All File Changes

v343_preview2 to v343_base (2017-01-03 to 2017-01-09) v343

• confs/preview.hg.conf
  • lines changed 244, context: html, text, full: html, text
    36e5c4048cccad714ede81bf08596363368c5ee8 Sun Jan 8 01:13:27 2017 -0800
    Installing updated hg.conf files from UCSC servers
• src/hg/cirm/cdw/cdwMakeFileTags/cdwMakeFileTags.c
  • lines changed 32, context: html, text, full: html, text
    482523a14c95bb1819b4e3ee74ed0037b7fd1b4f Thu Jan 5 12:54:52 2017 -0800
    responding to most of Kate's code review feedback refs #18611
  • lines changed 211, context: html, text, full: html, text
    c69dea1a62dba064ed5f3053ccb428e15f8d63de Thu Jan 5 14:02:10 2017 -0800
    Refactoring cdwMakeFileTags refs #18611
  • lines changed 77, context: html, text, full: html, text
    7dc6b81fd111ac609870542a0da4fc2bf4faa98c Thu Jan 5 16:23:57 2017 -0800
    A little more refactoring in preparation for moving SQL creation stuff to library.
  • lines changed 320, context: html, text, full: html, text
    7c6fc748aa7b23971669dc686510dcbff030d045 Thu Jan 5 16:42:52 2017 -0800
    Moving a bunch of the SQL creation code to library.
• src/hg/hgTracks/hgTracks.c
  • lines changed 5, context: html, text, full: html, text
    86ab10b2e387dfeb4505329c84ad399d44fcc1d6 Wed Jan 4 11:43:05 2017 -0800
    changing UK to US spelling, refs #18513
  • lines changed 6, context: html, text, full: html, text
    1965a8b005056af919bddb9b0fdf0b83128a9dd9 Wed Jan 4 14:05:35 2017 -0800
    adding more keyboard shortcut docs, refs #18618
  • lines changed 10, context: html, text, full: html, text
    ad9d7082c4e74d57f07a8bf5170fead4aad8a81f Fri Jan 6 11:16:53 2017 -0800
    fix a problem with visibility of composites #18544
  • lines changed 10, context: html, text, full: html, text
    032fa2c2ef16227175694f6181e38a7372b48a24 Fri Jan 6 13:08:09 2017 -0800
    Revert "fix a problem with visibility of composites #18544" This reverts commit ad9d7082c4e74d57f07a8bf5170fead4aad8a81f.
• src/hg/htdocs/images/cdwImages/qbg_krgSeurat.png
  • lines changed 0, context: html, text, full: html, text
    f3ab7e342f8505623ec061de505843d34c25222c Wed Jan 4 09:54:11 2017 -0800
    Updating the quality of the home page image that links to a data set page, refs #17870
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    1234f3ad8d68b1865c6010b29ae2d9ab488f54d5 Mon Jan 9 09:57:37 2017 -0800
    New version number v343
• src/hg/lib/hdb.c
  • lines changed 4, context: html, text, full: html, text
    f6def44785079440787ef7b1c05660e6d16f992b Wed Jan 4 11:01:51 2017 -0800
    If hTableExists is passed a db that doesn't exist (e.g. from all.joiner), it should return FALSE instead of crashing. fixes #18586
• src/hg/lib/hui.c
  • lines changed 4, context: html, text, full: html, text
    c2f1001f2ab451206060861ed977f5d0c12726c1 Fri Jan 6 14:55:51 2017 -0800
    yet more attempt to squash bug from #18544
• src/hg/makeDb/doc/mm10.txt
  • lines changed 61, context: html, text, full: html, text
    f7a3a16fa73c8252f32f4ec3e97552d0e75419d4 Wed Jan 4 12:46:13 2017 -0800
    adding mouse strain VCF track refs #18305
• src/hg/makeDb/trackDb/human/hg18/evofoldV2.html
  • lines changed 1, context: html, text, full: html, text
