Commits for markd

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

177eed0b0b757749adcc17bcc92eb767536e458e Fri Jan 10 10:13:42 2020 -0800

• added mustSeek function
  • src/inc/common.h - lines changed 3, context: html, text, full: html, text
  • src/lib/common.c - lines changed 20, context: html, text, full: html, text

9be14bbf98fbe84c898cf038fa80c3f9124a2ee6 Sat Jan 11 13:29:12 2020 -0800

• added madvise call after mmap to improve performance
  • src/gfServer/gfServer.c - lines changed 5, context: html, text, full: html, text

c3c65fde6dd5aa6f20860c7113eb9ee22cf35b96 Wed Jan 15 08:37:28 2020 -0800

• Initial pass at 64bit blat index
  • src/gfServer/gfServer.c - lines changed 13, context: html, text, full: html, text
  • src/inc/bits.h - lines changed 26, context: html, text, full: html, text
  • src/inc/genoFind.h - lines changed 29, context: html, text, full: html, text
  • src/inc/ooc.h - lines changed 2, context: html, text, full: html, text
  • src/jkOwnLib/genoFind.c - lines changed 59, context: html, text, full: html, text
  • src/jkOwnLib/ooc.c - lines changed 2, context: html, text, full: html, text
  • src/jkOwnLib/patSpace.c - lines changed 1, context: html, text, full: html, text
  • src/lib/bits.c - lines changed 73, context: html, text, full: html, text

67918e4571e0a4002aa554ea78b2a1bbb592e4d9 Thu Jan 16 10:40:29 2020 -0800

• 64bit blat work
  • src/jkOwnLib/genoFind.c - lines changed 6, context: html, text, full: html, text

369c64d12a80d2b2690e87cfd4ece9b968824f23 Thu Jan 16 11:13:25 2020 -0800

• Revert "64bit blat work" This reverts commit 13f9e552cf168647c7044e339108f2ece5151ad5.
  • src/jkOwnLib/genoFind.c - lines changed 6, 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/gfServer/gfServer.c - lines changed 13, context: html, text, full: html, text
  • src/inc/bits.h - lines changed 26, context: html, text, full: html, text
  • src/inc/genoFind.h - lines changed 29, context: html, text, full: html, text
  • src/inc/ooc.h - lines changed 2, context: html, text, full: html, text
  • src/jkOwnLib/genoFind.c - lines changed 58, context: html, text, full: html, text
  • src/jkOwnLib/ooc.c - lines changed 2, context: html, text, full: html, text
  • src/jkOwnLib/patSpace.c - lines changed 1, context: html, text, full: html, text
  • src/lib/bits.c - lines changed 73, context: html, text, full: html, text

89ea68569377014dcce51081880a7e0ebfcc1d7f Sat Jun 27 12:47:34 2020 -0700

• fixed error in merge
  • src/jkOwnLib/genoFind.c - lines changed 1, context: html, text, full: html, text

0a10e299786e9b470b55b2f02b9718ec6c4e4bb4 Sat Jun 27 15:33:26 2020 -0700

• move genoFind build, save, and load to a library
  • src/gfServer/gfServer.c - lines changed 231, context: html, text, full: html, text
  • src/inc/genoFind.h - lines changed 26, context: html, text, full: html, text
  • src/jkOwnLib/genoFind.c - lines changed 235, context: html, text, full: html, text

766edf73c99da98b3935f42c234d14acf08c2c0e Sat Jun 27 19:37:45 2020 -0700

• move index building to a separate gfServer subcommand
  • src/gfServer/gfServer.c - lines changed 30, context: html, text, full: html, text
  • src/gfServer/tests/testIndexFile - lines changed 1, context: html, text, full: html, text
  • src/gfServer/tests/testIndexFileTrans - lines changed 1, context: html, text, full: html, text

