File Changes for markd

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

• confs/asia.hg.conf
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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
• 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
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    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
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    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
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    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/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 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
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    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 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
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    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
    ee8ef81c6d82157859f16548a27726f4b7421891 Mon Jul 6 19:22:14 2020 -0700
    added support for perSeqMax in dynamic server
• src/gfServer/tests/expected/testIndexFile.out
  • 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/testIndexFileTrans
  • lines changed 94, 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/testIndexFileTrans.out
  • lines changed 94, 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/testNib
  • lines changed 24, 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/testNib.out
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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
• src/gfServer/tests/expected/testPcr
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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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• src/gfServer/tests/expected/testProtNib
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    ee8ef81c6d82157859f16548a27726f4b7421891 Mon Jul 6 19:22:14 2020 -0700
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• src/gfServer/tests/expected/testProtNib.out
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    ee8ef81c6d82157859f16548a27726f4b7421891 Mon Jul 6 19:22:14 2020 -0700
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• src/gfServer/tests/expected/testProtTwoBit
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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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• src/gfServer/tests/expected/testTransNib
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    ee8ef81c6d82157859f16548a27726f4b7421891 Mon Jul 6 19:22:14 2020 -0700
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• src/gfServer/tests/expected/testTransNib.out
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    ee8ef81c6d82157859f16548a27726f4b7421891 Mon Jul 6 19:22:14 2020 -0700
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• src/gfServer/tests/expected/testTransTwoBit
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    ee8ef81c6d82157859f16548a27726f4b7421891 Mon Jul 6 19:22:14 2020 -0700
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• src/gfServer/tests/expected/testTransTwoBit.out
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    ee8ef81c6d82157859f16548a27726f4b7421891 Mon Jul 6 19:22:14 2020 -0700
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• src/gfServer/tests/expected/testTwoBit
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    ee8ef81c6d82157859f16548a27726f4b7421891 Mon Jul 6 19:22:14 2020 -0700
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• src/gfServer/tests/expected/testTwoBit.out
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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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• src/gfServer/tests/input/AB000095.fa
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    5fcdf45fee21aa88247a68df00575e2865a9478e Sun Jun 28 14:50:30 2020 -0700
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• src/gfServer/tests/input/AB000220.fa
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    5fcdf45fee21aa88247a68df00575e2865a9478e Sun Jun 28 14:50:30 2020 -0700
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• src/gfServer/tests/input/crea.mrna
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    ecacb0a15e8ddbe9b2e62381e30621ba70f82d8f Sun Jun 28 14:36:10 2020 -0700
    dynamic server tests working
• src/gfServer/tests/input/repeat.fa
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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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    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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    5fcdf45fee21aa88247a68df00575e2865a9478e Sun Jun 28 14:50:30 2020 -0700
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• src/gfServer/tests/input/testPcr.fa
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    54a643b32015c6a4672bd540b4bf7a94a751e1ce Wed Feb 3 12:45:46 2021 -0800
    added unit test of gfServer dynamic PCR
• src/gfServer/tests/testDynServer
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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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    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/testDynServerPcr
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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
• src/gfServer/tests/testDynServerTrans
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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
• src/gfServer/tests/testDynServerWithDir
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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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    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
    added support for perSeqMax in dynamic server
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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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    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
    added support for perSeqMax in dynamic server
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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
    added support for perSeqMax in dynamic server
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    36f8f6fb024b20cc523cdf9ebde7491eca84fd7c Sun Dec 6 20:33:20 2020 -0800
    multiple request per connect works except hgBlat
• src/gfServer/tests/testProtNib
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    ee8ef81c6d82157859f16548a27726f4b7421891 Mon Jul 6 19:22:14 2020 -0700
    added support for perSeqMax in dynamic server
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    36f8f6fb024b20cc523cdf9ebde7491eca84fd7c Sun Dec 6 20:33:20 2020 -0800
    multiple request per connect works except hgBlat
• src/gfServer/tests/testProtTwoBit
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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/testTransNib
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    ee8ef81c6d82157859f16548a27726f4b7421891 Mon Jul 6 19:22:14 2020 -0700
    added support for perSeqMax in dynamic server
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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
    added support for perSeqMax in dynamic server
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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
    merge with master
• src/hca/fromGeo/geoToHcaStorm/geoToHcaStorm.c
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/hca/hcaColorCells/hcaColorCells.c
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/hca/hcaColorCells/makefile
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• 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
    merge with master
• src/hca/hcaUnifyMatrix/makefile
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• 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
    merge with master
• 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
    merge with master
• src/hca/hcat/mysite/hcat/api_urls.py
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/hca/hcat/mysite/hcat/index_urls.py
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
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• src/hca/hcat/mysite/hcat/models.py
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
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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
    merge with master
• src/hca/hcat/mysite/templates/hcat/index.html
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/hca/hcat/mysite/versions.txt
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
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• 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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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