    fb3b804476f2405df3cf8c10fe468c28f12a38d5 Tue Jan 3 15:57:14 2017 -0800
    Fixing bad urls, no RM
• src/hg/makeDb/trackDb/human/hg18/pgSnp.html
  • lines changed 2, context: html, text, full: html, text
    fb3b804476f2405df3cf8c10fe468c28f12a38d5 Tue Jan 3 15:57:14 2017 -0800
    Fixing bad urls, no RM
• src/hg/makeDb/trackDb/human/hg18/wgEncodeChromatinMap.html
  • lines changed 2, context: html, text, full: html, text
    fb3b804476f2405df3cf8c10fe468c28f12a38d5 Tue Jan 3 15:57:14 2017 -0800
    Fixing bad urls, no RM
• src/hg/makeDb/trackDb/human/hg18/wgEncodeChromatinMapRelease2.html
  • lines changed 2, context: html, text, full: html, text
    fb3b804476f2405df3cf8c10fe468c28f12a38d5 Tue Jan 3 15:57:14 2017 -0800
    Fixing bad urls, no RM
• src/hg/makeDb/trackDb/human/hg19/pgSnp.html
  • lines changed 2, context: html, text, full: html, text
    fb3b804476f2405df3cf8c10fe468c28f12a38d5 Tue Jan 3 15:57:14 2017 -0800
    Fixing bad urls, no RM
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.release2.html
  • lines changed 3, context: html, text, full: html, text
    fb3b804476f2405df3cf8c10fe468c28f12a38d5 Tue Jan 3 15:57:14 2017 -0800
    Fixing bad urls, no RM
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.release2.html
  • lines changed 2, context: html, text, full: html, text
    fb3b804476f2405df3cf8c10fe468c28f12a38d5 Tue Jan 3 15:57:14 2017 -0800
    Fixing bad urls, no RM
• src/hg/makeDb/trackDb/human/hg38/hg38Patch9.html
  • lines changed 2, context: html, text, full: html, text
    1b33e95605347d7b91df12c2c1020fedb2d996ae Mon Jan 9 09:08:56 2017 -0800
    adding GRC hg38Patch9 per rafs #18274
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    1b33e95605347d7b91df12c2c1020fedb2d996ae Mon Jan 9 09:08:56 2017 -0800
    adding GRC hg38Patch9 per rafs #18274
• src/hg/makeDb/trackDb/human/snp141.shared.html
  • lines changed 10, context: html, text, full: html, text
    12f4e58b8104338509056104dce72a79b1ffd983 Wed Jan 4 08:17:09 2017 -0800
    added changes to human/snp.shared.html per refs #17960
• src/hg/makeDb/trackDb/human/snp142.shared.html
  • lines changed 11, context: html, text, full: html, text
    12f4e58b8104338509056104dce72a79b1ffd983 Wed Jan 4 08:17:09 2017 -0800
    added changes to human/snp.shared.html per refs #17960
• src/hg/makeDb/trackDb/human/snp144.shared.html
  • lines changed 11, context: html, text, full: html, text
    12f4e58b8104338509056104dce72a79b1ffd983 Wed Jan 4 08:17:09 2017 -0800
    added changes to human/snp.shared.html per refs #17960
• src/hg/makeDb/trackDb/human/snp146.shared.html
  • lines changed 11, context: html, text, full: html, text
    12f4e58b8104338509056104dce72a79b1ffd983 Wed Jan 4 08:17:09 2017 -0800
    added changes to human/snp.shared.html per refs #17960
• src/hg/makeDb/trackDb/human/snp147.shared.html
  • lines changed 11, context: html, text, full: html, text
    12f4e58b8104338509056104dce72a79b1ffd983 Wed Jan 4 08:17:09 2017 -0800
    added changes to human/snp.shared.html per refs #17960
• src/hg/oneShot/freen/freen.c
  • lines changed 12, context: html, text, full: html, text
    a559984d5d4096c3616590f1e90fd92bafb2e28a Thu Jan 5 14:09:28 2017 -0800
    Freen helps debug a udcCache/linefile issue.
