All File Changes

v411_base to v412_preview (2021-03-01 to 2021-03-08) v412

• confs/asia.hg.conf
  • lines changed 4, context: html, text, full: html, text
    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• confs/euro.hg.conf
  • lines changed 4, context: html, text, full: html, text
    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
  • lines changed 4, context: html, text, full: html, text
    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• confs/hgwbeta.hg.conf
  • lines changed 1, context: html, text, full: html, text
    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
  • lines changed 4, context: html, text, full: html, text
    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• confs/hgwdev.hg.conf
  • lines changed 11, context: html, text, full: html, text
    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
  • lines changed 3, context: html, text, full: html, text
    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• confs/rr.hg.conf
  • lines changed 1, context: html, text, full: html, text
    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
  • lines changed 4, context: html, text, full: html, text
    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/browserbox/root/updateBrowser.sh
  • lines changed 16, context: html, text, full: html, text
    50b94a07ac1c74bc32ca230dd9c66ee36ad20d94 Mon Mar 1 15:54:10 2021 -0800
    GBiB: Move cgi-bin and htdocs symlinks out so that old and new gbibs receive the symlinks instead of just old gbibs, refs #26943
• src/gfClient/gfClient.c
  • lines changed 11, context: html, text, full: html, text
    e764efe5d0e596213c72e69f028df0a667d0a83c Mon Jun 29 00:43:22 2020 +0000
    gfClient working with blat server running under xinetd
  • lines changed 2, context: html, text, full: html, text
    a74c645505a135d5c1e923afe477cdeb9c15bded Wed Jul 8 22:27:42 2020 -0700
    added including multiple container directoies in genome dir path to gfServer
  • lines changed 11, context: html, text, full: html, text
    25d4c33f3e224c9d571876326ceccb46530005b0 Wed Jul 8 23:09:57 2020 -0700
    changed variable name to be more accurate
  • lines changed 21, context: html, text, full: html, text
    95030f73f067d8e8f9221a09c1811784607e4e72 Fri Jul 10 17:51:29 2020 -0700
    split dynamic server genomeDataPrefix into genome and genomeDataDir. More verbose, but clearer
  • lines changed 3, context: html, text, full: html, text
    63120154609787691150cc8a67a1aad40455481c Wed Oct 14 13:09:06 2020 -0700
    separate -genomeDir into -genome and -genomeDataDir
  • lines changed 7, context: html, text, full: html, text
    f683064dc6a998206665b484790ef9d561e6c8a7 Sat Dec 5 22:42:53 2020 -0800
    initial conversion to gfServer connection to object
  • lines changed 9, context: html, text, full: html, text
    36f8f6fb024b20cc523cdf9ebde7491eca84fd7c Sun Dec 6 20:33:20 2020 -0800
    multiple request per connect works except hgBlat
  • lines changed 8, context: html, text, full: html, text
    a4b45fbe8156dfa9881f586b830a2e6a6338d58f Wed Dec 9 11:35:20 2020 -0800
    fixed undetect change in signature
  • lines changed 1, context: html, text, full: html, text
    a2819277576ffc91069261a03b358213afe2cb3b Wed Feb 3 15:30:27 2021 -0800
    allow gfPcr to query dynamic servers
• src/gfClient/makefile
  • lines changed 15, context: html, text, full: html, text
    f683064dc6a998206665b484790ef9d561e6c8a7 Sat Dec 5 22:42:53 2020 -0800
    initial conversion to gfServer connection to object
• src/gfServer/AB000095.fa
  • lines changed 49, context: html, text, full: html, text
    5fcdf45fee21aa88247a68df00575e2865a9478e Sun Jun 28 14:50:30 2020 -0700
    moved old test data files to tests/input
• src/gfServer/AB000220.fa
  • lines changed 39, context: html, text, full: html, text
    5fcdf45fee21aa88247a68df00575e2865a9478e Sun Jun 28 14:50:30 2020 -0700
    moved old test data files to tests/input
• src/gfServer/README.blat
  • lines changed 16, context: html, text, full: html, text
    36f8f6fb024b20cc523cdf9ebde7491eca84fd7c Sun Dec 6 20:33:20 2020 -0800
    multiple request per connect works except hgBlat
• src/gfServer/blat-xinetd.example
  • lines changed 33, context: html, text, full: html, text
    87a162ccdc3ac94525fc1011dec5bc10e2cf2171 Thu Jul 2 16:12:57 2020 -0700
    web blat working
• src/gfServer/design.txt
  • lines changed 48, context: html, text, full: html, text
    65f00dd6b049342f185de41542e9c968ec3e98d3 Wed Dec 9 21:31:03 2020 -0800
    added gfServer design overview
  • lines changed 4, context: html, text, full: html, text
    3c5f6de8a9739eb8ddaf1cb233460e0bba9e5321 Fri Dec 11 21:32:23 2020 -0800
    fixed documention issues
• src/gfServer/gfServer.c
  • lines changed 236, context: html, text, full: html, text
    a1c950cde18a4b977dc47c4528dfa6a9357a1f0f Mon Jul 13 19:13:08 2015 -0700
    Option for gfServer to save index as an mmap file on disk to speed startup.
  • lines changed 5, context: html, text, full: html, text
    9be14bbf98fbe84c898cf038fa80c3f9124a2ee6 Sat Jan 11 13:29:12 2020 -0800
    added madvise call after mmap to improve performance
  • lines changed 13, context: html, text, full: html, text
    c3c65fde6dd5aa6f20860c7113eb9ee22cf35b96 Wed Jan 15 08:37:28 2020 -0800
    Initial pass at 64bit blat index
  • lines changed 13, context: html, text, full: html, text
    ef2b0974644900d17bdc4e0a2c8056e995832282 Thu Jan 16 11:14:03 2020 -0800
    Revert "Initial pass at 64bit blat index" This reverts commit 85f6ef8de85a89781978add2ed98fb158718cd40.
  • lines changed 231, context: html, text, full: html, text
    0a10e299786e9b470b55b2f02b9718ec6c4e4bb4 Sat Jun 27 15:33:26 2020 -0700
    move genoFind build, save, and load to a library
  • lines changed 30, context: html, text, full: html, text
    766edf73c99da98b3935f42c234d14acf08c2c0e Sat Jun 27 19:37:45 2020 -0700
    move index building to a separate gfServer subcommand
  • lines changed 159, context: html, text, full: html, text
    ecacb0a15e8ddbe9b2e62381e30621ba70f82d8f Sun Jun 28 14:36:10 2020 -0700
    dynamic server tests working
  • lines changed 13, context: html, text, full: html, text
    e764efe5d0e596213c72e69f028df0a667d0a83c Mon Jun 29 00:43:22 2020 +0000
    gfClient working with blat server running under xinetd
  • lines changed 2, context: html, text, full: html, text
    b6d7e4446453c3ab019b30024741247171a2f040 Mon Jun 29 20:04:40 2020 +0000
    make sure data is 64-bit aligned, store offsets in headers to simplify
  • lines changed 49, context: html, text, full: html, text
    c99b62d7865a828f8f41c6e82dd36cbd2dd26780 Wed Jul 1 21:45:43 2020 -0700
    hgBlat mostly works
  • lines changed 84, context: html, text, full: html, text
    ef850e264ac840b515b825f34314c36d58ccbcbe Thu Jul 2 11:12:15 2020 -0700
    added info command similar to status to support hgBlat
  • lines changed 3, context: html, text, full: html, text
    87a162ccdc3ac94525fc1011dec5bc10e2cf2171 Thu Jul 2 16:12:57 2020 -0700
    web blat working
  • lines changed 7, context: html, text, full: html, text
    0ede364a2dcb452681933d5a3579b4f05d90a245 Sun Jul 5 15:16:27 2020 -0700
    fixed bug where totalSeqSize was not stored in index, now hgBlat works
  • lines changed 7, context: html, text, full: html, text
    84dba0006acf65324bb843abee1e11ad02c0a912 Sun Jul 5 20:01:10 2020 -0700
    some cleanup about hgBlat
  • lines changed 47, context: html, text, full: html, text
    ee8ef81c6d82157859f16548a27726f4b7421891 Mon Jul 6 19:22:14 2020 -0700
    added support for perSeqMax in dynamic server
  • lines changed 38, context: html, text, full: html, text
    a74c645505a135d5c1e923afe477cdeb9c15bded Wed Jul 8 22:27:42 2020 -0700
    added including multiple container directoies in genome dir path to gfServer
  • lines changed 46, context: html, text, full: html, text
    95030f73f067d8e8f9221a09c1811784607e4e72 Fri Jul 10 17:51:29 2020 -0700
    split dynamic server genomeDataPrefix into genome and genomeDataDir. More verbose, but clearer
  • lines changed 50, context: html, text, full: html, text
    9186d6410c3266a7069c81e642c9ea22dc981191 Sun Oct 25 20:12:47 2020 -0700
    merged master
  • lines changed 151, context: html, text, full: html, text
    36f8f6fb024b20cc523cdf9ebde7491eca84fd7c Sun Dec 6 20:33:20 2020 -0800
    multiple request per connect works except hgBlat
  • lines changed 33, context: html, text, full: html, text
    e9492dbfa8a68aee133893d4b02475b0aec27bb9 Sun Dec 6 23:48:42 2020 -0800
    webblat and hgBlat working
  • lines changed 115, context: html, text, full: html, text
    88485cfa7f13affa28ec5765fe9b2db90cce42b6 Tue Dec 8 21:02:15 2020 -0800
    hgPcr working
  • lines changed 1, context: html, text, full: html, text
    a4100d62e1f3a6864f70e651b6b41517c662f496 Wed Dec 9 21:34:41 2020 -0800
    improved doc on reserved files
  • lines changed 6, context: html, text, full: html, text
    be5104801a919dd2668e935b265b669940c9199a Wed Dec 9 22:05:45 2020 -0800
    added check for attempting to access outside of gfServer root
  • lines changed 3, context: html, text, full: html, text
    cb757269cca8bc473f97d588a2f3737acaf0fb41 Wed Dec 9 22:11:32 2020 -0800
    dropped support for absolute genomeDataDir
  • lines changed 4, context: html, text, full: html, text
    3c5f6de8a9739eb8ddaf1cb233460e0bba9e5321 Fri Dec 11 21:32:23 2020 -0800
    fixed documention issues
  • lines changed 1, context: html, text, full: html, text
    54a643b32015c6a4672bd540b4bf7a94a751e1ce Wed Feb 3 12:45:46 2021 -0800
    added unit test of gfServer dynamic PCR
  • lines changed 1, context: html, text, full: html, text
    382b9a0900ae6fc988915de7a27c62318f55f172 Wed Feb 3 13:44:59 2021 -0800
    remove redundant newline
  • lines changed 33, context: html, text, full: html, text
    c16b3edf4c88aed3d6cf1da68118fca1f8855593 Wed Feb 3 16:31:12 2021 -0800
    add debug logging of index parameters
  • lines changed 25, context: html, text, full: html, text
    f7d577042a7e3e41c1121082febb7ff25020bf0b Sun Feb 28 13:19:19 2021 -0800
    have gfServer check that index files match the required naming convention
• src/gfServer/makefile
  • lines changed 3, context: html, text, full: html, text
    a1c950cde18a4b977dc47c4528dfa6a9357a1f0f Mon Jul 13 19:13:08 2015 -0700
    Option for gfServer to save index as an mmap file on disk to speed startup.
