: html, text
    5f7b28612df1ff4e29c31020b33f8fee9c097b11 Tue Oct 10 12:35:00 2023 -0700
    Check for refseq historical old table existence before querying them for hgvs terms, refs #26016
  • lines changed 47, context: html, text, full: html, text
    c9ddf4ca037d9b61b462b77da54bc2f5b14726be Wed Oct 11 12:05:59 2023 -0700
    Revert historical refSeq track changes This reverts the following commits 5f7b28612df1ff4e29c31020b33f8fee9c097b11 346fa22af4717e4d8bdaa6a22a873ac4324c357b d2346420237f134dff79722739380d022c5ec48d fbcacfcd4a8baadb31fca8b07c8f831580c31c82 db4660fe604ccb1b21aa3b5dfe3421cf8ac662eb bbca1ee6f90a46e7a139434849dbf32bd206b522
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 2, context: html, text, full: html, text
    307976d1f4c1ecbc73a55dea1f6348c19c1336b8 Mon Oct 9 20:08:42 2023 -0700
    adding GCA_026545065.1_CHOZN_v2.4 Chinese hamster (CHO-K1 CHOZN v2.4 2022) per user request refs #29545
  • lines changed 2, context: html, text, full: html, text
    c377565e4de6eefa3ed568504aab0c9934282d01 Tue Oct 10 08:21:09 2023 -0700
    adding 2 bacteria Streptomyces ambofaciens per user request refs #29545
  • lines changed 1, context: html, text, full: html, text
    72ef049d74b7d9bce6d78508f5b8de6ea8587541 Thu Oct 12 22:37:19 2023 -0700
    adding GCA_030013775.1_ASM3001377v1 Florida manatee (CSIC 2023) per user request an updated version of GCA_000243295.1_TriManLat1.0 refs #29545
  • lines changed 1, context: html, text, full: html, text
    b72524bd512ddebff3f125a1a1df7f701c4ed49f Fri Oct 13 08:57:48 2023 -0700
    adding GCA_021461655.1_ASM2146165v1 flatworm S.japonicum (SjaV3_Hu 2022) per user request refs #29545
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    c377565e4de6eefa3ed568504aab0c9934282d01 Tue Oct 10 08:21:09 2023 -0700
    adding 2 bacteria Streptomyces ambofaciens per user request refs #29545
• src/hg/makeDb/doc/hg19.gencode.txt
  • lines changed 40, context: html, text, full: html, text
    308bed30e11953a0dc802743c98181ce7f409dd9 Tue Oct 10 20:23:18 2023 -0700
    import of pre-release of GENCODE V45, VM34, and V45lift37
• src/hg/makeDb/doc/hg38/gencode.txt
  • lines changed 39, context: html, text, full: html, text
    308bed30e11953a0dc802743c98181ce7f409dd9 Tue Oct 10 20:23:18 2023 -0700
    import of pre-release of GENCODE V45, VM34, and V45lift37
• src/hg/makeDb/doc/hg38/hprc90way.txt
  • lines changed 40, context: html, text, full: html, text
    3cbcd195f375a1368615ca50be236375507e010f Mon Oct 9 15:01:49 2023 -0700
    added correct construction of the maf summary table refs #31561
• src/hg/makeDb/doc/hg38/hprcChain.txt
  • lines changed 307, context: html, text, full: html, text
    393037b58276445a2af3ca72e7299eb2b39d5e9d Fri Oct 13 16:37:36 2023 -0700
    move some doc files around
  • lines changed 193, context: html, text, full: html, text
    2e2674507b0968331df3f081e65b08678f860ca3 Sat Oct 14 16:45:14 2023 -0700
    some cleanup of the HPRC tracks
• src/hg/makeDb/doc/hg38/hprcInDel.txt
  • lines changed 7, context: html, text, full: html, text
    2e2674507b0968331df3f081e65b08678f860ca3 Sat Oct 14 16:45:14 2023 -0700
    some cleanup of the HPRC tracks
  • lines changed 31, context: html, text, full: html, text
    e3be616148276adf5583f752c462be025e59fe68 Sun Oct 15 15:26:29 2023 -0700
    add HPRC indels track
• src/hg/makeDb/doc/hg38/hprcPggbChain.txt
  • lines changed 66, context: html, text, full: html, text
    393037b58276445a2af3ca72e7299eb2b39d5e9d Fri Oct 13 16:37:36 2023 -0700
    move some doc files around
• src/hg/makeDb/doc/hg38/hprcReChain.txt
  • lines changed 207, context: html, text, full: html, text