  • lines changed 12, context: html, text, full: html, text
    172697d2287cc4e093dcd2d925d1b5f2c7795d78 Fri Jan 6 10:34:20 2017 -0800
    freen tests tagStormQuery.
  • lines changed 1, context: html, text, full: html, text
    b5a2415fd25848d2f4ab8e0bcc1565e2556b52ca Fri Jan 6 13:31:59 2017 -0800
    Adding tagStanzaFindInHash and tagStanzaFree functions.
• src/hg/utils/vai.pl
  • lines changed 1, context: html, text, full: html, text
    53a2e1ae6b18669a39f8d9fdd929c754f974f367 Fri Jan 6 09:44:31 2017 -0800
    Fixing option spec for udcCache. refs #12216 note-43
• src/inc/tagStorm.h
  • lines changed 3, context: html, text, full: html, text
    fb7235db79dcef536a49fad74529c2384887bc40 Tue Jan 3 14:01:36 2017 -0800
    Added utility function to remove empty stanzas.
  • lines changed 2, context: html, text, full: html, text
    9208d427b15fa0a175639d40a83bd52bda75f5c6 Thu Jan 5 17:13:08 2017 -0800
    Adding two parameters to tagStormWriteAsFlatTab, and deleting a redundant static routine.
  • lines changed 19, context: html, text, full: html, text
    23ba0ea430e9e60f9b33a778fa5430b12c99a3a8 Fri Jan 6 10:33:46 2017 -0800
    Creating a tagStormQuery library function. Refactoring some stuff from the tagStormQuery command line utility into library.
  • lines changed 14, context: html, text, full: html, text
    b5a2415fd25848d2f4ab8e0bcc1565e2556b52ca Fri Jan 6 13:31:59 2017 -0800
    Adding tagStanzaFindInHash and tagStanzaFree functions.
• src/inc/tagToSql.h
  • lines changed 41, context: html, text, full: html, text
    7c6fc748aa7b23971669dc686510dcbff030d045 Thu Jan 5 16:42:52 2017 -0800
    Moving a bunch of the SQL creation code to library.
  • lines changed 2, context: html, text, full: html, text
    6f9e439038e3587389b3fad29d4e24476f4485c2 Thu Jan 5 22:55:42 2017 -0800
    Adding -schema flag to tagStormInfo
• src/lib/fieldedTable.c
  • lines changed 2, context: html, text, full: html, text
    2682dc0d4299d8c72f892e6345faa7a516ea1425 Thu Jan 5 15:34:01 2017 -0800
    Making it so that fieldedTable tab-sep-files first (label) line need not start with a #
• src/lib/linefile.c
  • lines changed 1, context: html, text, full: html, text
    936343c3167fc0fde1b54dca286c018689ff9025 Wed Jan 4 14:19:22 2017 -0800
    Making lineIx work for udcFile case.
• src/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    ab485115a26471d12034a441d7ff48f2972d15d7 Thu Jan 5 16:43:05 2017 -0800
    Moving a bunch of the SQL creation code to library.
• src/lib/tagStorm.c
  • lines changed 37, context: html, text, full: html, text
    fb7235db79dcef536a49fad74529c2384887bc40 Tue Jan 3 14:01:36 2017 -0800
    Added utility function to remove empty stanzas.
  • lines changed 43, context: html, text, full: html, text
    9208d427b15fa0a175639d40a83bd52bda75f5c6 Thu Jan 5 17:13:08 2017 -0800
    Adding two parameters to tagStormWriteAsFlatTab, and deleting a redundant static routine.
  • lines changed 89, context: html, text, full: html, text
    23ba0ea430e9e60f9b33a778fa5430b12c99a3a8 Fri Jan 6 10:33:46 2017 -0800
    Creating a tagStormQuery library function. Refactoring some stuff from the tagStormQuery command line utility into library.
  • lines changed 36, context: html, text, full: html, text
    b5a2415fd25848d2f4ab8e0bcc1565e2556b52ca Fri Jan 6 13:31:59 2017 -0800
    Adding tagStanzaFindInHash and tagStanzaFree functions.