  • lines changed 1, context: html, text, full: html, text
    ecacb0a15e8ddbe9b2e62381e30621ba70f82d8f Sun Jun 28 14:36:10 2020 -0700
    dynamic server tests working
  • lines changed 14, context: html, text, full: html, text
    ee8ef81c6d82157859f16548a27726f4b7421891 Mon Jul 6 19:22:14 2020 -0700
    added support for perSeqMax in dynamic server
  • lines changed 1, context: html, text, full: html, text
    a74c645505a135d5c1e923afe477cdeb9c15bded Wed Jul 8 22:27:42 2020 -0700
    added including multiple container directoies in genome dir path to gfServer
  • lines changed 1, context: html, text, full: html, text
    54a643b32015c6a4672bd540b4bf7a94a751e1ce Wed Feb 3 12:45:46 2021 -0800
    added unit test of gfServer dynamic PCR
• src/gfServer/repeat.fa
  • lines changed 7, context: html, text, full: html, text
    5fcdf45fee21aa88247a68df00575e2865a9478e Sun Jun 28 14:50:30 2020 -0700
    moved old test data files to tests/input
• src/gfServer/test1.fa
  • lines changed 11, context: html, text, full: html, text
    5fcdf45fee21aa88247a68df00575e2865a9478e Sun Jun 28 14:50:30 2020 -0700
    moved old test data files to tests/input
• src/gfServer/test1.nib
  • lines changed 0, context: html, text, full: html, text
    5fcdf45fee21aa88247a68df00575e2865a9478e Sun Jun 28 14:50:30 2020 -0700
    moved old test data files to tests/input
• src/gfServer/test2.fa
  • lines changed 7, context: html, text, full: html, text
    5fcdf45fee21aa88247a68df00575e2865a9478e Sun Jun 28 14:50:30 2020 -0700
    moved old test data files to tests/input
• src/gfServer/test3.fa
  • lines changed 9, context: html, text, full: html, text
    5fcdf45fee21aa88247a68df00575e2865a9478e Sun Jun 28 14:50:30 2020 -0700
    moved old test data files to tests/input
• src/gfServer/tests/dynTester
  • lines changed 143, context: html, text, full: html, text
    fab119b260a64f40ea3db632486e0823a0c0f493 Tue Jun 30 18:33:39 2020 +0000
    forgot to add test driver
  • lines changed 1, context: html, text, full: html, text
    c99b62d7865a828f8f41c6e82dd36cbd2dd26780 Wed Jul 1 21:45:43 2020 -0700
    hgBlat mostly works
  • lines changed 19, context: html, text, full: html, text
    ef850e264ac840b515b825f34314c36d58ccbcbe Thu Jul 2 11:12:15 2020 -0700
    added info command similar to status to support hgBlat
  • lines changed 9, context: html, text, full: html, text
    0ede364a2dcb452681933d5a3579b4f05d90a245 Sun Jul 5 15:16:27 2020 -0700
    fixed bug where totalSeqSize was not stored in index, now hgBlat works
  • lines changed 1, context: html, text, full: html, text
    a74c645505a135d5c1e923afe477cdeb9c15bded Wed Jul 8 22:27:42 2020 -0700
    added including multiple container directoies in genome dir path to gfServer
  • lines changed 20, context: html, text, full: html, text
    95030f73f067d8e8f9221a09c1811784607e4e72 Fri Jul 10 17:51:29 2020 -0700
    split dynamic server genomeDataPrefix into genome and genomeDataDir. More verbose, but clearer
  • lines changed 22, context: html, text, full: html, text
    36f8f6fb024b20cc523cdf9ebde7491eca84fd7c Sun Dec 6 20:33:20 2020 -0800
    multiple request per connect works except hgBlat
  • lines changed 42, context: html, text, full: html, text
    54a643b32015c6a4672bd540b4bf7a94a751e1ce Wed Feb 3 12:45:46 2021 -0800
    added unit test of gfServer dynamic PCR
• src/gfServer/tests/expected/testDynServer
  • lines changed 44, context: html, text, full: html, text
    ecacb0a15e8ddbe9b2e62381e30621ba70f82d8f Sun Jun 28 14:36:10 2020 -0700
    dynamic server tests working
  • lines changed 38, context: html, text, full: html, text
    e764efe5d0e596213c72e69f028df0a667d0a83c Mon Jun 29 00:43:22 2020 +0000
    gfClient working with blat server running under xinetd
  • lines changed 12, context: html, text, full: html, text
    c99b62d7865a828f8f41c6e82dd36cbd2dd26780 Wed Jul 1 21:45:43 2020 -0700
    hgBlat mostly works
  • lines changed 9, context: html, text, full: html, text
    ef850e264ac840b515b825f34314c36d58ccbcbe Thu Jul 2 11:12:15 2020 -0700
    added info command similar to status to support hgBlat
  • lines changed 52, context: html, text, full: html, text
    ee8ef81c6d82157859f16548a27726f4b7421891 Mon Jul 6 19:22:14 2020 -0700
    added support for perSeqMax in dynamic server
• src/gfServer/tests/expected/testDynServer.out
  • lines changed 52, context: html, text, full: html, text
    ee8ef81c6d82157859f16548a27726f4b7421891 Mon Jul 6 19:22:14 2020 -0700
    added support for perSeqMax in dynamic server
  • lines changed 3, context: html, text, full: html, text
    95030f73f067d8e8f9221a09c1811784607e4e72 Fri Jul 10 17:51:29 2020 -0700
    split dynamic server genomeDataPrefix into genome and genomeDataDir. More verbose, but clearer
  • lines changed 1, context: html, text, full: html, text
    f683064dc6a998206665b484790ef9d561e6c8a7 Sat Dec 5 22:42:53 2020 -0800
    initial conversion to gfServer connection to object
  • lines changed 2, context: html, text, full: html, text
    36f8f6fb024b20cc523cdf9ebde7491eca84fd7c Sun Dec 6 20:33:20 2020 -0800
    multiple request per connect works except hgBlat
  • lines changed 1, context: html, text, full: html, text
    365534e1a97dc9250ff85e367a7786989662281d Mon Dec 14 14:01:20 2020 -0800
    updated gfServer version
• src/gfServer/tests/expected/testDynServerPcr.out
  • lines changed 29, context: html, text, full: html, text
    54a643b32015c6a4672bd540b4bf7a94a751e1ce Wed Feb 3 12:45:46 2021 -0800
    added unit test of gfServer dynamic PCR
  • lines changed 12, context: html, text, full: html, text
    f67d0a4b041b6553076c7fb9128772f5116231b3 Sun Feb 28 13:08:56 2021 -0800
    updated expected results due to previous fix
• src/gfServer/tests/expected/testDynServerPerSeqMax.out
  • lines changed 52, context: html, text, full: html, text
    a74c645505a135d5c1e923afe477cdeb9c15bded Wed Jul 8 22:27:42 2020 -0700
    added including multiple container directoies in genome dir path to gfServer
  • lines changed 3, context: html, text, full: html, text
    95030f73f067d8e8f9221a09c1811784607e4e72 Fri Jul 10 17:51:29 2020 -0700
    split dynamic server genomeDataPrefix into genome and genomeDataDir. More verbose, but clearer
  • lines changed 1, context: html, text, full: html, text
    f683064dc6a998206665b484790ef9d561e6c8a7 Sat Dec 5 22:42:53 2020 -0800
    initial conversion to gfServer connection to object
  • lines changed 2, context: html, text, full: html, text
    36f8f6fb024b20cc523cdf9ebde7491eca84fd7c Sun Dec 6 20:33:20 2020 -0800
    multiple request per connect works except hgBlat
  • lines changed 1, context: html, text, full: html, text
    365534e1a97dc9250ff85e367a7786989662281d Mon Dec 14 14:01:20 2020 -0800
    updated gfServer version
• src/gfServer/tests/expected/testDynServerTrans
  • lines changed 188, context: html, text, full: html, text
    ecacb0a15e8ddbe9b2e62381e30621ba70f82d8f Sun Jun 28 14:36:10 2020 -0700
    dynamic server tests working
  • lines changed 90, context: html, text, full: html, text
    e764efe5d0e596213c72e69f028df0a667d0a83c Mon Jun 29 00:43:22 2020 +0000
    gfClient working with blat server running under xinetd
  • lines changed 12, context: html, text, full: html, text
    c99b62d7865a828f8f41c6e82dd36cbd2dd26780 Wed Jul 1 21:45:43 2020 -0700
    hgBlat mostly works
  • lines changed 9, context: html, text, full: html, text
    ef850e264ac840b515b825f34314c36d58ccbcbe Thu Jul 2 11:12:15 2020 -0700
    added info command similar to status to support hgBlat
  • lines changed 196, context: html, text, full: html, text
    ee8ef81c6d82157859f16548a27726f4b7421891 Mon Jul 6 19:22:14 2020 -0700
    added support for perSeqMax in dynamic server
• src/gfServer/tests/expected/testDynServerTrans.out
  • lines changed 196, context: html, text, full: html, text
    ee8ef81c6d82157859f16548a27726f4b7421891 Mon Jul 6 19:22:14 2020 -0700
    added support for perSeqMax in dynamic server
  • lines changed 3, context: html, text, full: html, text
    95030f73f067d8e8f9221a09c1811784607e4e72 Fri Jul 10 17:51:29 2020 -0700
    split dynamic server genomeDataPrefix into genome and genomeDataDir. More verbose, but clearer
  • lines changed 1, context: html, text, full: html, text
    f683064dc6a998206665b484790ef9d561e6c8a7 Sat Dec 5 22:42:53 2020 -0800
    initial conversion to gfServer connection to object
  • lines changed 2, context: html, text, full: html, text
    36f8f6fb024b20cc523cdf9ebde7491eca84fd7c Sun Dec 6 20:33:20 2020 -0800
    multiple request per connect works except hgBlat
  • lines changed 2, context: html, text, full: html, text
    88485cfa7f13affa28ec5765fe9b2db90cce42b6 Tue Dec 8 21:02:15 2020 -0800
    hgPcr working
  • lines changed 1, context: html, text, full: html, text
    365534e1a97dc9250ff85e367a7786989662281d Mon Dec 14 14:01:20 2020 -0800
    updated gfServer version
• src/gfServer/tests/expected/testDynServerWithDir.out
  • lines changed 52, context: html, text, full: html, text
    a74c645505a135d5c1e923afe477cdeb9c15bded Wed Jul 8 22:27:42 2020 -0700
    added including multiple container directoies in genome dir path to gfServer
  • lines changed 3, context: html, text, full: html, text
    95030f73f067d8e8f9221a09c1811784607e4e72 Fri Jul 10 17:51:29 2020 -0700
    split dynamic server genomeDataPrefix into genome and genomeDataDir. More verbose, but clearer
  • lines changed 1, context: html, text, full: html, text
    f683064dc6a998206665b484790ef9d561e6c8a7 Sat Dec 5 22:42:53 2020 -0800
    initial conversion to gfServer connection to object
  • lines changed 2, context: html, text, full: html, text
    36f8f6fb024b20cc523cdf9ebde7491eca84fd7c Sun Dec 6 20:33:20 2020 -0800
    multiple request per connect works except hgBlat
  • lines changed 1, context: html, text, full: html, text
    365534e1a97dc9250ff85e367a7786989662281d Mon Dec 14 14:01:20 2020 -0800
    updated gfServer version
• src/gfServer/tests/expected/testIndexFile
  • lines changed 20, context: html, text, full: html, text
    a1c950cde18a4b977dc47c4528dfa6a9357a1f0f Mon Jul 13 19:13:08 2015 -0700
    Option for gfServer to save index as an mmap file on disk to speed startup.