    65a0fd8af813529a001a714b3c550b0063c9de6e Thu Oct 12 13:18:46 2023 -0700
    re-chain the reChains and re-net the reNets refs #31561
  • lines changed 315, context: html, text, full: html, text
    393037b58276445a2af3ca72e7299eb2b39d5e9d Fri Oct 13 16:37:36 2023 -0700
    move some doc files around
• src/hg/makeDb/doc/hg38/hprcRearrange.txt
  • lines changed 8, context: html, text, full: html, text
    2e2674507b0968331df3f081e65b08678f860ca3 Sat Oct 14 16:45:14 2023 -0700
    some cleanup of the HPRC tracks
• src/hg/makeDb/doc/hg38/ncbiRefSeq.txt
  • lines changed 81, context: html, text, full: html, text
    c9ddf4ca037d9b61b462b77da54bc2f5b14726be Wed Oct 11 12:05:59 2023 -0700
    Revert historical refSeq track changes This reverts the following commits 5f7b28612df1ff4e29c31020b33f8fee9c097b11 346fa22af4717e4d8bdaa6a22a873ac4324c357b d2346420237f134dff79722739380d022c5ec48d fbcacfcd4a8baadb31fca8b07c8f831580c31c82 db4660fe604ccb1b21aa3b5dfe3421cf8ac662eb bbca1ee6f90a46e7a139434849dbf32bd206b522
• src/hg/makeDb/doc/hg38/tabulaSapiens.txt
  • lines changed 83, context: html, text, full: html, text
    f48cccce86f5cc987b4532e7267f036a1ee4f3c5 Tue Oct 10 13:01:18 2023 -0700
    work on tabula sapiens but stuck on missing metadata
• src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    b72524bd512ddebff3f125a1a1df7f701c4ed49f Fri Oct 13 08:57:48 2023 -0700
    adding GCA_021461655.1_ASM2146165v1 flatworm S.japonicum (SjaV3_Hu 2022) per user request refs #29545
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    307976d1f4c1ecbc73a55dea1f6348c19c1336b8 Mon Oct 9 20:08:42 2023 -0700
    adding GCA_026545065.1_CHOZN_v2.4 Chinese hamster (CHO-K1 CHOZN v2.4 2022) per user request refs #29545
  • lines changed 1, context: html, text, full: html, text
    72ef049d74b7d9bce6d78508f5b8de6ea8587541 Thu Oct 12 22:37:19 2023 -0700
    adding GCA_030013775.1_ASM3001377v1 Florida manatee (CSIC 2023) per user request an updated version of GCA_000243295.1_TriManLat1.0 refs #29545
• src/hg/makeDb/doc/mm39/gencode.txt
  • lines changed 36, context: html, text, full: html, text
    308bed30e11953a0dc802743c98181ce7f409dd9 Tue Oct 10 20:23:18 2023 -0700
    import of pre-release of GENCODE V45, VM34, and V45lift37
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
  • lines changed 12, context: html, text, full: html, text
    308bed30e11953a0dc802743c98181ce7f409dd9 Tue Oct 10 20:23:18 2023 -0700
    import of pre-release of GENCODE V45, VM34, and V45lift37
• src/hg/makeDb/schema/all.joiner
  • lines changed 277, context: html, text, full: html, text
    308bed30e11953a0dc802743c98181ce7f409dd9 Tue Oct 10 20:23:18 2023 -0700
    import of pre-release of GENCODE V45, VM34, and V45lift37
• src/hg/makeDb/trackDb/human/covidHgiGwas.ra
  • lines changed 4, context: html, text, full: html, text
    279143838dbbba19a628e2f0658bc856deba6c95 Mon Oct 9 14:51:40 2023 -0700
    Removing tracks from the covid bluebar group to make room for HPRC, refs #32213
• src/hg/makeDb/trackDb/human/hg19/knownGene.alpha.ra
  • lines changed 9, context: html, text, full: html, text
    7cd6003587e1e514ef27f1f7c8ed2d244630c21b Fri Oct 13 14:30:34 2023 -0700
    first pass at hg19 GENCODE knownGene
• src/hg/makeDb/trackDb/human/hg19/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    308bed30e11953a0dc802743c98181ce7f409dd9 Tue Oct 10 20:23:18 2023 -0700
    import of pre-release of GENCODE V45, VM34, and V45lift37
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    7cd6003587e1e514ef27f1f7c8ed2d244630c21b Fri Oct 13 14:30:34 2023 -0700
    first pass at hg19 GENCODE knownGene
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV45lift37.html