• src/lib/tagToSql.c
  • lines changed 310, context: html, text, full: html, text
    7c6fc748aa7b23971669dc686510dcbff030d045 Thu Jan 5 16:42:52 2017 -0800
    Moving a bunch of the SQL creation code to library.
  • lines changed 41, context: html, text, full: html, text
    6f9e439038e3587389b3fad29d4e24476f4485c2 Thu Jan 5 22:55:42 2017 -0800
    Adding -schema flag to tagStormInfo
• src/tagStorm/makefile
  • lines changed 4, context: html, text, full: html, text
    115188883ac5352c028bba63ba80029a57092cad Thu Jan 5 15:11:58 2017 -0800
    Adding tagStormToTab
  • lines changed 4, context: html, text, full: html, text
    820a2723dbd2cf156feb9024944dae88c66779c9 Thu Jan 5 17:11:09 2017 -0800
    First cut of utility to convert tagStorm to a sql command.
  • lines changed 4, context: html, text, full: html, text
    00f51e93f637bbae2d53d2eea1372cf0b5b1a754 Fri Jan 6 00:02:26 2017 -0800
    First cut of tagStormCheck
• src/tagStorm/tagStormCheck/makefile
  • lines changed 3, context: html, text, full: html, text
    00f51e93f637bbae2d53d2eea1372cf0b5b1a754 Fri Jan 6 00:02:26 2017 -0800
    First cut of tagStormCheck
• src/tagStorm/tagStormCheck/tagStormCheck.c
  • lines changed 193, context: html, text, full: html, text
    00f51e93f637bbae2d53d2eea1372cf0b5b1a754 Fri Jan 6 00:02:26 2017 -0800
    First cut of tagStormCheck
  • lines changed 51, context: html, text, full: html, text
    c841119661494598a15654915bb653f54a4a4345 Fri Jan 6 00:16:16 2017 -0800
    Improving usage message and allowing wildcards in tag names in schema.
  • lines changed 2, context: html, text, full: html, text
    c2a85e74b442edb31a7d365c4695d0db2be2da14 Fri Jan 6 00:20:21 2017 -0800
    Improving punctuation in usage message.
  • lines changed 27, context: html, text, full: html, text
    9f14c73b4c289b89cfaf94f88ab39ee0264dc8f5 Fri Jan 6 13:33:36 2017 -0800
    Improving normal passes check output. Fixing bug in quoted value handling.
• src/tagStorm/tagStormCheck/test.schema
  • lines changed 18, context: html, text, full: html, text
    805eeb76b27646c80769d264e39a4216209f2832 Fri Jan 6 00:17:46 2017 -0800
    Adding test files.
  • lines changed 2, context: html, text, full: html, text
    e9adb17a7dab941d267a6093eb10dd13eb3cd568 Fri Jan 6 00:19:08 2017 -0800
    Improving test set
• src/tagStorm/tagStormCheck/test.tags
  • lines changed 164, context: html, text, full: html, text
    805eeb76b27646c80769d264e39a4216209f2832 Fri Jan 6 00:17:46 2017 -0800
    Adding test files.
• src/tagStorm/tagStormDeleteTags/tagStormDeleteTags.c
  • lines changed 1, context: html, text, full: html, text
    fd56da452ba9cb650dec208215b764cd110c40ae Tue Jan 3 11:23:15 2017 -0800
    Making usage statement more consistent.
• src/tagStorm/tagStormFromTab/tagStormFromTab.c
  • lines changed 2, context: html, text, full: html, text
    0fccc72cfec3b269d9002dde99b3cc263265fb7b Thu Jan 5 15:34:19 2017 -0800
    Explaining that the # in the label line is now optional.
• src/tagStorm/tagStormHoist/tagStormHoist.c
  • lines changed 3, context: html, text, full: html, text
    9290d3bf91d0817cd34569bfffbc6d67907ce841 Tue Jan 3 14:03:00 2017 -0800
    Removing empty stanzas, which no longer end up screwing up hierarchy on read.