  • lines changed 20, context: html, text, full: html, text
    ee8ef81c6d82157859f16548a27726f4b7421891 Mon Jul 6 19:22:14 2020 -0700
    added support for perSeqMax in dynamic server
• src/gfServer/tests/expected/testIndexFile.out
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    ee8ef81c6d82157859f16548a27726f4b7421891 Mon Jul 6 19:22:14 2020 -0700
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    a1c950cde18a4b977dc47c4528dfa6a9357a1f0f Mon Jul 13 19:13:08 2015 -0700
    Option for gfServer to save index as an mmap file on disk to speed startup.
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    ee8ef81c6d82157859f16548a27726f4b7421891 Mon Jul 6 19:22:14 2020 -0700
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    ee8ef81c6d82157859f16548a27726f4b7421891 Mon Jul 6 19:22:14 2020 -0700
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    ee8ef81c6d82157859f16548a27726f4b7421891 Mon Jul 6 19:22:14 2020 -0700
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    a74c645505a135d5c1e923afe477cdeb9c15bded Wed Jul 8 22:27:42 2020 -0700
    added including multiple container directoies in genome dir path to gfServer
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    ee8ef81c6d82157859f16548a27726f4b7421891 Mon Jul 6 19:22:14 2020 -0700
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    a74c645505a135d5c1e923afe477cdeb9c15bded Wed Jul 8 22:27:42 2020 -0700
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    ee8ef81c6d82157859f16548a27726f4b7421891 Mon Jul 6 19:22:14 2020 -0700
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    ee8ef81c6d82157859f16548a27726f4b7421891 Mon Jul 6 19:22:14 2020 -0700
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    ee8ef81c6d82157859f16548a27726f4b7421891 Mon Jul 6 19:22:14 2020 -0700
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    ee8ef81c6d82157859f16548a27726f4b7421891 Mon Jul 6 19:22:14 2020 -0700
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    ee8ef81c6d82157859f16548a27726f4b7421891 Mon Jul 6 19:22:14 2020 -0700
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    ee8ef81c6d82157859f16548a27726f4b7421891 Mon Jul 6 19:22:14 2020 -0700
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    ee8ef81c6d82157859f16548a27726f4b7421891 Mon Jul 6 19:22:14 2020 -0700
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    ee8ef81c6d82157859f16548a27726f4b7421891 Mon Jul 6 19:22:14 2020 -0700
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    ee8ef81c6d82157859f16548a27726f4b7421891 Mon Jul 6 19:22:14 2020 -0700
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    a74c645505a135d5c1e923afe477cdeb9c15bded Wed Jul 8 22:27:42 2020 -0700
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    5fcdf45fee21aa88247a68df00575e2865a9478e Sun Jun 28 14:50:30 2020 -0700
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    5fcdf45fee21aa88247a68df00575e2865a9478e Sun Jun 28 14:50:30 2020 -0700
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    ecacb0a15e8ddbe9b2e62381e30621ba70f82d8f Sun Jun 28 14:36:10 2020 -0700
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    5fcdf45fee21aa88247a68df00575e2865a9478e Sun Jun 28 14:50:30 2020 -0700
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    54a643b32015c6a4672bd540b4bf7a94a751e1ce Wed Feb 3 12:45:46 2021 -0800
    added unit test of gfServer dynamic PCR
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    ecacb0a15e8ddbe9b2e62381e30621ba70f82d8f Sun Jun 28 14:36:10 2020 -0700
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    ee8ef81c6d82157859f16548a27726f4b7421891 Mon Jul 6 19:22:14 2020 -0700
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    a74c645505a135d5c1e923afe477cdeb9c15bded Wed Jul 8 22:27:42 2020 -0700
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    95030f73f067d8e8f9221a09c1811784607e4e72 Fri Jul 10 17:51:29 2020 -0700
    split dynamic server genomeDataPrefix into genome and genomeDataDir. More verbose, but clearer
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    36f8f6fb024b20cc523cdf9ebde7491eca84fd7c Sun Dec 6 20:33:20 2020 -0800
    multiple request per connect works except hgBlat
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    54a643b32015c6a4672bd540b4bf7a94a751e1ce Wed Feb 3 12:45:46 2021 -0800
    added unit test of gfServer dynamic PCR
• src/gfServer/tests/testDynServerPerSeqMax
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    ee8ef81c6d82157859f16548a27726f4b7421891 Mon Jul 6 19:22:14 2020 -0700
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    a74c645505a135d5c1e923afe477cdeb9c15bded Wed Jul 8 22:27:42 2020 -0700
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    95030f73f067d8e8f9221a09c1811784607e4e72 Fri Jul 10 17:51:29 2020 -0700
    split dynamic server genomeDataPrefix into genome and genomeDataDir. More verbose, but clearer
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    36f8f6fb024b20cc523cdf9ebde7491eca84fd7c Sun Dec 6 20:33:20 2020 -0800
    multiple request per connect works except hgBlat
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    ee8ef81c6d82157859f16548a27726f4b7421891 Mon Jul 6 19:22:14 2020 -0700
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    a74c645505a135d5c1e923afe477cdeb9c15bded Wed Jul 8 22:27:42 2020 -0700
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    95030f73f067d8e8f9221a09c1811784607e4e72 Fri Jul 10 17:51:29 2020 -0700
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    36f8f6fb024b20cc523cdf9ebde7491eca84fd7c Sun Dec 6 20:33:20 2020 -0800
    multiple request per connect works except hgBlat
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    a74c645505a135d5c1e923afe477cdeb9c15bded Wed Jul 8 22:27:42 2020 -0700
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    95030f73f067d8e8f9221a09c1811784607e4e72 Fri Jul 10 17:51:29 2020 -0700
    split dynamic server genomeDataPrefix into genome and genomeDataDir. More verbose, but clearer
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    36f8f6fb024b20cc523cdf9ebde7491eca84fd7c Sun Dec 6 20:33:20 2020 -0800
    multiple request per connect works except hgBlat
• src/gfServer/tests/testIndexFile
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    a1c950cde18a4b977dc47c4528dfa6a9357a1f0f Mon Jul 13 19:13:08 2015 -0700
    Option for gfServer to save index as an mmap file on disk to speed startup.
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    766edf73c99da98b3935f42c234d14acf08c2c0e Sat Jun 27 19:37:45 2020 -0700
    move index building to a separate gfServer subcommand
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    ecacb0a15e8ddbe9b2e62381e30621ba70f82d8f Sun Jun 28 14:36:10 2020 -0700
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    ee8ef81c6d82157859f16548a27726f4b7421891 Mon Jul 6 19:22:14 2020 -0700
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    36f8f6fb024b20cc523cdf9ebde7491eca84fd7c Sun Dec 6 20:33:20 2020 -0800
    multiple request per connect works except hgBlat
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    f7d577042a7e3e41c1121082febb7ff25020bf0b Sun Feb 28 13:19:19 2021 -0800
    have gfServer check that index files match the required naming convention
• src/gfServer/tests/testIndexFileTrans
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    a1c950cde18a4b977dc47c4528dfa6a9357a1f0f Mon Jul 13 19:13:08 2015 -0700
    Option for gfServer to save index as an mmap file on disk to speed startup.
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    766edf73c99da98b3935f42c234d14acf08c2c0e Sat Jun 27 19:37:45 2020 -0700
    move index building to a separate gfServer subcommand
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    ecacb0a15e8ddbe9b2e62381e30621ba70f82d8f Sun Jun 28 14:36:10 2020 -0700
    dynamic server tests working
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    ee8ef81c6d82157859f16548a27726f4b7421891 Mon Jul 6 19:22:14 2020 -0700
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    36f8f6fb024b20cc523cdf9ebde7491eca84fd7c Sun Dec 6 20:33:20 2020 -0800
    multiple request per connect works except hgBlat
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    f7d577042a7e3e41c1121082febb7ff25020bf0b Sun Feb 28 13:19:19 2021 -0800
    have gfServer check that index files match the required naming convention
• src/gfServer/tests/testPcr
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    ee8ef81c6d82157859f16548a27726f4b7421891 Mon Jul 6 19:22:14 2020 -0700
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    36f8f6fb024b20cc523cdf9ebde7491eca84fd7c Sun Dec 6 20:33:20 2020 -0800
    multiple request per connect works except hgBlat
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    ee8ef81c6d82157859f16548a27726f4b7421891 Mon Jul 6 19:22:14 2020 -0700
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    36f8f6fb024b20cc523cdf9ebde7491eca84fd7c Sun Dec 6 20:33:20 2020 -0800
    multiple request per connect works except hgBlat
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    ee8ef81c6d82157859f16548a27726f4b7421891 Mon Jul 6 19:22:14 2020 -0700
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    36f8f6fb024b20cc523cdf9ebde7491eca84fd7c Sun Dec 6 20:33:20 2020 -0800
    multiple request per connect works except hgBlat
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    ee8ef81c6d82157859f16548a27726f4b7421891 Mon Jul 6 19:22:14 2020 -0700
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    36f8f6fb024b20cc523cdf9ebde7491eca84fd7c Sun Dec 6 20:33:20 2020 -0800
    multiple request per connect works except hgBlat
• src/gfServer/tests/testTransTwoBit
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    ee8ef81c6d82157859f16548a27726f4b7421891 Mon Jul 6 19:22:14 2020 -0700
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    36f8f6fb024b20cc523cdf9ebde7491eca84fd7c Sun Dec 6 20:33:20 2020 -0800
    multiple request per connect works except hgBlat
• src/gfServer/xinetd-example.conf
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    e764efe5d0e596213c72e69f028df0a667d0a83c Mon Jun 29 00:43:22 2020 +0000
    gfClient working with blat server running under xinetd
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    d8a949135724f97cfc92b52111ac223fece3dbf5 Mon Jun 29 14:53:25 2020 -0700
    got entire tree compliing with geneFind changes
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    c99b62d7865a828f8f41c6e82dd36cbd2dd26780 Wed Jul 1 21:45:43 2020 -0700
    hgBlat mostly works
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    87a162ccdc3ac94525fc1011dec5bc10e2cf2171 Thu Jul 2 16:12:57 2020 -0700
    web blat working
• src/hca/LICENSE
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
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• src/hca/fromGeo/geoToHcaStorm/geoToHcaStorm.c
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
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• src/hca/hcaColorCells/hcaColorCells.c
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
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• src/hca/hcaColorCells/makefile
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
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• src/hca/hcaColorCells/typeColors.tsv
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
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• src/hca/hcaUnifyMatrix/hcaUnifyMatrix.c
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
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• src/hca/hcaUnifyMatrix/makefile
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
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• src/hca/hcaUnpack5/hcaUnpack5.c
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
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• src/hca/hcaUnpack5/makefile
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
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• src/hca/hcat/hcatParseParth/hcatParseParth.c
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
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• src/hca/hcat/mysite/hcat/admin.py
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
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• src/hca/hcat/mysite/hcat/api.py
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
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• src/hca/hcat/mysite/hcat/api_urls.py
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
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• src/hca/hcat/mysite/hcat/index_urls.py
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• src/hca/hcat/mysite/hcat/models.py
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• src/hca/hcat/mysite/hcat/views.py
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
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• src/hca/hcat/mysite/mysite/urls.py
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
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• src/hca/hcat/mysite/templates/hcat/index.html
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
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• src/hca/hcat/mysite/versions.txt
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• src/hg/cirm/cdw/cdwMakeValidFile/cdwMakeValidFile.c
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    426b7a4e4fb45d6bb248ff00572c3cc62aa472d8 Wed Mar 3 18:00:08 2021 -0800
    Fix compiler complaint. This code is from 2014.
• src/hg/featureBits/featureBits.c
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    d248ea47e2ffed0b22206642ad3477c1213ec5cc Wed Mar 3 14:15:32 2021 -0800
    add -countBlocks option. Support bigBeds.