  • lines changed 32, context: html, text, full: html, text
    308bed30e11953a0dc802743c98181ce7f409dd9 Tue Oct 10 20:23:18 2023 -0700
    import of pre-release of GENCODE V45, VM34, and V45lift37
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV45lift37.ra
  • lines changed 210, context: html, text, full: html, text
    308bed30e11953a0dc802743c98181ce7f409dd9 Tue Oct 10 20:23:18 2023 -0700
    import of pre-release of GENCODE V45, VM34, and V45lift37
• src/hg/makeDb/trackDb/human/hg38/chainNetHumanExperiment.ra
  • lines changed 1, context: html, text, full: html, text
    bab374b08238b22ae463c600ca193b469af1544f Wed Oct 11 10:55:12 2023 -0700
    move HPRC test tracks to experimental track group and rename netsReHprc to hprcNets refs #31561
• src/hg/makeDb/trackDb/human/hg38/chainsHprc.ra
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    e9db1da60585f8d0f7abda5494a5741348d6a3b5 Wed Oct 11 10:02:04 2023 -0700
    a renaming of the ReChains refs #31561
  • lines changed 1, context: html, text, full: html, text
    bab374b08238b22ae463c600ca193b469af1544f Wed Oct 11 10:55:12 2023 -0700
    move HPRC test tracks to experimental track group and rename netsReHprc to hprcNets refs #31561
• src/hg/makeDb/trackDb/human/hg38/hprc90way.html
  • lines changed 36, context: html, text, full: html, text
    2f2e49b55d15cd34a675325aec6e08ee0e36a233 Mon Oct 9 15:11:47 2023 -0700
    starting proper description page for this track refs #31561
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    f79cd21c0f6ffea6776fc04b53a61b10b59dd947 Tue Oct 10 14:30:11 2023 -0700
    adding documentation for HPRC tracks refs #31561
• src/hg/makeDb/trackDb/human/hg38/hprcArr.ra
  • lines changed 22, context: html, text, full: html, text
    e3be616148276adf5583f752c462be025e59fe68 Sun Oct 15 15:26:29 2023 -0700
    add HPRC indels track
• src/hg/makeDb/trackDb/human/hg38/hprcChain.ra
  • lines changed 1, context: html, text, full: html, text
    bab374b08238b22ae463c600ca193b469af1544f Wed Oct 11 10:55:12 2023 -0700
    move HPRC test tracks to experimental track group and rename netsReHprc to hprcNets refs #31561
• src/hg/makeDb/trackDb/human/hg38/hprcChains.html
  • lines changed 70, context: html, text, full: html, text
    e9db1da60585f8d0f7abda5494a5741348d6a3b5 Wed Oct 11 10:02:04 2023 -0700
    a renaming of the ReChains refs #31561
  • lines changed 17, context: html, text, full: html, text
    2e2674507b0968331df3f081e65b08678f860ca3 Sat Oct 14 16:45:14 2023 -0700
    some cleanup of the HPRC tracks
• src/hg/makeDb/trackDb/human/hg38/hprcChains.ra
  • lines changed 820, context: html, text, full: html, text
    e9db1da60585f8d0f7abda5494a5741348d6a3b5 Wed Oct 11 10:02:04 2023 -0700
    a renaming of the ReChains refs #31561
• src/hg/makeDb/trackDb/human/hg38/hprcCoverage.ra
  • lines changed 1, context: html, text, full: html, text
    bab374b08238b22ae463c600ca193b469af1544f Wed Oct 11 10:55:12 2023 -0700
    move HPRC test tracks to experimental track group and rename netsReHprc to hprcNets refs #31561
• src/hg/makeDb/trackDb/human/hg38/hprcCoverage97.ra
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    2e2674507b0968331df3f081e65b08678f860ca3 Sat Oct 14 16:45:14 2023 -0700
    some cleanup of the HPRC tracks
• src/hg/makeDb/trackDb/human/hg38/hprcNets.html
  • lines changed 69, context: html, text, full: html, text
    bab374b08238b22ae463c600ca193b469af1544f Wed Oct 11 10:55:12 2023 -0700
    move HPRC test tracks to experimental track group and rename netsReHprc to hprcNets refs #31561
• src/hg/makeDb/trackDb/human/hg38/hprcNets.ra
  • lines changed 820, context: html, text, full: html, text