ecacb0a15e8ddbe9b2e62381e30621ba70f82d8f Sun Jun 28 14:36:10 2020 -0700

• dynamic server tests working
  • src/gfServer/gfServer.c - lines changed 159, context: html, text, full: html, text
  • src/gfServer/makefile - lines changed 1, context: html, text, full: html, text
  • src/gfServer/tests/expected/testDynServer - lines changed 44, context: html, text, full: html, text
  • src/gfServer/tests/expected/testDynServerTrans - lines changed 188, context: html, text, full: html, text
  • src/gfServer/tests/input/crea.mrna - lines changed 2, context: html, text, full: html, text
  • src/gfServer/tests/testDynServer - lines changed 13, context: html, text, full: html, text
  • src/gfServer/tests/testDynServerTrans - lines changed 13, context: html, text, full: html, text
  • src/gfServer/tests/testIndexFile - lines changed 7, context: html, text, full: html, text
  • src/gfServer/tests/testIndexFileTrans - lines changed 7, context: html, text, full: html, text
  • src/jkOwnLib/genoFind.c - lines changed 3, context: html, text, full: html, text
  • src/jkOwnLib/gfBlatLib.c - lines changed 1, 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/AB000095.fa - lines changed 49, context: html, text, full: html, text
  • src/gfServer/AB000220.fa - lines changed 39, context: html, text, full: html, text
  • src/gfServer/repeat.fa - lines changed 7, context: html, text, full: html, text
  • src/gfServer/test1.fa - lines changed 11, context: html, text, full: html, text
  • src/gfServer/test1.nib - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/gfServer/test2.fa - lines changed 7, context: html, text, full: html, text
  • src/gfServer/test3.fa - lines changed 9, context: html, text, full: html, text
  • src/gfServer/tests/input/AB000095.fa - lines changed 49, context: html, text, full: html, text
  • src/gfServer/tests/input/AB000220.fa - lines changed 39, context: html, text, full: html, text
  • src/gfServer/tests/input/repeat.fa - lines changed 7, context: html, text, full: html, text
  • src/gfServer/tests/input/test1.fa - lines changed 11, context: html, text, full: html, text
  • src/gfServer/tests/input/test1.nib - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/gfServer/tests/input/test2.fa - lines changed 7, context: html, text, full: html, text
  • src/gfServer/tests/input/test3.fa - lines changed 9, context: html, text, full: html, text

e764efe5d0e596213c72e69f028df0a667d0a83c Mon Jun 29 00:43:22 2020 +0000

• gfClient working with blat server running under xinetd
  • src/gfClient/gfClient.c - lines changed 11, context: html, text, full: html, text
  • src/gfServer/gfServer.c - lines changed 13, context: html, text, full: html, text
  • src/gfServer/tests/expected/testDynServer - lines changed 38, context: html, text, full: html, text
  • src/gfServer/tests/expected/testDynServerTrans - lines changed 90, context: html, text, full: html, text
  • src/gfServer/xinetd-example.conf - lines changed 31, context: html, text, full: html, text
  • src/inc/genoFind.h - lines changed 3, context: html, text, full: html, text
  • src/jkOwnLib/genoFind.c - lines changed 11, context: html, text, full: html, text
  • src/jkOwnLib/gfBlatLib.c - lines changed 20, 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
  • src/gfServer/gfServer.c - lines changed 2, context: html, text, full: html, text
  • src/inc/common.h - lines changed 5, context: html, text, full: html, text
  • src/inc/genoFind.h - lines changed 6, context: html, text, full: html, text
  • src/jkOwnLib/genoFind.c - lines changed 382, context: html, text, full: html, text
  • src/lib/common.c - lines changed 14, context: html, text, full: html, text

fab119b260a64f40ea3db632486e0823a0c0f493 Tue Jun 30 18:33:39 2020 +0000

• forgot to add test driver
  • src/gfServer/tests/dynTester - lines changed 143, context: html, text, full: html, text

d8a949135724f97cfc92b52111ac223fece3dbf5 Mon Jun 29 14:53:25 2020 -0700

• got entire tree compliing with geneFind changes
  • src/gfServer/xinetd-example.conf - lines changed 1, context: html, text, full: html, text
  • src/hg/hgBlat/hgBlat.c - lines changed 5, context: html, text, full: html, text
  • src/hg/lib/coordConv.c - lines changed 2, context: html, text, full: html, text
  • src/webBlat/webBlat.c - lines changed 5, context: html, text, full: html, text

c99b62d7865a828f8f41c6e82dd36cbd2dd26780 Wed Jul 1 21:45:43 2020 -0700

• hgBlat mostly works
  • src/gfServer/gfServer.c - lines changed 49, context: html, text, full: html, text
  • src/gfServer/tests/dynTester - lines changed 1, context: html, text, full: html, text
  • src/gfServer/tests/expected/testDynServer - lines changed 12, context: html, text, full: html, text
  • src/gfServer/tests/expected/testDynServerTrans - lines changed 12, context: html, text, full: html, text
  • src/gfServer/xinetd-example.conf - lines changed 2, context: html, text, full: html, text
  • src/hg/hgBlat/hgBlat.c - lines changed 59, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html - lines changed 5, context: html, text, full: html, text
  • src/hg/inc/trackHub.h - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/trackHub.c - lines changed 21, context: html, text, full: html, text
  • src/jkOwnLib/gfBlatLib.c - lines changed 8, context: html, text, full: html, text