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    14a7e9de4b1e9c2cc6fd6c1b4912c147afd05064 Fri Mar 5 10:56:27 2021 -0800
    fix up usage message to make it clearer that bigBeds are allowed and that the tool does a bitwise AND
• src/hg/geneBounds/clusterGenes/clusterGenes.c
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
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• src/hg/geneBounds/clusterGenes/tests/expected/ignoreBasesTinyTest.gl
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
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• src/hg/geneBounds/clusterGenes/tests/input/Mt-tRNA.gp
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• src/hg/geneBounds/clusterGenes/tests/makefile
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• src/hg/hgBlat/hgBlat.c
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    d8a949135724f97cfc92b52111ac223fece3dbf5 Mon Jun 29 14:53:25 2020 -0700
    got entire tree compliing with geneFind changes
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    c99b62d7865a828f8f41c6e82dd36cbd2dd26780 Wed Jul 1 21:45:43 2020 -0700
    hgBlat mostly works
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    f50fee44b129d516772f00d7a1d00be2f3953e6f Thu Jul 2 11:50:46 2020 -0700
    hgBlat appears to be working
  • lines changed 14, context: html, text, full: html, text
    0ede364a2dcb452681933d5a3579b4f05d90a245 Sun Jul 5 15:16:27 2020 -0700
    fixed bug where totalSeqSize was not stored in index, now hgBlat works
  • lines changed 94, context: html, text, full: html, text
    84dba0006acf65324bb843abee1e11ad02c0a912 Sun Jul 5 20:01:10 2020 -0700
    some cleanup about hgBlat
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    a74c645505a135d5c1e923afe477cdeb9c15bded Wed Jul 8 22:27:42 2020 -0700
    added including multiple container directoies in genome dir path to gfServer
  • lines changed 45, context: html, text, full: html, text
    95030f73f067d8e8f9221a09c1811784607e4e72 Fri Jul 10 17:51:29 2020 -0700
    split dynamic server genomeDataPrefix into genome and genomeDataDir. More verbose, but clearer
  • lines changed 80, context: html, text, full: html, text
    9186d6410c3266a7069c81e642c9ea22dc981191 Sun Oct 25 20:12:47 2020 -0700
    merged master
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    f683064dc6a998206665b484790ef9d561e6c8a7 Sat Dec 5 22:42:53 2020 -0800
    initial conversion to gfServer connection to object
  • lines changed 14, context: html, text, full: html, text
    36f8f6fb024b20cc523cdf9ebde7491eca84fd7c Sun Dec 6 20:33:20 2020 -0800
    multiple request per connect works except hgBlat
  • lines changed 35, context: html, text, full: html, text
    e9492dbfa8a68aee133893d4b02475b0aec27bb9 Sun Dec 6 23:48:42 2020 -0800
    webblat and hgBlat working
  • lines changed 35, context: html, text, full: html, text
    88485cfa7f13affa28ec5765fe9b2db90cce42b6 Tue Dec 8 21:02:15 2020 -0800
    hgPcr working
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    f16dbe1fef6a6fd83d63fbc7e060b21262b43bf5 Mon Feb 8 15:26:55 2021 -0800
    don't include dynamic gfServer in blat of all genomes
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    73c09a61e57baf2a2ab6548c2a2bfe0cf3303600 Thu Mar 4 11:11:57 2021 -0800
    provide hint to look in systems logs when blat server failes
• src/hg/hgGateway/hgGateway.c
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/hg/hgGateway/hgGateway.html
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
• src/hg/hgGene/hgGene.c
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
• src/hg/hgGene/hgGeneData/Human/links.ra
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
• src/hg/hgGene/malaCards.c
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
• src/hg/hgGene/sequence.c
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
• src/hg/hgHubConnect/hgHubConnect.c
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/hg/hgMenubar/hgMenubar.c
  • lines changed 14, context: html, text, full: html, text
    7b7b0c1b25ef841ec99db2fc02b225a1999015af Tue Feb 2 10:19:17 2021 -0800
    Allow menubar links to hgTracks to use the current web browser window size for hgTracks image width
• src/hg/hgPcr/hgPcr.c
  • lines changed 33, context: html, text, full: html, text
    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
  • lines changed 33, context: html, text, full: html, text
    88485cfa7f13affa28ec5765fe9b2db90cce42b6 Tue Dec 8 21:02:15 2020 -0800
    hgPcr working
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    94a2d41644d235ec3702d8189ec52036e739000a Sun Feb 28 14:23:10 2021 -0800
    merge master into branch
• src/hg/hgPhyloPlace/hgPhyloPlace.c
  • lines changed 428, context: html, text, full: html, text
    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
  • lines changed 18, context: html, text, full: html, text
    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
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    68b2af5491e6f6bf71448ef639ac524823998e2a Fri Mar 5 15:27:26 2021 -0800
    Add embed & link to CDC Genomic Epi Toolkit training module for UShER.
• src/hg/hgPhyloPlace/makefile
  • lines changed 29, context: html, text, full: html, text
    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
• src/hg/hgPhyloPlace/parsimonyProto.c
  • lines changed 275, context: html, text, full: html, text
    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
• src/hg/hgPhyloPlace/parsimonyProto.h
  • lines changed 42, context: html, text, full: html, text
    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
• src/hg/hgPhyloPlace/phyloPlace.c
  • lines changed 1581, context: html, text, full: html, text
    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
  • lines changed 11, context: html, text, full: html, text
    e9cd3eef710ba3141d58ef119006b7d2327e5b7f Wed Dec 9 13:52:01 2020 -0800
    fixed accidently backout of master changes in the last merge
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
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    af86e1b9d932d0834eee1be7fe2ca77166203c48 Wed Mar 3 18:37:10 2021 -0800
    Add row of quick download links between button row and summary table.
  • lines changed 45, context: html, text, full: html, text
    e267c9ec78e654975dbcd0bb8d5b4bf393187269 Thu Mar 4 15:39:32 2021 -0800
    Add ZIP file of subtree JSON & Newick files for download. Add subtree numbers to the filenames so it's not all trashDir soup.
  • lines changed 26, context: html, text, full: html, text
    3d0cfdfcc3d36bb37899de639d21a1211ba52680 Thu Mar 4 17:49:44 2021 -0800
    Change 'comprehensive subtree' to 'single subtree' and add mouseovers to 'view in *' buttons. Thx Russ.
• src/hg/hgPhyloPlace/phyloPlace.h
  • lines changed 161, context: html, text, full: html, text
    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
  • lines changed 3, context: html, text, full: html, text
    3d0cfdfcc3d36bb37899de639d21a1211ba52680 Thu Mar 4 17:49:44 2021 -0800
    Change 'comprehensive subtree' to 'single subtree' and add mouseovers to 'view in *' buttons. Thx Russ.
• src/hg/hgPhyloPlace/phyloPlaceMain.c
  • lines changed 40, context: html, text, full: html, text
    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/hg/hgPhyloPlace/runUsher.c
  • lines changed 767, context: html, text, full: html, text
    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
  • lines changed 11, context: html, text, full: html, text
    e267c9ec78e654975dbcd0bb8d5b4bf393187269 Thu Mar 4 15:39:32 2021 -0800
    Add ZIP file of subtree JSON & Newick files for download. Add subtree numbers to the filenames so it's not all trashDir soup.
  • lines changed 2, context: html, text, full: html, text
    3d0cfdfcc3d36bb37899de639d21a1211ba52680 Thu Mar 4 17:49:44 2021 -0800
    Change 'comprehensive subtree' to 'single subtree' and add mouseovers to 'view in *' buttons. Thx Russ.
• src/hg/hgPhyloPlace/treeToAuspiceJson.c
  • lines changed 467, context: html, text, full: html, text
    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
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    e9cd3eef710ba3141d58ef119006b7d2327e5b7f Wed Dec 9 13:52:01 2020 -0800
    fixed accidently backout of master changes in the last merge
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/hg/hgPhyloPlace/vcfFromFasta.c
  • lines changed 519, context: html, text, full: html, text
    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
  • lines changed 2, context: html, text, full: html, text
    e267c9ec78e654975dbcd0bb8d5b4bf393187269 Thu Mar 4 15:39:32 2021 -0800
    Add ZIP file of subtree JSON & Newick files for download. Add subtree numbers to the filenames so it's not all trashDir soup.
• src/hg/hgPhyloPlace/writeCustomTracks.c
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/hg/hgPublicSessions/hgPublicSessions.c
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
• src/hg/hgTrackUi/hgTrackUi.c
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    8b044d5f4044e8450db06f21481249e95bec7f85 Wed Mar 3 17:07:11 2021 -0800
    Multi-region link on hgTrackUi now turns track on in dense if it was hidden. Responding to QA note 22. refs #26385
• src/hg/hgTracks/barChartTrack.c
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/hg/hgTracks/bigBedTrack.c
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/hg/hgTracks/cds.c
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    e9cd3eef710ba3141d58ef119006b7d2327e5b7f Wed Dec 9 13:52:01 2020 -0800
    fixed accidently backout of master changes in the last merge
• src/hg/hgTracks/config.c
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
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    e9cd3eef710ba3141d58ef119006b7d2327e5b7f Wed Dec 9 13:52:01 2020 -0800
    fixed accidently backout of master changes in the last merge
  • lines changed 1, context: html, text, full: html, text
    35b3c483895c5ee49ad380200a342db959da6d3f Thu Mar 4 17:07:25 2021 -0800
    Add multi-region mode and improve layout a bit on position box popup. refs #26385
• src/hg/hgTracks/extTools.c
  • lines changed 1, context: html, text, full: html, text
    c2e376e7b6d980f41ff903e6374378d668f11770 Thu Oct 22 14:41:52 2020 -0700
    Multi-region features for sparse tracks. With virt->multi, needs debug. refs #26385
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    a0a09fc6e6c25f19d12fec548b834b931976207d Mon Dec 28 12:27:56 2020 -0800
    Minor cleanup. refs #26385
• src/hg/hgTracks/hgTracks.c
  • lines changed 34, context: html, text, full: html, text
    c2e376e7b6d980f41ff903e6374378d668f11770 Thu Oct 22 14:41:52 2020 -0700
    Multi-region features for sparse tracks. With virt->multi, needs debug. refs #26385
  • lines changed 22, context: html, text, full: html, text
    9e9fdcd37b60aa4186eeea2b2c61df277dbfeb5a Thu Oct 22 15:48:16 2020 -0700
    Add multi-region button to position line and lighten highlights on alternating regions. Part of improving multi-region features for sparse track use. refs #26385
  • lines changed 99, context: html, text, full: html, text
    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
  • lines changed 24, context: html, text, full: html, text
    e9cd3eef710ba3141d58ef119006b7d2327e5b7f Wed Dec 9 13:52:01 2020 -0800
    fixed accidently backout of master changes in the last merge
  • lines changed 1, context: html, text, full: html, text
    425201196cb484fc22f36b66dcd15f370de800c8 Mon Dec 28 10:52:54 2020 -0800
    Better var name, slight color tweak on multi-region alt coloring change (for better visibility). refs #26385
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    87b7884a455030761304f18056a4e8a265b8cfaa Fri Jan 8 09:35:47 2021 -0800
    Resolving merge conflict
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    dcb87cc5b6d91351982761d957b1564b005acf9b Fri Jan 8 14:47:16 2021 -0800
    Fix merge problem
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    981add832de5beb7820a5337a4958f77d66aaad2 Fri Jan 8 14:48:43 2021 -0800
    Fix whitespace
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
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    0ba941dfe2f00a5f8e62a44264489fd9253e504d Thu Feb 25 16:20:53 2021 -0800
    Fix missed virt->multi changes. TODO: #define.