    bab374b08238b22ae463c600ca193b469af1544f Wed Oct 11 10:55:12 2023 -0700
    move HPRC test tracks to experimental track group and rename netsReHprc to hprcNets refs #31561
• src/hg/makeDb/trackDb/human/hg38/hprcVCF.html
  • lines changed 70, context: html, text, full: html, text
    f79cd21c0f6ffea6776fc04b53a61b10b59dd947 Tue Oct 10 14:30:11 2023 -0700
    adding documentation for HPRC tracks refs #31561
• src/hg/makeDb/trackDb/human/hg38/hprcVCF.ra
  • lines changed 54, context: html, text, full: html, text
    f79cd21c0f6ffea6776fc04b53a61b10b59dd947 Tue Oct 10 14:30:11 2023 -0700
    adding documentation for HPRC tracks refs #31561
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    0dda631e8d39f48e611efe3538d5ae87f2713b28 Tue Oct 10 14:44:41 2023 -0700
    duplicate tag removed refs #31561
• src/hg/makeDb/trackDb/human/hg38/hprcVCFTest.html
  • lines changed 69, context: html, text, full: html, text
    f79cd21c0f6ffea6776fc04b53a61b10b59dd947 Tue Oct 10 14:30:11 2023 -0700
    adding documentation for HPRC tracks refs #31561
• src/hg/makeDb/trackDb/human/hg38/hprcVCFTest.ra
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    f79cd21c0f6ffea6776fc04b53a61b10b59dd947 Tue Oct 10 14:30:11 2023 -0700
    adding documentation for HPRC tracks refs #31561
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    bab374b08238b22ae463c600ca193b469af1544f Wed Oct 11 10:55:12 2023 -0700
    move HPRC test tracks to experimental track group and rename netsReHprc to hprcNets refs #31561
• src/hg/makeDb/trackDb/human/hg38/netsReHprc.ra
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    bab374b08238b22ae463c600ca193b469af1544f Wed Oct 11 10:55:12 2023 -0700
    move HPRC test tracks to experimental track group and rename netsReHprc to hprcNets refs #31561
• src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
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    308bed30e11953a0dc802743c98181ce7f409dd9 Tue Oct 10 20:23:18 2023 -0700
    import of pre-release of GENCODE V45, VM34, and V45lift37
• src/hg/makeDb/trackDb/human/hg38/trackDb.hprc90way.ra
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    5ed8b946589b8a171e8c3849fd0e1640859c64bf Mon Oct 9 15:20:01 2023 -0700
    starting proper description page for this track refs #31561
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    279143838dbbba19a628e2f0658bc856deba6c95 Mon Oct 9 14:51:40 2023 -0700
    Removing tracks from the covid bluebar group to make room for HPRC, refs #32213
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    d2b3b8afbf6b9864777b688eb53629c97322ef04 Tue Oct 10 14:51:41 2023 -0700
    move all the HPRC VCF experiements to their own container refs #31561
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    e9db1da60585f8d0f7abda5494a5741348d6a3b5 Wed Oct 11 10:02:04 2023 -0700
    a renaming of the ReChains refs #31561
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    bab374b08238b22ae463c600ca193b469af1544f Wed Oct 11 10:55:12 2023 -0700
    move HPRC test tracks to experimental track group and rename netsReHprc to hprcNets refs #31561
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    c9ddf4ca037d9b61b462b77da54bc2f5b14726be Wed Oct 11 12:05:59 2023 -0700
    Revert historical refSeq track changes This reverts the following commits 5f7b28612df1ff4e29c31020b33f8fee9c097b11 346fa22af4717e4d8bdaa6a22a873ac4324c357b d2346420237f134dff79722739380d022c5ec48d fbcacfcd4a8baadb31fca8b07c8f831580c31c82 db4660fe604ccb1b21aa3b5dfe3421cf8ac662eb bbca1ee6f90a46e7a139434849dbf32bd206b522
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV45.html