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• src/hg/geneBounds/clusterGenes/tests/makefile
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
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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
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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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    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
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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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    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
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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
    webblat and hgBlat working
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    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
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    88485cfa7f13affa28ec5765fe9b2db90cce42b6 Tue Dec 8 21:02:15 2020 -0800
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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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    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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    88485cfa7f13affa28ec5765fe9b2db90cce42b6 Tue Dec 8 21:02:15 2020 -0800
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    6d36881dee4bc2a4256614638aec4dddf3c26f44 Wed Jan 27 19:33:09 2021 -0800
    recommend creating index with -stepSize=5
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    71a2c73633337ab11c6344fee8c077e13daf815b Tue Feb 2 12:03:42 2021 -0800
    move most doc on setting up dynamic blat servers to the wiki
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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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    d8a949135724f97cfc92b52111ac223fece3dbf5 Mon Jun 29 14:53:25 2020 -0700
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    bff6869213fd1af019c635141ceab9d3078e959d Thu Oct 15 10:38:36 2020 -0700
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    f683064dc6a998206665b484790ef9d561e6c8a7 Sat Dec 5 22:42:53 2020 -0800
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    36f8f6fb024b20cc523cdf9ebde7491eca84fd7c Sun Dec 6 20:33:20 2020 -0800
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
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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/utils/phyloRenameAndPrune/phyloRenameAndPrune.c
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
• src/hg/utils/tdbQuery/tdbQuery.c
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
• src/hg/utils/vcfRenameAndPrune/vcfRenameAndPrune.c
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
• src/hg/utils/vcfToBed/vcfToBed.c
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
• src/hg/utils/vcfToHgvs/tests/expected/stopLoss.tab
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
• src/inc/bits.h
  • lines changed 26, context: html, text, full: html, text
    c3c65fde6dd5aa6f20860c7113eb9ee22cf35b96 Wed Jan 15 08:37:28 2020 -0800
    Initial pass at 64bit blat index
  • lines changed 26, 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/inc/cheapcgi.h
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• 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
  • lines changed 8, 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
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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/inc/common.mk
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/inc/fieldedTable.h
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    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• 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
  • lines changed 29, context: html, text, full: html, text
    c3c65fde6dd5aa6f20860c7113eb9ee22cf35b96 Wed Jan 15 08:37:28 2020 -0800
    Initial pass at 64bit blat index
  • lines changed 29, 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.
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    0a10e299786e9b470b55b2f02b9718ec6c4e4bb4 Sat Jun 27 15:33:26 2020 -0700
    move genoFind build, save, and load to a library
  • lines changed 3, context: html, text, full: html, text
    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
  • lines changed 3, 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 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
  • 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
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    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
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    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
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    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.
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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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    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
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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
  • 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
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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
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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
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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
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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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    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
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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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    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
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    87a162ccdc3ac94525fc1011dec5bc10e2cf2171 Thu Jul 2 16:12:57 2020 -0700
    web blat working
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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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    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
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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/jkOwnLib/patSpace.c
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    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
• 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
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    06d7be056190c14b85e71bc12523f18ea6815b5e Mon Dec 7 00:50:29 2020 -0800
    BLAT mmap index support merge with master
• src/utils/wordLine/wordLine.c
  • lines changed 10, context: html, text, full: html, text
    be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800
    merge with master
• src/webBlat/install.txt
  • lines changed 36, context: html, text, full: html, text
    87a162ccdc3ac94525fc1011dec5bc10e2cf2171 Thu Jul 2 16:12:57 2020 -0700
    web blat working
  • lines changed 4, context: html, text, full: html, text
    36f8f6fb024b20cc523cdf9ebde7491eca84fd7c Sun Dec 6 20:33:20 2020 -0800
    multiple request per connect works except hgBlat
  • lines changed 5, context: html, text, full: html, text
    e9492dbfa8a68aee133893d4b02475b0aec27bb9 Sun Dec 6 23:48:42 2020 -0800
    webblat and hgBlat working
  • lines changed 3, context: html, text, full: html, text
    88485cfa7f13affa28ec5765fe9b2db90cce42b6 Tue Dec 8 21:02:15 2020 -0800
    hgPcr working
• src/webBlat/webBlat.c
  • lines changed 5, context: html, text, full: html, text
    d8a949135724f97cfc92b52111ac223fece3dbf5 Mon Jun 29 14:53:25 2020 -0700
    got entire tree compliing with geneFind changes
  • lines changed 4, context: html, text, full: html, text
    16991e5fb7819460241f38f184a9e46311994598 Thu Jul 2 16:58:23 2020 -0700
    web blat really working now
  • lines changed 4, 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 15, context: html, text, full: html, text
    36f8f6fb024b20cc523cdf9ebde7491eca84fd7c Sun Dec 6 20:33:20 2020 -0800
    multiple request per connect works except hgBlat
  • lines changed 9, context: html, text, full: html, text
    3d71b2793b72fd0f6f4ff1511bb93cf3b6b76497 Sun Jan 3 14:01:54 2021 -0800
    fixed parameter change errors in blatSuite
• src/webBlat/webBlat.cfg
  • lines changed 4, context: html, text, full: html, text
    87a162ccdc3ac94525fc1011dec5bc10e2cf2171 Thu Jul 2 16:12:57 2020 -0700
    web blat working
  • lines changed 4, context: html, text, full: html, text
    e1ae6056b95e1f21e3889bd190108a8f71ca222e Wed Dec 9 08:25:02 2020 -0800
    fixed example that was incorrectly modified