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    f53faebbe7aeb41c71623aeaea19cac84fb728af Thu Feb 25 16:47:50 2021 -0800
    Remove now-redundant multi-region button. Change exit button to be more informative. refs #26385
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    f1065efe3aadb9b2f83c1a3a0a48afd9a47d9153 Mon Mar 1 15:57:17 2021 -0800
    implement wiggleWindow that forces a track into density coverage mode when the window exceeds a specified width
  • lines changed 6, context: html, text, full: html, text
    d6e12e6e9c7dc09ef516984f150664165a48d9df Tue Mar 2 16:54:21 2021 -0800
    Tweak MR exit button label and mouseover. refs #26385
  • lines changed 5, context: html, text, full: html, text
    6da74d6034610d2ce3fe7ac708110c0e0e3d3a1c Tue Mar 2 17:02:43 2021 -0800
    Define string literal for multi-region chrom name. refs #26385
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    3acf3830a00e2e600b62a41a4c4d56a6c2ef4a23 Wed Mar 3 10:12:36 2021 -0800
    Add link to COVID landing page to virus browser footer. refs #27117
  • lines changed 1, context: html, text, full: html, text
    35b3c483895c5ee49ad380200a342db959da6d3f Thu Mar 4 17:07:25 2021 -0800
    Add multi-region mode and improve layout a bit on position box popup. refs #26385
  • lines changed 20, context: html, text, full: html, text
    a8be2f912e75d724a5d0d313e8488e82fd28e4ec Fri Mar 5 12:32:20 2021 -0800
    Retire 'exit multi-region' button idea. With multi-region button on position line and more informative mouseovers and popups it should be easier now for new multi-region users to exit. refs #26385
  • lines changed 3, context: html, text, full: html, text
    a8f242d425795e25ce0e0cce6d7cec9d8d8a3b6a Fri Mar 5 12:43:40 2021 -0800
    Context sensitive mouseover for multi-region button. refs #26385
• src/hg/hgTracks/hgTracks.h
  • lines changed 3, context: html, text, full: html, text
    c2e376e7b6d980f41ff903e6374378d668f11770 Thu Oct 22 14:41:52 2020 -0700
    Multi-region features for sparse tracks. With virt->multi, needs debug. refs #26385
  • lines changed 1, context: html, text, full: html, text
    9e9fdcd37b60aa4186eeea2b2c61df277dbfeb5a Thu Oct 22 15:48:16 2020 -0700
    Add multi-region button to position line and lighten highlights on alternating regions. Part of improving multi-region features for sparse track use. refs #26385
  • lines changed 16, context: html, text, full: html, text
    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
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    e9cd3eef710ba3141d58ef119006b7d2327e5b7f Wed Dec 9 13:52:01 2020 -0800
    fixed accidently backout of master changes in the last merge
  • lines changed 1, context: html, text, full: html, text
    425201196cb484fc22f36b66dcd15f370de800c8 Mon Dec 28 10:52:54 2020 -0800
    Better var name, slight color tweak on multi-region alt coloring change (for better visibility). refs #26385
  • lines changed 2, context: html, text, full: html, text
    a0a09fc6e6c25f19d12fec548b834b931976207d Mon Dec 28 12:27:56 2020 -0800
    Minor cleanup. refs #26385
  • lines changed 2, context: html, text, full: html, text
    f1065efe3aadb9b2f83c1a3a0a48afd9a47d9153 Mon Mar 1 15:57:17 2021 -0800
    implement wiggleWindow that forces a track into density coverage mode when the window exceeds a specified width
  • lines changed 3, context: html, text, full: html, text
    6da74d6034610d2ce3fe7ac708110c0e0e3d3a1c Tue Mar 2 17:02:43 2021 -0800
    Define string literal for multi-region chrom name. refs #26385
• src/hg/hgTracks/imageV2.c
  • lines changed 7, context: html, text, full: html, text
    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
  • lines changed 1, context: html, text, full: html, text
    0ba941dfe2f00a5f8e62a44264489fd9253e504d Thu Feb 25 16:20:53 2021 -0800
    Fix missed virt->multi changes. TODO: #define.
  • lines changed 1, context: html, text, full: html, text
    6da74d6034610d2ce3fe7ac708110c0e0e3d3a1c Tue Mar 2 17:02:43 2021 -0800
    Define string literal for multi-region chrom name. refs #26385
• src/hg/hgTracks/lolly.h
  • lines changed 1, context: html, text, full: html, text
    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
• src/hg/hgTracks/lollyTrack.c
  • lines changed 115, context: html, text, full: html, text
    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
  • lines changed 93, context: html, text, full: html, text
    e9cd3eef710ba3141d58ef119006b7d2327e5b7f Wed Dec 9 13:52:01 2020 -0800
    fixed accidently backout of master changes in the last merge
• src/hg/hgTracks/mainMain.c
  • lines changed 1, context: html, text, full: html, text
    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
• src/hg/hgTracks/simpleTracks.c
  • lines changed 1, context: html, text, full: html, text
    c2e376e7b6d980f41ff903e6374378d668f11770 Thu Oct 22 14:41:52 2020 -0700
    Multi-region features for sparse tracks. With virt->multi, needs debug. refs #26385
  • lines changed 1, context: html, text, full: html, text
    9e9fdcd37b60aa4186eeea2b2c61df277dbfeb5a Thu Oct 22 15:48:16 2020 -0700
    Add multi-region button to position line and lighten highlights on alternating regions. Part of improving multi-region features for sparse track use. refs #26385
  • lines changed 116, context: html, text, full: html, text
    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
  • lines changed 1, context: html, text, full: html, text
    e9cd3eef710ba3141d58ef119006b7d2327e5b7f Wed Dec 9 13:52:01 2020 -0800
    fixed accidently backout of master changes in the last merge
  • lines changed 1, context: html, text, full: html, text
    425201196cb484fc22f36b66dcd15f370de800c8 Mon Dec 28 10:52:54 2020 -0800
    Better var name, slight color tweak on multi-region alt coloring change (for better visibility). refs #26385
  • lines changed 9, context: html, text, full: html, text
    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
  • lines changed 18, context: html, text, full: html, text
    f1065efe3aadb9b2f83c1a3a0a48afd9a47d9153 Mon Mar 1 15:57:17 2021 -0800
    implement wiggleWindow that forces a track into density coverage mode when the window exceeds a specified width
  • lines changed 2, context: html, text, full: html, text
    2126da777ab1677598eeb020127005477ee51ac9 Tue Mar 2 14:49:29 2021 -0800
    when counting overlaps for density coverage, make zero width elements cover a single base.
• src/hg/hgTracks/snakeTrack.c
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/hg/hgTracks/vcfTrack.c
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    da3eb1b03ab9bd4ef7a02e120297d9293143ff3c Thu Feb 4 16:50:34 2021 -0800
    don't attempt to connect to database for blat results user input, including hubs
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    8b044d5f4044e8450db06f21481249e95bec7f85 Wed Mar 3 17:07:11 2021 -0800
    Multi-region link on hgTrackUi now turns track on in dense if it was hidden. Responding to QA note 22. refs #26385
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    e1487d60d004ee8de24e6e1e7dfd12919104e19d Thu Mar 4 09:37:02 2021 -0800
    allow use of blat custom track in DNA extra color/case options #23045
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    e674e530d83be9a0408a4e35c8940547c0b07a8b Fri Mar 5 10:12:57 2021 -0800
    Adding documentation for Protein-translated BLAT having different results, refs #26658
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    ec353cf62c93231178f40d06f4e7df7bfb283ee9 Fri Mar 5 15:49:19 2021 -0800
    Added link to CDC Genomic Epi Toolkit training module for UShER.
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    c99b62d7865a828f8f41c6e82dd36cbd2dd26780 Wed Jul 1 21:45:43 2020 -0700
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    a74c645505a135d5c1e923afe477cdeb9c15bded Wed Jul 8 22:27:42 2020 -0700
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    95030f73f067d8e8f9221a09c1811784607e4e72 Fri Jul 10 17:51:29 2020 -0700
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    88485cfa7f13affa28ec5765fe9b2db90cce42b6 Tue Dec 8 21:02:15 2020 -0800
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    03e853f795d04dbdd939c9fbef0186cc339bafde Mon Jan 25 18:02:10 2021 -0800
    Adding example on how to make gfidx files and updating the doc, refs #26658
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    7ffff6bd3e03eb510a4324993ab2da5812bd036d Wed Jan 27 10:11:04 2021 -0800
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    6d36881dee4bc2a4256614638aec4dddf3c26f44 Wed Jan 27 19:33:09 2021 -0800
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    71a2c73633337ab11c6344fee8c077e13daf815b Tue Feb 2 12:03:42 2021 -0800
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    a38ee8e9f00ea181dab4374a2a1589ad2e9731d0 Tue Mar 2 16:48:02 2021 -0800
    Announcing the CADD tracks for hg19 and hg38, refs #18492
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    50d9c48ac1cbb26bfbbb5e132f69d5391d782f7d Wed Mar 3 08:08:34 2021 -0800
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    d1043a6f746fc5a39c7e13ff94224349304d1d35 Wed Mar 3 12:01:01 2021 -0800
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    744e6a65e839abcb8d67881d4dbb74ac21948fbd Wed Mar 3 12:03:36 2021 -0800
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    1d818f2b16ef453c7a9021949fd77ec4acf3d8d7 Thu Mar 4 17:52:03 2021 -0800
    Announcing refSeq update refs #26428
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    bb99f79b6364b8a88a8712726acdee19cf18c3b5 Fri Mar 5 15:21:08 2021 -0800
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    a38ee8e9f00ea181dab4374a2a1589ad2e9731d0 Tue Mar 2 16:48:02 2021 -0800
    Announcing the CADD tracks for hg19 and hg38, refs #18492
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    1d818f2b16ef453c7a9021949fd77ec4acf3d8d7 Thu Mar 4 17:52:03 2021 -0800
    Announcing refSeq update refs #26428
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    0ede364a2dcb452681933d5a3579b4f05d90a245 Sun Jul 5 15:16:27 2020 -0700
    fixed bug where totalSeqSize was not stored in index, now hgBlat works
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    c2e376e7b6d980f41ff903e6374378d668f11770 Thu Oct 22 14:41:52 2020 -0700
    Multi-region features for sparse tracks. With virt->multi, needs debug. refs #26385
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    7aa4e34c4a9855457ff806186ba65594e03ae6ac Wed Dec 30 16:03:35 2020 -0800
    First cut support for multiRegionBedUrl setting. refs #26385
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    8b044d5f4044e8450db06f21481249e95bec7f85 Wed Mar 3 17:07:11 2021 -0800
    Multi-region link on hgTrackUi now turns track on in dense if it was hidden. Responding to QA note 22. refs #26385
• src/hg/inc/protobuf.h
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
• src/hg/inc/trackDb.h
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/hg/inc/trackHub.h
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    c99b62d7865a828f8f41c6e82dd36cbd2dd26780 Wed Jul 1 21:45:43 2020 -0700
    hgBlat mostly works
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    a74c645505a135d5c1e923afe477cdeb9c15bded Wed Jul 8 22:27:42 2020 -0700
    added including multiple container directoies in genome dir path to gfServer
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    95030f73f067d8e8f9221a09c1811784607e4e72 Fri Jul 10 17:51:29 2020 -0700
    split dynamic server genomeDataPrefix into genome and genomeDataDir. More verbose, but clearer
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
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    88485cfa7f13affa28ec5765fe9b2db90cce42b6 Tue Dec 8 21:02:15 2020 -0800
    hgPcr working
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/hg/inc/trackLayout.h
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
• src/hg/inc/versionInfo.h
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
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    e9cd3eef710ba3141d58ef119006b7d2327e5b7f Wed Dec 9 13:52:01 2020 -0800
    fixed accidently backout of master changes in the last merge
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/hg/js/ajax.js
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
• src/hg/js/hgGateway.js
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/hg/js/hgTracks.js
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    c2e376e7b6d980f41ff903e6374378d668f11770 Thu Oct 22 14:41:52 2020 -0700
    Multi-region features for sparse tracks. With virt->multi, needs debug. refs #26385
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
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    28b9aa965d7f2e912fcad511f85e46b122e42261 Wed Feb 10 16:46:09 2021 -0800
    Surface up any warnings or errors that came about from an ajax update, refs #26847
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    35b3c483895c5ee49ad380200a342db959da6d3f Thu Mar 4 17:07:25 2021 -0800
    Add multi-region mode and improve layout a bit on position box popup. refs #26385
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    23cc4593ea500af7329317e9ce60875dd458233a Fri Mar 5 12:12:51 2021 -0800
    Rejecting idea of MR exit button here. Removing useless OK button. refs #26385
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    b84c039e779dc79ed16f6828cc17f30a7fae88a1 Fri Mar 5 12:53:24 2021 -0800