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    308bed30e11953a0dc802743c98181ce7f409dd9 Tue Oct 10 20:23:18 2023 -0700
    import of pre-release of GENCODE V45, VM34, and V45lift37
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV45.ra
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    308bed30e11953a0dc802743c98181ce7f409dd9 Tue Oct 10 20:23:18 2023 -0700
    import of pre-release of GENCODE V45, VM34, and V45lift37
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    279143838dbbba19a628e2f0658bc856deba6c95 Mon Oct 9 14:51:40 2023 -0700
    Removing tracks from the covid bluebar group to make room for HPRC, refs #32213
• src/hg/makeDb/trackDb/mouse/mm10/knownGene.html
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    d5932e4051a4885f0036831cdfc5fbf1eb08a499 Tue Oct 10 17:16:27 2023 -0700
    Fixing broken blog links, refs #32439
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.gencode.ra
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    308bed30e11953a0dc802743c98181ce7f409dd9 Tue Oct 10 20:23:18 2023 -0700
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    308bed30e11953a0dc802743c98181ce7f409dd9 Tue Oct 10 20:23:18 2023 -0700
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• src/hg/makeDb/trackDb/mouse/mm39/wgEncodeGencodeVM34.ra
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    308bed30e11953a0dc802743c98181ce7f409dd9 Tue Oct 10 20:23:18 2023 -0700
    import of pre-release of GENCODE V45, VM34, and V45lift37
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    c9ddf4ca037d9b61b462b77da54bc2f5b14726be Wed Oct 11 12:05:59 2023 -0700
    Revert historical refSeq track changes This reverts the following commits 5f7b28612df1ff4e29c31020b33f8fee9c097b11 346fa22af4717e4d8bdaa6a22a873ac4324c357b d2346420237f134dff79722739380d022c5ec48d fbcacfcd4a8baadb31fca8b07c8f831580c31c82 db4660fe604ccb1b21aa3b5dfe3421cf8ac662eb bbca1ee6f90a46e7a139434849dbf32bd206b522
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    d5932e4051a4885f0036831cdfc5fbf1eb08a499 Tue Oct 10 17:16:27 2023 -0700
    Fixing broken blog links, refs #32439
• src/hg/utils/bigChainArrange/bigChainArrange.c
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    e3be616148276adf5583f752c462be025e59fe68 Sun Oct 15 15:26:29 2023 -0700
    add HPRC indels track
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    e3be616148276adf5583f752c462be025e59fe68 Sun Oct 15 15:26:29 2023 -0700
    add HPRC indels track
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    c38f77acf5cf110d960192b5242a76c04ff33d54 Sun Oct 15 15:21:16 2023 -0700
    added chainDupFilter which addresses a problem in axtChain where duplicated blocks are not chained
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    c38f77acf5cf110d960192b5242a76c04ff33d54 Sun Oct 15 15:21:16 2023 -0700
    added chainDupFilter which addresses a problem in axtChain where duplicated blocks are not chained
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    c9ddf4ca037d9b61b462b77da54bc2f5b14726be Wed Oct 11 12:05:59 2023 -0700
    Revert historical refSeq track changes This reverts the following commits 5f7b28612df1ff4e29c31020b33f8fee9c097b11 346fa22af4717e4d8bdaa6a22a873ac4324c357b d2346420237f134dff79722739380d022c5ec48d fbcacfcd4a8baadb31fca8b07c8f831580c31c82 db4660fe604ccb1b21aa3b5dfe3421cf8ac662eb bbca1ee6f90a46e7a139434849dbf32bd206b522
• src/hg/utils/hgvsToVcf/tests/expected/clinVarChanges.vcf
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    c9ddf4ca037d9b61b462b77da54bc2f5b14726be Wed Oct 11 12:05:59 2023 -0700