ef850e264ac840b515b825f34314c36d58ccbcbe Thu Jul 2 11:12:15 2020 -0700

• added info command similar to status to support hgBlat
  • src/gfServer/gfServer.c - lines changed 84, context: html, text, full: html, text
  • src/gfServer/tests/dynTester - lines changed 19, context: html, text, full: html, text
  • src/gfServer/tests/expected/testDynServer - lines changed 9, context: html, text, full: html, text
  • src/gfServer/tests/expected/testDynServerTrans - lines changed 9, context: html, text, full: html, text

f50fee44b129d516772f00d7a1d00be2f3953e6f Thu Jul 2 11:50:46 2020 -0700

• hgBlat appears to be working
  • src/hg/hgBlat/hgBlat.c - lines changed 57, context: html, text, full: html, text

87a162ccdc3ac94525fc1011dec5bc10e2cf2171 Thu Jul 2 16:12:57 2020 -0700

• web blat working
  • src/gfServer/blat-xinetd.example - lines changed 33, context: html, text, full: html, text
  • src/gfServer/gfServer.c - lines changed 3, context: html, text, full: html, text
  • src/gfServer/xinetd-example.conf - lines changed 33, context: html, text, full: html, text
  • src/inc/gfWebLib.h - lines changed 1, context: html, text, full: html, text
  • src/jkOwnLib/gfWebLib.c - lines changed 60, context: html, text, full: html, text
  • src/webBlat/install.txt - lines changed 36, context: html, text, full: html, text
  • src/webBlat/webBlat.cfg - lines changed 4, context: html, text, full: html, text

16991e5fb7819460241f38f184a9e46311994598 Thu Jul 2 16:58:23 2020 -0700

• web blat really working now
  • src/webBlat/webBlat.c - lines changed 4, 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
  • src/gfServer/gfServer.c - lines changed 7, context: html, text, full: html, text
  • src/gfServer/tests/dynTester - lines changed 9, context: html, text, full: html, text
  • src/hg/hgBlat/hgBlat.c - lines changed 14, context: html, text, full: html, text
  • src/hg/inc/blatServers.h - lines changed 2, context: html, text, full: html, text
  • src/hg/lib/blatServers.as - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/blatServers.c - lines changed 8, context: html, text, full: html, text
  • src/hg/lib/blatServers.sql - lines changed 1, context: html, text, full: html, text
  • src/inc/genoFind.h - lines changed 3, context: html, text, full: html, text
  • src/jkOwnLib/genoFind.c - lines changed 13, context: html, text, full: html, text