    Tweak wording on position info popup. refs #26385
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    e5469e2dd98bc8aeacbc6e77fc6b344aebe6327e Mon Mar 8 07:00:03 2021 -0800
    fixing mouseclick problem for gene tracks, refs #26687
• src/hg/js/hui.js
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/hg/js/mouseOver.js
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
• src/hg/js/subCfg.js
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
• src/hg/lib/barChartUi.c
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/hg/lib/blatServers.as
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    0ede364a2dcb452681933d5a3579b4f05d90a245 Sun Jul 5 15:16:27 2020 -0700
    fixed bug where totalSeqSize was not stored in index, now hgBlat works
• src/hg/lib/blatServers.c
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    0ede364a2dcb452681933d5a3579b4f05d90a245 Sun Jul 5 15:16:27 2020 -0700
    fixed bug where totalSeqSize was not stored in index, now hgBlat works
• src/hg/lib/blatServers.sql
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    0ede364a2dcb452681933d5a3579b4f05d90a245 Sun Jul 5 15:16:27 2020 -0700
    fixed bug where totalSeqSize was not stored in index, now hgBlat works
• src/hg/lib/cart.c
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/hg/lib/cartDb.c
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
• src/hg/lib/clinvarSubLolly.as
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/hg/lib/coordConv.c
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    d8a949135724f97cfc92b52111ac223fece3dbf5 Mon Jun 29 14:53:25 2020 -0700
    got entire tree compliing with geneFind changes
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    bff6869213fd1af019c635141ceab9d3078e959d Thu Oct 15 10:38:36 2020 -0700
    fixed missing function arguments not detect due to lack of dependency checking
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    f683064dc6a998206665b484790ef9d561e6c8a7 Sat Dec 5 22:42:53 2020 -0800
    initial conversion to gfServer connection to object
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    36f8f6fb024b20cc523cdf9ebde7491eca84fd7c Sun Dec 6 20:33:20 2020 -0800
    multiple request per connect works except hgBlat
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    88485cfa7f13affa28ec5765fe9b2db90cce42b6 Tue Dec 8 21:02:15 2020 -0800
    hgPcr working
• src/hg/lib/customFactory.c
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
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    e1487d60d004ee8de24e6e1e7dfd12919104e19d Thu Mar 4 09:37:02 2021 -0800
    allow use of blat custom track in DNA extra color/case options #23045
• src/hg/lib/customTrack.c
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/hg/lib/defaultCart.as
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
• src/hg/lib/defaultCart.sql
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
• src/hg/lib/gencodeBGP.as
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/hg/lib/hAnno.c
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
• src/hg/lib/hdb.c
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/hg/lib/hgFind.c
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    c2e376e7b6d980f41ff903e6374378d668f11770 Thu Oct 22 14:41:52 2020 -0700
    Multi-region features for sparse tracks. With virt->multi, needs debug. refs #26385
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    a0a09fc6e6c25f19d12fec548b834b931976207d Mon Dec 28 12:27:56 2020 -0800
    Minor cleanup. refs #26385
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/hg/lib/hgMaf.c
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/hg/lib/hubConnect.c
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/hg/lib/hui.c
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
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    7aa4e34c4a9855457ff806186ba65594e03ae6ac Wed Dec 30 16:03:35 2020 -0800
    First cut support for multiRegionBedUrl setting. refs #26385
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    0c511f781581025b2963c78ef87f090435fa2a73 Mon Jan 4 16:13:07 2021 -0800
    Create trashfile for custom bed url, as multi-region code doesn't currently handle custom bed file (maybe change this later). refs #26385
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    d772009c6a70cb89a5baa33bc58499f1286827cb Fri Jan 8 09:21:34 2021 -0800
    Add padding to multi-region view and custom track generated by multiRegionBedUrl setting. refs #26385
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    bd998f55bff39941de393c98ae3bb5e26ebdd836 Wed Feb 24 16:45:44 2021 -0800
    Changes to link wording, from review input. refs #26385
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    d4c1526c6c8d7a2b709fbeaa336bfc01c4a76ed5 Tue Mar 2 14:53:56 2021 -0800
    add density coverage option to bigBeds
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    c9c3b2b4a6fb478e5cd4c8b987af8647e1ed5ee6 Wed Mar 3 09:51:12 2021 -0800
    Tweak link wording. refs #26385
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    b57070bef85b2c81db85b865075f2dfd3822b021 Wed Mar 3 09:58:45 2021 -0800
    Trivial text change. refs #26385
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    8b044d5f4044e8450db06f21481249e95bec7f85 Wed Mar 3 17:07:11 2021 -0800
    Multi-region link on hgTrackUi now turns track on in dense if it was hidden. Responding to QA note 22. refs #26385
• src/hg/lib/mafGene.c
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/hg/lib/makefile
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
• src/hg/lib/mane.as
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
• src/hg/lib/protobuf.c
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
• src/hg/lib/psl.as
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/hg/lib/simpleBarChartBed.as
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/hg/lib/tests/expected/hgvs/validTerms.txt
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
• src/hg/lib/tests/input/hgvs/validTerms.txt
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
• src/hg/lib/trackDbCache.c
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/hg/lib/trackDbCustom.c
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/hg/lib/trackHub.c
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    c99b62d7865a828f8f41c6e82dd36cbd2dd26780 Wed Jul 1 21:45:43 2020 -0700
    hgBlat mostly works
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    a74c645505a135d5c1e923afe477cdeb9c15bded Wed Jul 8 22:27:42 2020 -0700
    added including multiple container directoies in genome dir path to gfServer
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    95030f73f067d8e8f9221a09c1811784607e4e72 Fri Jul 10 17:51:29 2020 -0700
    split dynamic server genomeDataPrefix into genome and genomeDataDir. More verbose, but clearer
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
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    88485cfa7f13affa28ec5765fe9b2db90cce42b6 Tue Dec 8 21:02:15 2020 -0800
    hgPcr working
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/hg/lib/trackLayout.c
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
• src/hg/lib/variantProjector.c
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    04f1eb41233f2cd7dd80fb51f36eda1462f2899f Wed Mar 3 15:26:23 2021 -0800
    Code review feedback: ';;' --> ';'. refs #27102
• src/hg/lib/web.c
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    7b7b0c1b25ef841ec99db2fc02b225a1999015af Tue Feb 2 10:19:17 2021 -0800
    Allow menubar links to hgTracks to use the current web browser window size for hgTracks image width
• src/hg/lib/wiggleCart.c
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/hg/liftOver/liftOver.c
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/hg/makeDb/doc/asmHubs/README.txt
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    e9cd3eef710ba3141d58ef119006b7d2327e5b7f Wed Dec 9 13:52:01 2020 -0800
    fixed accidently backout of master changes in the last merge
• src/hg/makeDb/doc/asmHubs/asmHubList.pl
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    c7691c65d7065503634bab2c3468c66da1d83bba Tue Mar 2 13:36:23 2021 -0800
    script to produce list of assembly hubs refs #26953
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    50d655bec99c9e0a4f201ced82513d4c936af575 Wed Mar 3 20:14:44 2021 -0800
    now creating useOneFile hub.txt files for each individual hub and separate files for download and adding blat servers for hubs on hgwdev refs #26658
• src/hg/makeDb/doc/asmHubs/asmHubs.mk
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
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    50d655bec99c9e0a4f201ced82513d4c936af575 Wed Mar 3 20:14:44 2021 -0800
    now creating useOneFile hub.txt files for each individual hub and separate files for download and adding blat servers for hubs on hgwdev refs #26658
• src/hg/makeDb/doc/asmHubs/commonHtml.pm
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
• src/hg/makeDb/doc/asmHubs/hgdownload.index.html
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/hg/makeDb/doc/asmHubs/master.run.list
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
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    e9cd3eef710ba3141d58ef119006b7d2327e5b7f Wed Dec 9 13:52:01 2020 -0800
    fixed accidently backout of master changes in the last merge
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/hg/makeDb/doc/asmHubs/mkGenomes.pl
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    50d655bec99c9e0a4f201ced82513d4c936af575 Wed Mar 3 20:14:44 2021 -0800
    now creating useOneFile hub.txt files for each individual hub and separate files for download and adding blat servers for hubs on hgwdev refs #26658
• src/hg/makeDb/doc/asmHubs/mkSymLinks.pl
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
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    50d655bec99c9e0a4f201ced82513d4c936af575 Wed Mar 3 20:14:44 2021 -0800
    now creating useOneFile hub.txt files for each individual hub and separate files for download and adding blat servers for hubs on hgwdev refs #26658
• src/hg/makeDb/doc/asmHubs/runBuild
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
• src/hg/makeDb/doc/asmHubs/sendToHgdownload.sh
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    50d655bec99c9e0a4f201ced82513d4c936af575 Wed Mar 3 20:14:44 2021 -0800
    now creating useOneFile hub.txt files for each individual hub and separate files for download and adding blat servers for hubs on hgwdev refs #26658
• src/hg/makeDb/doc/asmHubs/trackData.pl
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    50d655bec99c9e0a4f201ced82513d4c936af575 Wed Mar 3 20:14:44 2021 -0800
    now creating useOneFile hub.txt files for each individual hub and separate files for download and adding blat servers for hubs on hgwdev refs #26658
• src/hg/makeDb/doc/bacteriaAsmHub/bacteria.orderList.tsv
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    574f7095d8e9ca85e7a9f553293e940b246a91e0 Thu Mar 4 17:53:29 2021 -0800
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    76a9aca93d79779eb06c977825e5688c9c2d0f47 Wed Mar 3 11:43:03 2021 -0800
    Adding the pennantIcon for the announcement. Adding scoreFilterLimits for the CADD track, refs #18492
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    458a7adb89d69f13d1378e8902af527423a1f36e Thu Mar 4 14:09:15 2021 -0800
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    76a9aca93d79779eb06c977825e5688c9c2d0f47 Wed Mar 3 11:43:03 2021 -0800
    Adding the pennantIcon for the announcement. Adding scoreFilterLimits for the CADD track, refs #18492
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    458a7adb89d69f13d1378e8902af527423a1f36e Thu Mar 4 14:09:15 2021 -0800
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    c2e376e7b6d980f41ff903e6374378d668f11770 Thu Oct 22 14:41:52 2020 -0700
    Multi-region features for sparse tracks. With virt->multi, needs debug. refs #26385
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    03ae1252cec23efcd1fdfd14504c80ef327878f8 Mon Mar 1 16:08:19 2021 -0800
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    c6a61db1102453d3428e9e5f926e37de8acd673d Thu Mar 4 09:40:01 2021 -0800
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    83148f6863903c0d0395d17d6b727c337defbffd Thu Mar 4 09:12:16 2021 -0800
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    a0d381e86081dc1e4d53c8a519a30db607d30c7f Thu Mar 4 13:40:57 2021 -0800
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    Adding pennantIcon to ncbiRefSeq update refs #26248
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    First cut support for multiRegionBedUrl setting. refs #26385
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    9707698a681e0089ab2d04955a70d1e1594e8a8f Tue Mar 2 15:33:40 2021 -0800
    Except cytoBandIdeo from track description page check in hubCheck, refs #27108
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• src/hg/utils/otto/sarscov2phylo/bioSampleIdToText.sh
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• src/hg/utils/otto/sarscov2phylo/gbMetadataAddBioSample.pl
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    396fc7273c589cc83a4107a365fe67aa28b4457e Fri Mar 5 15:34:32 2021 -0800
    If BioSample date is more complete than GenBank date, use it.