• src/tagStorm/tagStormHoist/test.in
  • lines changed 93, context: html, text, full: html, text
    fb7235db79dcef536a49fad74529c2384887bc40 Tue Jan 3 14:01:36 2017 -0800
    Added utility function to remove empty stanzas.
  • lines changed 2, context: html, text, full: html, text
    7a486464076e1ff5b2fe46878a915747d0f15c9c Tue Jan 3 14:13:42 2017 -0800
    Making test set more comprehensive.
• src/tagStorm/tagStormInfo/tagStormInfo.c
  • lines changed 94, context: html, text, full: html, text
    6f9e439038e3587389b3fad29d4e24476f4485c2 Thu Jan 5 22:55:42 2017 -0800
    Adding -schema flag to tagStormInfo
  • lines changed 41, context: html, text, full: html, text
    ec02f84b0ca8f5935250c47470699cc80028c1e6 Fri Jan 6 01:47:55 2017 -0800
    Adding looseSchema and tightSchema options.
• src/tagStorm/tagStormInfo/tests/expected.counts
  • lines changed 5, context: html, text, full: html, text
    66fcc2e08e33ad612c14003b08e851dbe44987b3 Thu Jan 5 22:53:36 2017 -0800
    Updating test sets
• src/tagStorm/tagStormInfo/tests/expected.out
  • lines changed 5, context: html, text, full: html, text
    66fcc2e08e33ad612c14003b08e851dbe44987b3 Thu Jan 5 22:53:36 2017 -0800
    Updating test sets
• src/tagStorm/tagStormInfo/tests/expected.schema
  • lines changed 17, context: html, text, full: html, text
    66fcc2e08e33ad612c14003b08e851dbe44987b3 Thu Jan 5 22:53:36 2017 -0800
    Updating test sets
• src/tagStorm/tagStormInfo/tests/expected.vals
  • lines changed 19, context: html, text, full: html, text
    66fcc2e08e33ad612c14003b08e851dbe44987b3 Thu Jan 5 22:53:36 2017 -0800
    Updating test sets
• src/tagStorm/tagStormInfo/tests/makefile
  • lines changed 3, context: html, text, full: html, text
    66fcc2e08e33ad612c14003b08e851dbe44987b3 Thu Jan 5 22:53:36 2017 -0800
    Updating test sets
• src/tagStorm/tagStormInfo/tests/test.in
  • lines changed 20, context: html, text, full: html, text
    3363c3080fa54a4489af441559d44e52f2face7b Fri Jan 6 00:21:07 2017 -0800
    Improving test set.
• src/tagStorm/tagStormQuery/tagStormQuery.c
  • lines changed 6, context: html, text, full: html, text
    42314f49b54ee7e450fea7797bf25c74b8c5f743 Thu Jan 5 14:05:51 2017 -0800
    Cleaning up usage statement. refs #18611
  • lines changed 10, context: html, text, full: html, text
    23ba0ea430e9e60f9b33a778fa5430b12c99a3a8 Fri Jan 6 10:33:46 2017 -0800
    Creating a tagStormQuery library function. Refactoring some stuff from the tagStormQuery command line utility into library.
• src/tagStorm/tagStormReformat/tagStormReformat.c
  • lines changed 1, context: html, text, full: html, text
    92a933c2508762a11c12fbd3375551258894c987 Thu Jan 5 17:13:28 2017 -0800
    Adding two parameters to tagStormWriteAsFlatTab, and deleting a redundant static routine.
• src/tagStorm/tagStormToSql/makefile
  • lines changed 3, context: html, text, full: html, text
    820a2723dbd2cf156feb9024944dae88c66779c9 Thu Jan 5 17:11:09 2017 -0800
    First cut of utility to convert tagStorm to a sql command.
• src/tagStorm/tagStormToSql/tagStormToSql.c
  • lines changed 99, context: html, text, full: html, text
    820a2723dbd2cf156feb9024944dae88c66779c9 Thu Jan 5 17:11:09 2017 -0800
    First cut of utility to convert tagStorm to a sql command.