84dba0006acf65324bb843abee1e11ad02c0a912 Sun Jul 5 20:01:10 2020 -0700

• some cleanup about hgBlat
  • src/gfServer/gfServer.c - lines changed 7, context: html, text, full: html, text
  • src/hg/hgBlat/hgBlat.c - 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/gfServer.c - lines changed 47, context: html, text, full: html, text
  • src/gfServer/makefile - lines changed 14, context: html, text, full: html, text
  • src/gfServer/tests/expected/testDynServer - lines changed 52, context: html, text, full: html, text
  • src/gfServer/tests/expected/testDynServer.out - lines changed 52, context: html, text, full: html, text
  • src/gfServer/tests/expected/testDynServerTrans - lines changed 196, context: html, text, full: html, text
  • src/gfServer/tests/expected/testDynServerTrans.out - lines changed 196, context: html, text, full: html, text
  • src/gfServer/tests/expected/testIndexFile - lines changed 20, context: html, text, full: html, text
  • src/gfServer/tests/expected/testIndexFile.out - lines changed 20, context: html, text, full: html, text
  • src/gfServer/tests/expected/testIndexFileTrans - lines changed 94, context: html, text, full: html, text
  • src/gfServer/tests/expected/testIndexFileTrans.out - lines changed 94, context: html, text, full: html, text
  • src/gfServer/tests/expected/testNib - lines changed 24, context: html, text, full: html, text
  • src/gfServer/tests/expected/testNib.out - lines changed 24, context: html, text, full: html, text
  • src/gfServer/tests/expected/testPcr - lines changed 18, context: html, text, full: html, text
  • src/gfServer/tests/expected/testPcr.out - lines changed 18, context: html, text, full: html, text
  • src/gfServer/tests/expected/testProtNib - lines changed 38, context: html, text, full: html, text
  • src/gfServer/tests/expected/testProtNib.out - lines changed 38, context: html, text, full: html, text
  • src/gfServer/tests/expected/testProtTwoBit - lines changed 38, context: html, text, full: html, text
  • src/gfServer/tests/expected/testProtTwoBit.out - lines changed 38, context: html, text, full: html, text
  • src/gfServer/tests/expected/testTransNib - lines changed 94, context: html, text, full: html, text
  • src/gfServer/tests/expected/testTransNib.out - lines changed 94, context: html, text, full: html, text
  • src/gfServer/tests/expected/testTransTwoBit - lines changed 94, context: html, text, full: html, text
  • src/gfServer/tests/expected/testTransTwoBit.out - lines changed 94, context: html, text, full: html, text
  • src/gfServer/tests/expected/testTwoBit - lines changed 21, context: html, text, full: html, text
  • src/gfServer/tests/expected/testTwoBit.out - lines changed 21, context: html, text, full: html, text
  • src/gfServer/tests/testDynServer - lines changed 2, context: html, text, full: html, text
  • src/gfServer/tests/testDynServerPerSeqMax - lines changed 15, context: html, text, full: html, text
  • src/gfServer/tests/testDynServerTrans - lines changed 2, context: html, text, full: html, text
  • src/gfServer/tests/testIndexFile - lines changed 2, context: html, text, full: html, text
  • src/gfServer/tests/testIndexFileTrans - lines changed 2, context: html, text, full: html, text
  • src/gfServer/tests/testPcr - lines changed 5, context: html, text, full: html, text
  • src/gfServer/tests/testProtNib - lines changed 2, context: html, text, full: html, text
  • src/gfServer/tests/testProtTwoBit - lines changed 3, context: html, text, full: html, text
  • src/gfServer/tests/testTransNib - lines changed 3, context: html, text, full: html, text
  • src/gfServer/tests/testTransTwoBit - 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
  • src/gfClient/gfClient.c - lines changed 2, context: html, text, full: html, text
  • src/gfServer/gfServer.c - lines changed 38, context: html, text, full: html, text
  • src/gfServer/makefile - lines changed 1, context: html, text, full: html, text
  • src/gfServer/tests/dynTester - lines changed 1, context: html, text, full: html, text
  • src/gfServer/tests/expected/testDynServerPerSeqMax.out - lines changed 52, context: html, text, full: html, text
  • src/gfServer/tests/expected/testDynServerWithDir.out - lines changed 52, context: html, text, full: html, text
  • src/gfServer/tests/expected/testNib.out - lines changed 19, context: html, text, full: html, text
  • src/gfServer/tests/expected/testPcr.out - lines changed 6, context: html, text, full: html, text
  • src/gfServer/tests/expected/testTwoBit.out - lines changed 19, context: html, text, full: html, text
  • src/gfServer/tests/testDynServer - lines changed 6, context: html, text, full: html, text
  • src/gfServer/tests/testDynServerPerSeqMax - lines changed 6, context: html, text, full: html, text
  • src/gfServer/tests/testDynServerTrans - lines changed 6, context: html, text, full: html, text
  • src/gfServer/tests/testDynServerWithDir - lines changed 16, context: html, text, full: html, text
  • src/hg/hgBlat/hgBlat.c - lines changed 23, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html - lines changed 51, context: html, text, full: html, text
  • src/hg/inc/trackHub.h - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/trackHub.c - lines changed 7, context: html, text, full: html, text
  • src/inc/common.h - lines changed 8, context: html, text, full: html, text
  • src/inc/genoFind.h - lines changed 3, context: html, text, full: html, text
  • src/inc/gfWebLib.h - lines changed 1, context: html, text, full: html, text
  • src/jkOwnLib/genoFind.c - lines changed 2, context: html, text, full: html, text
  • src/jkOwnLib/gfBlatLib.c - lines changed 15, context: html, text, full: html, text
  • src/webBlat/webBlat.c - lines changed 4, context: html, text, full: html, text