• src/hg/utils/otto/sarscov2phylo/getCogUk.sh
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    4da885c024760ff033a7bf8a3a5ea38a3eb37852 Mon Mar 1 14:08:12 2021 -0800
    Instead of running nextclade on all COG-UK sequences every night, run it only on new sequences.
• src/hg/utils/otto/sarscov2phylo/getNcbi.sh
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    56405fd76d2760549a7fe511384e534f240ac79e Wed Mar 3 18:45:30 2021 -0800
    Clean up a bit when done.
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    a501a677b1027e7103b547e54b0e2ee286ca09e7 Fri Mar 5 15:39:35 2021 -0800
    Make getNcbi.sh more efficient: fetch only new IDs from BioSample; run nextclade and pangolin only on new sequences.
• src/hg/utils/otto/sarscov2phylo/getRelease.sh
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• src/hg/utils/otto/sarscov2phylo/gisaidFromChunks.sh
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    1abdb5501f3d2e51d0b48cd016c30f79bb9c12c6 Wed Mar 3 18:46:33 2021 -0800
    Run nextclade and pangolin on my manually downloaded chunks of GISAID sequences and combine them into something similar to nextmeta and nextfasta downloads.
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    a6793cc4a84d4e1450fea53b558378e9f9659c64 Fri Mar 5 15:36:53 2021 -0800
    Don't need -x for this script, steps are all straightforward.
• src/hg/utils/otto/sarscov2phylo/installSarsCov2Phylo.sh
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    4da885c024760ff033a7bf8a3a5ea38a3eb37852 Mon Mar 1 14:08:12 2021 -0800
    Instead of running nextclade on all COG-UK sequences every night, run it only on new sequences.
• src/hg/utils/otto/sarscov2phylo/nextcladeNcbi.sh
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    a501a677b1027e7103b547e54b0e2ee286ca09e7 Fri Mar 5 15:39:35 2021 -0800
    Make getNcbi.sh more efficient: fetch only new IDs from BioSample; run nextclade and pangolin only on new sequences.
• src/hg/utils/otto/sarscov2phylo/pangolinNcbi.sh
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    a501a677b1027e7103b547e54b0e2ee286ca09e7 Fri Mar 5 15:39:35 2021 -0800
    Make getNcbi.sh more efficient: fetch only new IDs from BioSample; run nextclade and pangolin only on new sequences.
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• src/hg/utils/otto/sarscov2phylo/searchAllSarsCov2BioSample.sh
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
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    7a2d50434d3fac99adc005ed3a68f9f00f92f9bf Wed Mar 3 18:43:53 2021 -0800
    Let some other script call getCogUk.sh and getNcbi.sh. Preserve ncov-ingest mappings in case of duplicates. Update local nextmeta-ish file with ID mapping when done.
• src/hg/utils/otto/sarscov2phylo/updatePublic.sh
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    4da885c024760ff033a7bf8a3a5ea38a3eb37852 Mon Mar 1 14:08:12 2021 -0800
    Instead of running nextclade on all COG-UK sequences every night, run it only on new sequences.
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    d13f0bd04427ad790fae74040413acded3189386 Wed Mar 3 18:45:00 2021 -0800
    Call gisaidFromChunks.sh and updateIdMapping.sh to keep those up to date. Eventually will want to update GISAID+public tree.
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    a501a677b1027e7103b547e54b0e2ee286ca09e7 Fri Mar 5 15:39:35 2021 -0800
    Make getNcbi.sh more efficient: fetch only new IDs from BioSample; run nextclade and pangolin only on new sequences.
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    4e46cbfb5a3e3c506b82234e1dbb774b99bb9168 Wed Mar 3 18:42:02 2021 -0800
    Add protobufs with nextclade and pangolin annotations to public tree archive dir. Update public-latest.* links in more cgi-bin* locations. Clean up a bit.
• src/hg/utils/otto/sarscov2phylo/updateSarsCov2Phylo.sh
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• src/hg/utils/otto/uniprot/doUniprot
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    fixed accidently backout of master changes in the last merge
• src/hg/utils/phyloRenameAndPrune/phyloRenameAndPrune.c
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• src/hg/utils/vcfRenameAndPrune/vcfRenameAndPrune.c
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• src/inc/bits.h
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    c3c65fde6dd5aa6f20860c7113eb9ee22cf35b96 Wed Jan 15 08:37:28 2020 -0800
    Initial pass at 64bit blat index
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    ef2b0974644900d17bdc4e0a2c8056e995832282 Thu Jan 16 11:14:03 2020 -0800
    Revert "Initial pass at 64bit blat index" This reverts commit 85f6ef8de85a89781978add2ed98fb158718cd40.
• src/inc/cheapcgi.h
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    4ea1cf8aafc507f79cb6cb779e4ffb6aa6adc43f Thu Mar 4 17:48:50 2021 -0800
    Added cgiMakeOnClickButtonWithMsg for a *non*-submit button with both mouseover title and javascript.
• src/inc/common.h
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    177eed0b0b757749adcc17bcc92eb767536e458e Fri Jan 10 10:13:42 2020 -0800
    added mustSeek function
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    b6d7e4446453c3ab019b30024741247171a2f040 Mon Jun 29 20:04:40 2020 +0000
    make sure data is 64-bit aligned, store offsets in headers to simplify
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    a74c645505a135d5c1e923afe477cdeb9c15bded Wed Jul 8 22:27:42 2020 -0700
    added including multiple container directoies in genome dir path to gfServer
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    36f8f6fb024b20cc523cdf9ebde7491eca84fd7c Sun Dec 6 20:33:20 2020 -0800
    multiple request per connect works except hgBlat
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• src/inc/common.mk
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• src/inc/filePath.h
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    fa416c484061b1e44519962435588916dc14a1f7 Wed Dec 9 22:04:07 2020 -0800
    added isSafeRelativePath and removed way too low-level verbose logging
• src/inc/genoFind.h
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    c3c65fde6dd5aa6f20860c7113eb9ee22cf35b96 Wed Jan 15 08:37:28 2020 -0800
    Initial pass at 64bit blat index
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    ef2b0974644900d17bdc4e0a2c8056e995832282 Thu Jan 16 11:14:03 2020 -0800
    Revert "Initial pass at 64bit blat index" This reverts commit 85f6ef8de85a89781978add2ed98fb158718cd40.
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    0a10e299786e9b470b55b2f02b9718ec6c4e4bb4 Sat Jun 27 15:33:26 2020 -0700
    move genoFind build, save, and load to a library
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    e764efe5d0e596213c72e69f028df0a667d0a83c Mon Jun 29 00:43:22 2020 +0000
    gfClient working with blat server running under xinetd
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    b6d7e4446453c3ab019b30024741247171a2f040 Mon Jun 29 20:04:40 2020 +0000
    make sure data is 64-bit aligned, store offsets in headers to simplify
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    0ede364a2dcb452681933d5a3579b4f05d90a245 Sun Jul 5 15:16:27 2020 -0700
    fixed bug where totalSeqSize was not stored in index, now hgBlat works
  • lines changed 3, context: html, text, full: html, text
    a74c645505a135d5c1e923afe477cdeb9c15bded Wed Jul 8 22:27:42 2020 -0700
    added including multiple container directoies in genome dir path to gfServer
  • lines changed 6, context: html, text, full: html, text
    95030f73f067d8e8f9221a09c1811784607e4e72 Fri Jul 10 17:51:29 2020 -0700
    split dynamic server genomeDataPrefix into genome and genomeDataDir. More verbose, but clearer
  • lines changed 15, context: html, text, full: html, text
    f683064dc6a998206665b484790ef9d561e6c8a7 Sat Dec 5 22:42:53 2020 -0800
    initial conversion to gfServer connection to object
  • lines changed 22, context: html, text, full: html, text
    36f8f6fb024b20cc523cdf9ebde7491eca84fd7c Sun Dec 6 20:33:20 2020 -0800
    multiple request per connect works except hgBlat
  • lines changed 12, context: html, text, full: html, text
    88485cfa7f13affa28ec5765fe9b2db90cce42b6 Tue Dec 8 21:02:15 2020 -0800
    hgPcr working
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    365534e1a97dc9250ff85e367a7786989662281d Mon Dec 14 14:01:20 2020 -0800
    updated gfServer version
• src/inc/gfPcrLib.h
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    88485cfa7f13affa28ec5765fe9b2db90cce42b6 Tue Dec 8 21:02:15 2020 -0800
    hgPcr working
• src/inc/gfWebLib.h
  • lines changed 1, context: html, text, full: html, text
    87a162ccdc3ac94525fc1011dec5bc10e2cf2171 Thu Jul 2 16:12:57 2020 -0700
    web blat working
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    a74c645505a135d5c1e923afe477cdeb9c15bded Wed Jul 8 22:27:42 2020 -0700
    added including multiple container directoies in genome dir path to gfServer
  • lines changed 2, context: html, text, full: html, text
    36f8f6fb024b20cc523cdf9ebde7491eca84fd7c Sun Dec 6 20:33:20 2020 -0800
    multiple request per connect works except hgBlat
• src/inc/hash.h
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/inc/linefile.h
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/inc/matrixMarket.h
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/inc/obscure.h
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/inc/ooc.h
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    c3c65fde6dd5aa6f20860c7113eb9ee22cf35b96 Wed Jan 15 08:37:28 2020 -0800
    Initial pass at 64bit blat index
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    ef2b0974644900d17bdc4e0a2c8056e995832282 Thu Jan 16 11:14:03 2020 -0800
    Revert "Initial pass at 64bit blat index" This reverts commit 85f6ef8de85a89781978add2ed98fb158718cd40.
• src/inc/phyloTree.h
  • lines changed 3, context: html, text, full: html, text
    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
• src/inc/portable.h
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/inc/psGfx.h
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/inc/sparseMatrix.h
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/inc/srcVersion.h
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
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    e9cd3eef710ba3141d58ef119006b7d2327e5b7f Wed Dec 9 13:52:01 2020 -0800
    fixed accidently backout of master changes in the last merge
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/inc/vMatrix.h
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/isPcr/gfPcr/gfPcr.c
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    3d71b2793b72fd0f6f4ff1511bb93cf3b6b76497 Sun Jan 3 14:01:54 2021 -0800
    fixed parameter change errors in blatSuite
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    a2819277576ffc91069261a03b358213afe2cb3b Wed Feb 3 15:30:27 2021 -0800
    allow gfPcr to query dynamic servers
• src/isPcr/webPcr/webPcr.c
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    3d71b2793b72fd0f6f4ff1511bb93cf3b6b76497 Sun Jan 3 14:01:54 2021 -0800
    fixed parameter change errors in blatSuite
• src/jkOwnLib/genoFind.c
  • lines changed 59, context: html, text, full: html, text
    c3c65fde6dd5aa6f20860c7113eb9ee22cf35b96 Wed Jan 15 08:37:28 2020 -0800
    Initial pass at 64bit blat index
  • lines changed 6, context: html, text, full: html, text
    67918e4571e0a4002aa554ea78b2a1bbb592e4d9 Thu Jan 16 10:40:29 2020 -0800
    64bit blat work
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    369c64d12a80d2b2690e87cfd4ece9b968824f23 Thu Jan 16 11:13:25 2020 -0800
    Revert "64bit blat work" This reverts commit 13f9e552cf168647c7044e339108f2ece5151ad5.