    Revert historical refSeq track changes This reverts the following commits 5f7b28612df1ff4e29c31020b33f8fee9c097b11 346fa22af4717e4d8bdaa6a22a873ac4324c357b d2346420237f134dff79722739380d022c5ec48d fbcacfcd4a8baadb31fca8b07c8f831580c31c82 db4660fe604ccb1b21aa3b5dfe3421cf8ac662eb bbca1ee6f90a46e7a139434849dbf32bd206b522
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    30d1e434dcd5b313f393eac770c8da2d4323d54f Fri Oct 13 11:45:13 2023 -0700
    Adding download & usher tree build scripts for several non-SARS-CoV-2 viruses. mpxv has been going for over a year, rsv & dengue for some months now. fluA is an incomplete work in progress, complicated by having 8 segments, greater distances, and different subtyping schemes for different segments and even for different types within the segments.
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    30d1e434dcd5b313f393eac770c8da2d4323d54f Fri Oct 13 11:45:13 2023 -0700
    Adding download & usher tree build scripts for several non-SARS-CoV-2 viruses. mpxv has been going for over a year, rsv & dengue for some months now. fluA is an incomplete work in progress, complicated by having 8 segments, greater distances, and different subtyping schemes for different segments and even for different types within the segments.
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    30d1e434dcd5b313f393eac770c8da2d4323d54f Fri Oct 13 11:45:13 2023 -0700
    Adding download & usher tree build scripts for several non-SARS-CoV-2 viruses. mpxv has been going for over a year, rsv & dengue for some months now. fluA is an incomplete work in progress, complicated by having 8 segments, greater distances, and different subtyping schemes for different segments and even for different types within the segments.
• src/hg/utils/otto/fluA/getNcbiFluA.sh
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    30d1e434dcd5b313f393eac770c8da2d4323d54f Fri Oct 13 11:45:13 2023 -0700
    Adding download & usher tree build scripts for several non-SARS-CoV-2 viruses. mpxv has been going for over a year, rsv & dengue for some months now. fluA is an incomplete work in progress, complicated by having 8 segments, greater distances, and different subtyping schemes for different segments and even for different types within the segments.
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    30d1e434dcd5b313f393eac770c8da2d4323d54f Fri Oct 13 11:45:13 2023 -0700
    Adding download & usher tree build scripts for several non-SARS-CoV-2 viruses. mpxv has been going for over a year, rsv & dengue for some months now. fluA is an incomplete work in progress, complicated by having 8 segments, greater distances, and different subtyping schemes for different segments and even for different types within the segments.
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    30d1e434dcd5b313f393eac770c8da2d4323d54f Fri Oct 13 11:45:13 2023 -0700
    Adding download & usher tree build scripts for several non-SARS-CoV-2 viruses. mpxv has been going for over a year, rsv & dengue for some months now. fluA is an incomplete work in progress, complicated by having 8 segments, greater distances, and different subtyping schemes for different segments and even for different types within the segments.
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    30d1e434dcd5b313f393eac770c8da2d4323d54f Fri Oct 13 11:45:13 2023 -0700
    Adding download & usher tree build scripts for several non-SARS-CoV-2 viruses. mpxv has been going for over a year, rsv & dengue for some months now. fluA is an incomplete work in progress, complicated by having 8 segments, greater distances, and different subtyping schemes for different segments and even for different types within the segments.