25d4c33f3e224c9d571876326ceccb46530005b0 Wed Jul 8 23:09:57 2020 -0700

• changed variable name to be more accurate
  • src/gfClient/gfClient.c - lines changed 11, 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
  • src/gfClient/gfClient.c - lines changed 21, context: html, text, full: html, text
  • src/gfServer/gfServer.c - lines changed 46, context: html, text, full: html, text
  • src/gfServer/tests/dynTester - lines changed 20, context: html, text, full: html, text
  • src/gfServer/tests/expected/testDynServer.out - lines changed 3, context: html, text, full: html, text
  • src/gfServer/tests/expected/testDynServerPerSeqMax.out - lines changed 3, context: html, text, full: html, text
  • src/gfServer/tests/expected/testDynServerTrans.out - lines changed 3, context: html, text, full: html, text
  • src/gfServer/tests/expected/testDynServerWithDir.out - lines changed 3, context: html, text, full: html, text
  • src/gfServer/tests/testDynServer - lines changed 1, context: html, text, full: html, text
  • src/gfServer/tests/testDynServerPerSeqMax - lines changed 1, context: html, text, full: html, text
  • src/gfServer/tests/testDynServerTrans - lines changed 1, context: html, text, full: html, text
  • src/gfServer/tests/testDynServerWithDir - lines changed 1, context: html, text, full: html, text
  • src/hg/hgBlat/hgBlat.c - lines changed 45, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html - lines changed 13, context: html, text, full: html, text
  • src/hg/inc/trackHub.h - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/trackHub.c - lines changed 3, context: html, text, full: html, text
  • src/inc/genoFind.h - lines changed 6, context: html, text, full: html, text
  • src/jkOwnLib/gfBlatLib.c - lines changed 20, context: html, text, full: html, text

63120154609787691150cc8a67a1aad40455481c Wed Oct 14 13:09:06 2020 -0700

• separate -genomeDir into -genome and -genomeDataDir
  • src/gfClient/gfClient.c - lines changed 3, 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
  • src/hg/lib/coordConv.c - lines changed 2, context: html, text, full: html, text
  • src/jkOwnLib/gfWebLib.c - lines changed 1, context: html, text, full: html, text

9186d6410c3266a7069c81e642c9ea22dc981191 Sun Oct 25 20:12:47 2020 -0700

• merged master
  • src/gfServer/gfServer.c - lines changed 50, context: html, text, full: html, text
  • src/hg/hgBlat/hgBlat.c - lines changed 80, context: html, text, full: html, text

f683064dc6a998206665b484790ef9d561e6c8a7 Sat Dec 5 22:42:53 2020 -0800

• initial conversion to gfServer connection to object
  • src/gfClient/gfClient.c - lines changed 7, context: html, text, full: html, text
  • src/gfClient/makefile - lines changed 15, context: html, text, full: html, text
  • src/gfServer/tests/expected/testDynServer.out - lines changed 1, context: html, text, full: html, text
  • src/gfServer/tests/expected/testDynServerPerSeqMax.out - lines changed 1, context: html, text, full: html, text
  • src/gfServer/tests/expected/testDynServerTrans.out - lines changed 1, context: html, text, full: html, text
  • src/gfServer/tests/expected/testDynServerWithDir.out - lines changed 1, context: html, text, full: html, text
  • src/hg/hgBlat/hgBlat.c - lines changed 27, context: html, text, full: html, text
  • src/hg/lib/coordConv.c - lines changed 6, context: html, text, full: html, text
  • src/inc/genoFind.h - lines changed 15, context: html, text, full: html, text
  • src/jkOwnLib/gfBlatLib.c - lines changed 27, context: html, text, full: html, text
  • src/jkOwnLib/gfPcrLib.c - lines changed 5, context: html, text, full: html, text
  • src/lib/gfNet.c - lines changed 20, context: html, text, full: html, text

36f8f6fb024b20cc523cdf9ebde7491eca84fd7c Sun Dec 6 20:33:20 2020 -0800

• multiple request per connect works except hgBlat
  • src/gfClient/gfClient.c - lines changed 9, context: html, text, full: html, text
  • src/gfServer/README.blat - lines changed 16, context: html, text, full: html, text
  • src/gfServer/gfServer.c - lines changed 151, context: html, text, full: html, text
  • src/gfServer/tests/dynTester - lines changed 22, context: html, text, full: html, text
  • src/gfServer/tests/expected/testDynServer.out - lines changed 2, context: html, text, full: html, text
  • src/gfServer/tests/expected/testDynServerPerSeqMax.out - lines changed 2, context: html, text, full: html, text
  • src/gfServer/tests/expected/testDynServerTrans.out - lines changed 2, context: html, text, full: html, text
  • src/gfServer/tests/expected/testDynServerWithDir.out - lines changed 2, context: html, text, full: html, text
  • src/gfServer/tests/testDynServer - lines changed 1, context: html, text, full: html, text
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e9492dbfa8a68aee133893d4b02475b0aec27bb9 Sun Dec 6 23:48:42 2020 -0800