  • lines changed 58, context: html, text, full: html, text
    ef2b0974644900d17bdc4e0a2c8056e995832282 Thu Jan 16 11:14:03 2020 -0800
    Revert "Initial pass at 64bit blat index" This reverts commit 85f6ef8de85a89781978add2ed98fb158718cd40.
  • lines changed 1, context: html, text, full: html, text
    89ea68569377014dcce51081880a7e0ebfcc1d7f Sat Jun 27 12:47:34 2020 -0700
    fixed error in merge
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    0a10e299786e9b470b55b2f02b9718ec6c4e4bb4 Sat Jun 27 15:33:26 2020 -0700
    move genoFind build, save, and load to a library
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    ecacb0a15e8ddbe9b2e62381e30621ba70f82d8f Sun Jun 28 14:36:10 2020 -0700
    dynamic server tests working
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    e764efe5d0e596213c72e69f028df0a667d0a83c Mon Jun 29 00:43:22 2020 +0000
    gfClient working with blat server running under xinetd
  • lines changed 382, context: html, text, full: html, text
    b6d7e4446453c3ab019b30024741247171a2f040 Mon Jun 29 20:04:40 2020 +0000
    make sure data is 64-bit aligned, store offsets in headers to simplify
  • lines changed 13, context: html, text, full: html, text
    0ede364a2dcb452681933d5a3579b4f05d90a245 Sun Jul 5 15:16:27 2020 -0700
    fixed bug where totalSeqSize was not stored in index, now hgBlat works
  • lines changed 2, context: html, text, full: html, text
    a74c645505a135d5c1e923afe477cdeb9c15bded Wed Jul 8 22:27:42 2020 -0700
    added including multiple container directoies in genome dir path to gfServer
  • lines changed 27, context: html, text, full: html, text
    36f8f6fb024b20cc523cdf9ebde7491eca84fd7c Sun Dec 6 20:33:20 2020 -0800
    multiple request per connect works except hgBlat
  • lines changed 2, context: html, text, full: html, text
    88485cfa7f13affa28ec5765fe9b2db90cce42b6 Tue Dec 8 21:02:15 2020 -0800
    hgPcr working
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    a4100d62e1f3a6864f70e651b6b41517c662f496 Wed Dec 9 21:34:41 2020 -0800
    improved doc on reserved files
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    fe48c5bed92448a3e0a599f2fe3123294fc0c7af Wed Feb 3 17:19:09 2021 -0800
    fixed initialization problem that prefected isPcr to work on dynamic servers
• src/jkOwnLib/gfBlatLib.c
  • lines changed 1, context: html, text, full: html, text
    ecacb0a15e8ddbe9b2e62381e30621ba70f82d8f Sun Jun 28 14:36:10 2020 -0700
    dynamic server tests working
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    e764efe5d0e596213c72e69f028df0a667d0a83c Mon Jun 29 00:43:22 2020 +0000
    gfClient working with blat server running under xinetd
  • lines changed 8, context: html, text, full: html, text
    c99b62d7865a828f8f41c6e82dd36cbd2dd26780 Wed Jul 1 21:45:43 2020 -0700
    hgBlat mostly works
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    a74c645505a135d5c1e923afe477cdeb9c15bded Wed Jul 8 22:27:42 2020 -0700
    added including multiple container directoies in genome dir path to gfServer
  • lines changed 20, context: html, text, full: html, text
    95030f73f067d8e8f9221a09c1811784607e4e72 Fri Jul 10 17:51:29 2020 -0700
    split dynamic server genomeDataPrefix into genome and genomeDataDir. More verbose, but clearer
  • lines changed 27, context: html, text, full: html, text
    f683064dc6a998206665b484790ef9d561e6c8a7 Sat Dec 5 22:42:53 2020 -0800
    initial conversion to gfServer connection to object
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    36f8f6fb024b20cc523cdf9ebde7491eca84fd7c Sun Dec 6 20:33:20 2020 -0800
    multiple request per connect works except hgBlat
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    88485cfa7f13affa28ec5765fe9b2db90cce42b6 Tue Dec 8 21:02:15 2020 -0800
    hgPcr working
• src/jkOwnLib/gfPcrLib.c
  • lines changed 5, context: html, text, full: html, text
    f683064dc6a998206665b484790ef9d561e6c8a7 Sat Dec 5 22:42:53 2020 -0800
    initial conversion to gfServer connection to object
  • lines changed 1, context: html, text, full: html, text
    36f8f6fb024b20cc523cdf9ebde7491eca84fd7c Sun Dec 6 20:33:20 2020 -0800
    multiple request per connect works except hgBlat
  • lines changed 1, context: html, text, full: html, text
    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
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    88485cfa7f13affa28ec5765fe9b2db90cce42b6 Tue Dec 8 21:02:15 2020 -0800
    hgPcr working
• src/jkOwnLib/gfWebLib.c
  • lines changed 60, context: html, text, full: html, text
    87a162ccdc3ac94525fc1011dec5bc10e2cf2171 Thu Jul 2 16:12:57 2020 -0700
    web blat working
  • lines changed 1, context: html, text, full: html, text
    bff6869213fd1af019c635141ceab9d3078e959d Thu Oct 15 10:38:36 2020 -0700
    fixed missing function arguments not detect due to lack of dependency checking
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    36f8f6fb024b20cc523cdf9ebde7491eca84fd7c Sun Dec 6 20:33:20 2020 -0800
    multiple request per connect works except hgBlat
• src/jkOwnLib/ooc.c
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    c3c65fde6dd5aa6f20860c7113eb9ee22cf35b96 Wed Jan 15 08:37:28 2020 -0800
    Initial pass at 64bit blat index
  • lines changed 2, context: html, text, full: html, text
    ef2b0974644900d17bdc4e0a2c8056e995832282 Thu Jan 16 11:14:03 2020 -0800
    Revert "Initial pass at 64bit blat index" This reverts commit 85f6ef8de85a89781978add2ed98fb158718cd40.
• src/jkOwnLib/patSpace.c
  • lines changed 1, context: html, text, full: html, text
    c3c65fde6dd5aa6f20860c7113eb9ee22cf35b96 Wed Jan 15 08:37:28 2020 -0800
    Initial pass at 64bit blat index
  • lines changed 1, context: html, text, full: html, text
    ef2b0974644900d17bdc4e0a2c8056e995832282 Thu Jan 16 11:14:03 2020 -0800
    Revert "Initial pass at 64bit blat index" This reverts commit 85f6ef8de85a89781978add2ed98fb158718cd40.
• src/lib/bamFile.c
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
• src/lib/bits.c
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    c3c65fde6dd5aa6f20860c7113eb9ee22cf35b96 Wed Jan 15 08:37:28 2020 -0800
    Initial pass at 64bit blat index
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    ef2b0974644900d17bdc4e0a2c8056e995832282 Thu Jan 16 11:14:03 2020 -0800
    Revert "Initial pass at 64bit blat index" This reverts commit 85f6ef8de85a89781978add2ed98fb158718cd40.
• src/lib/bwgCreate.c
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/lib/cheapcgi.c
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
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    4ea1cf8aafc507f79cb6cb779e4ffb6aa6adc43f Thu Mar 4 17:48:50 2021 -0800
    Added cgiMakeOnClickButtonWithMsg for a *non*-submit button with both mouseover title and javascript.
• src/lib/common.c
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    177eed0b0b757749adcc17bcc92eb767536e458e Fri Jan 10 10:13:42 2020 -0800
    added mustSeek function
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    b6d7e4446453c3ab019b30024741247171a2f040 Mon Jun 29 20:04:40 2020 +0000
    make sure data is 64-bit aligned, store offsets in headers to simplify
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    36f8f6fb024b20cc523cdf9ebde7491eca84fd7c Sun Dec 6 20:33:20 2020 -0800
    multiple request per connect works except hgBlat
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/lib/fieldedTable.c
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/lib/filePath.c
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    fa416c484061b1e44519962435588916dc14a1f7 Wed Dec 9 22:04:07 2020 -0800
    added isSafeRelativePath and removed way too low-level verbose logging
• src/lib/freeType.c
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
• src/lib/gfNet.c
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    f683064dc6a998206665b484790ef9d561e6c8a7 Sat Dec 5 22:42:53 2020 -0800
    initial conversion to gfServer connection to object
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    36f8f6fb024b20cc523cdf9ebde7491eca84fd7c Sun Dec 6 20:33:20 2020 -0800
    multiple request per connect works except hgBlat
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    88485cfa7f13affa28ec5765fe9b2db90cce42b6 Tue Dec 8 21:02:15 2020 -0800
    hgPcr working
• src/lib/hash.c
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/lib/log.c
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    36f8f6fb024b20cc523cdf9ebde7491eca84fd7c Sun Dec 6 20:33:20 2020 -0800
    multiple request per connect works except hgBlat
• src/lib/makefile
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/lib/matrixMarket.c
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/lib/obscure.c
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/lib/osunix.c
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/lib/phyloTree.c
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
• src/lib/psGfx.c
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/lib/pscmGfx.c
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/lib/psl.as
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/lib/sparseMatrix.c
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/lib/strex.c
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/lib/udc.c
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/lib/vMatrix.c
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/product/installer/README.md
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/product/installer/browserSetup.sh
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/product/mirrorDocs/makefile
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/product/mirrorDocs/staticPage.lua
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/product/mirrorManual.txt
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/tabFile/tabToTabDir/tabToTabDir.c
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/tabFile/tabToTabDir/tabToTabDir.doc
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/tabFile/tabToTabDir/tests/expected/donor_organ_cells.tsv
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/tabFile/tabToTabDir/tests/expected/lab_submitters.tsv
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/tabFile/tabToTabDir/tests/expected/unroll_test.tsv
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/tabFile/tabToTabDir/tests/input/spec.txt
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/tabFile/tabToTabDir/tests/test.x
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/tagStorm/tagStormFromTab/100.divSpec
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/tagStorm/tagStormFromTab/100.tab
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/tagStorm/tagStormFromTab/100.tag
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
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    87a162ccdc3ac94525fc1011dec5bc10e2cf2171 Thu Jul 2 16:12:57 2020 -0700
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    36f8f6fb024b20cc523cdf9ebde7491eca84fd7c Sun Dec 6 20:33:20 2020 -0800
    multiple request per connect works except hgBlat
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    e9492dbfa8a68aee133893d4b02475b0aec27bb9 Sun Dec 6 23:48:42 2020 -0800
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    16991e5fb7819460241f38f184a9e46311994598 Thu Jul 2 16:58:23 2020 -0700
    web blat really working now
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    added including multiple container directoies in genome dir path to gfServer
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    multiple request per connect works except hgBlat
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    87a162ccdc3ac94525fc1011dec5bc10e2cf2171 Thu Jul 2 16:12:57 2020 -0700
    web blat working
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    e1ae6056b95e1f21e3889bd190108a8f71ca222e Wed Dec 9 08:25:02 2020 -0800
    fixed example that was incorrectly modified