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    30d1e434dcd5b313f393eac770c8da2d4323d54f Fri Oct 13 11:45:13 2023 -0700
    Adding download & usher tree build scripts for several non-SARS-CoV-2 viruses. mpxv has been going for over a year, rsv & dengue for some months now. fluA is an incomplete work in progress, complicated by having 8 segments, greater distances, and different subtyping schemes for different segments and even for different types within the segments.
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    30d1e434dcd5b313f393eac770c8da2d4323d54f Fri Oct 13 11:45:13 2023 -0700
    Adding download & usher tree build scripts for several non-SARS-CoV-2 viruses. mpxv has been going for over a year, rsv & dengue for some months now. fluA is an incomplete work in progress, complicated by having 8 segments, greater distances, and different subtyping schemes for different segments and even for different types within the segments.
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    30d1e434dcd5b313f393eac770c8da2d4323d54f Fri Oct 13 11:45:13 2023 -0700
    Adding download & usher tree build scripts for several non-SARS-CoV-2 viruses. mpxv has been going for over a year, rsv & dengue for some months now. fluA is an incomplete work in progress, complicated by having 8 segments, greater distances, and different subtyping schemes for different segments and even for different types within the segments.
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    30d1e434dcd5b313f393eac770c8da2d4323d54f Fri Oct 13 11:45:13 2023 -0700
    Adding download & usher tree build scripts for several non-SARS-CoV-2 viruses. mpxv has been going for over a year, rsv & dengue for some months now. fluA is an incomplete work in progress, complicated by having 8 segments, greater distances, and different subtyping schemes for different segments and even for different types within the segments.
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    30d1e434dcd5b313f393eac770c8da2d4323d54f Fri Oct 13 11:45:13 2023 -0700
    Adding download & usher tree build scripts for several non-SARS-CoV-2 viruses. mpxv has been going for over a year, rsv & dengue for some months now. fluA is an incomplete work in progress, complicated by having 8 segments, greater distances, and different subtyping schemes for different segments and even for different types within the segments.
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    30d1e434dcd5b313f393eac770c8da2d4323d54f Fri Oct 13 11:45:13 2023 -0700
    Adding download & usher tree build scripts for several non-SARS-CoV-2 viruses. mpxv has been going for over a year, rsv & dengue for some months now. fluA is an incomplete work in progress, complicated by having 8 segments, greater distances, and different subtyping schemes for different segments and even for different types within the segments.
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    30d1e434dcd5b313f393eac770c8da2d4323d54f Fri Oct 13 11:45:13 2023 -0700
    Adding download & usher tree build scripts for several non-SARS-CoV-2 viruses. mpxv has been going for over a year, rsv & dengue for some months now. fluA is an incomplete work in progress, complicated by having 8 segments, greater distances, and different subtyping schemes for different segments and even for different types within the segments.
• src/hg/utils/otto/rsv/goya.A.clade-mutations.tsv
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    30d1e434dcd5b313f393eac770c8da2d4323d54f Fri Oct 13 11:45:13 2023 -0700
    Adding download & usher tree build scripts for several non-SARS-CoV-2 viruses. mpxv has been going for over a year, rsv & dengue for some months now. fluA is an incomplete work in progress, complicated by having 8 segments, greater distances, and different subtyping schemes for different segments and even for different types within the segments.
• src/hg/utils/otto/rsv/ramaekers.A.clade-mutations.tsv
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    30d1e434dcd5b313f393eac770c8da2d4323d54f Fri Oct 13 11:45:13 2023 -0700
    Adding download & usher tree build scripts for several non-SARS-CoV-2 viruses. mpxv has been going for over a year, rsv & dengue for some months now. fluA is an incomplete work in progress, complicated by having 8 segments, greater distances, and different subtyping schemes for different segments and even for different types within the segments.
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
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    fde35693549abfb2a22a4846bebfac38abdd5522 Fri Oct 13 09:38:49 2023 -0700
    Use Ns for positions in pango-masked UTR regions.

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