• webblat and hgBlat working
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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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e1ae6056b95e1f21e3889bd190108a8f71ca222e Wed Dec 9 08:25:02 2020 -0800

• fixed example that was incorrectly modified
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e791c48b268a2af9ac4e2866758661c513be61d2 Wed Dec 9 08:32:24 2020 -0800

• merged with master

a4b45fbe8156dfa9881f586b830a2e6a6338d58f Wed Dec 9 11:35:20 2020 -0800

• fixed undetect change in signature
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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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65f00dd6b049342f185de41542e9c968ec3e98d3 Wed Dec 9 21:31:03 2020 -0800

• added gfServer design overview
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a4100d62e1f3a6864f70e651b6b41517c662f496 Wed Dec 9 21:34:41 2020 -0800

• improved doc on reserved files
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fa416c484061b1e44519962435588916dc14a1f7 Wed Dec 9 22:04:07 2020 -0800

• added isSafeRelativePath and removed way too low-level verbose logging
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be5104801a919dd2668e935b265b669940c9199a Wed Dec 9 22:05:45 2020 -0800

• added check for attempting to access outside of gfServer root
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cb757269cca8bc473f97d588a2f3737acaf0fb41 Wed Dec 9 22:11:32 2020 -0800

• dropped support for absolute genomeDataDir
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3c5f6de8a9739eb8ddaf1cb233460e0bba9e5321 Fri Dec 11 21:32:23 2020 -0800

• fixed documention issues
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365534e1a97dc9250ff85e367a7786989662281d Mon Dec 14 14:01:20 2020 -0800

• updated gfServer version
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3d71b2793b72fd0f6f4ff1511bb93cf3b6b76497 Sun Jan 3 14:01:54 2021 -0800

• fixed parameter change errors in blatSuite
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be4311c07e14feb728abc6425ee606ffaa611a58 Fri Jan 22 06:46:58 2021 -0800

• merge with master
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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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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
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a2819277576ffc91069261a03b358213afe2cb3b Wed Feb 3 15:30:27 2021 -0800

• allow gfPcr to query dynamic servers
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c16b3edf4c88aed3d6cf1da68118fca1f8855593 Wed Feb 3 16:31:12 2021 -0800

• add debug logging of index parameters
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fe48c5bed92448a3e0a599f2fe3123294fc0c7af Wed Feb 3 17:19:09 2021 -0800

• fixed initialization problem that prefected isPcr to work on dynamic servers
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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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f16dbe1fef6a6fd83d63fbc7e060b21262b43bf5 Mon Feb 8 15:26:55 2021 -0800

• don't include dynamic gfServer in blat of all genomes
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f67d0a4b041b6553076c7fb9128772f5116231b3 Sun Feb 28 13:08:56 2021 -0800

• updated expected results due to previous fix
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f7d577042a7e3e41c1121082febb7ff25020bf0b Sun Feb 28 13:19:19 2021 -0800

• have gfServer check that index files match the required naming convention
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94a2d41644d235ec3702d8189ec52036e739000a Sun Feb 28 14:23:10 2021 -0800

• merge master into branch
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a7e5ec255bed61069a80919b5e5f48c850ee3c2c Mon Mar 1 15:00:01 2021 -0800

• added hubCheck -genome to support only checking one genome
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60499556c04cfbfd9197f76d1e1d0152a8d12614 Tue Mar 2 21:58:17 2021 -0800

• added option to build chrispr for hubs, doing this removed the no longer used gene track options
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96ec696511055773d2bc6f63d74dde41501e76b3 Wed Mar 3 12:35:02 2021 -0800

• Merge branch 'master' into gfserver-mmap-index

73c09a61e57baf2a2ab6548c2a2bfe0cf3303600 Thu Mar 4 11:11:57 2021 -0800

• provide hint to look in systems logs when blat server failes
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