• src/tagStorm/tagStormToTab/makefile
  • lines changed 3, context: html, text, full: html, text
    fffb473645d4ed13794dc747e23da9b701601920 Thu Jan 5 15:11:47 2017 -0800
    Adding tagStormToTab
• src/tagStorm/tagStormToTab/tagStormToTab.c
  • lines changed 42, context: html, text, full: html, text
    fffb473645d4ed13794dc747e23da9b701601920 Thu Jan 5 15:11:47 2017 -0800
    Adding tagStormToTab
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    4642a53a01e0ef9e1037164bb32c51e966f1400f Thu Jan 5 17:13:59 2017 -0800
    Adding noSharp and null options.
• src/userApps/Makefile
  • lines changed 7, context: html, text, full: html, text
    15b99aa056852e31fb0bd7c1f09c9979aab579d7 Fri Jan 6 10:51:46 2017 -0800
    eliminate problem echo statements that are not the same in all environments no redmine
• src/utils/qa/checkBOT.csh
  • lines changed 3, context: html, text, full: html, text
    76f2a1d645d0a52b31efe0a35b458d18b56e3d47 Fri Jan 6 11:39:05 2017 -0800
    fixed checkBOT.csh to get bottleneck info from hgnfs1 via ssh qateam@hgwbeta
  • lines changed 3, context: html, text, full: html, text
    cbee792305326b067cb6d6ee83390425ea85dab6 Fri Jan 6 11:45:58 2017 -0800
    fixed checkBOT.csh to work with all option and removed errant exit
• src/utils/qa/getPubHubContact.sh
  • lines changed 10, context: html, text, full: html, text
    b62da609cf70688466da60372a361df5488c75e6 Thu Jan 5 10:40:21 2017 -0800
    Adding check to see if user-supplied directory exists before accepting it. Also adding command that checks to see of there is a hubFiles directory in the supplied directory and creates it if it doesn't exist. refs #18603 #18316
• src/utils/qa/qaAutoTrack.sh
  • lines changed 97, context: html, text, full: html, text
    8c47f8c70bd398b723b695fa150b854a873f236f Thu Jan 5 12:27:33 2017 -0800
    Changed the way command-line options are supplied so that db and tableName are required arguments. Added three new options: -l allows you to specify output directory, -u allows you to specify the output URL, and -s allows you to suppress URL in the output. Changed it so that script can be more than once per day, subsequent log files include time in flie name, other minor changes to script structure and output. refs #12561
• src/utils/qa/weeklybld/buildEnv.csh
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    03e2ee670c8677e9628b7e766e1c8538b80d4276 Mon Jan 9 09:56:10 2017 -0800
    v343 final build refs #18555
• src/utils/rowsToCols/makefile
  • lines changed 1, context: html, text, full: html, text
    46a92bdf0870db480a98cc94c0958714a53e58d2 Fri Jan 6 10:01:44 2017 -0800
    our test target is test not tests
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    8c8f57d92bc18c71922447a3fbbc21ad1c82bf22 Fri Jan 6 11:51:47 2017 -0800
    renaming test directory to tests no redmine
• src/utils/rowsToCols/test/expected/comma
  • lines changed 3, context: html, text, full: html, text
    ba2e7617497f87ccc700f53802a7b7ed28bec07f Fri Jan 6 11:51:22 2017 -0800
    renaming test directory to tests no redmine
• src/utils/rowsToCols/test/expected/commaVarious
  • lines changed 4, context: html, text, full: html, text
    ba2e7617497f87ccc700f53802a7b7ed28bec07f Fri Jan 6 11:51:22 2017 -0800
    renaming test directory to tests no redmine
• src/utils/rowsToCols/test/expected/fixed
  • lines changed 3, context: html, text, full: html, text
    ba2e7617497f87ccc700f53802a7b7ed28bec07f Fri Jan 6 11:51:22 2017 -0800
    renaming test directory to tests no redmine
• src/utils/rowsToCols/test/expected/offsets
  • lines changed 3, context: html, text, full: html, text
    ba2e7617497f87ccc700f53802a7b7ed28bec07f Fri Jan 6 11:51:22 2017 -0800
    renaming test directory to tests no redmine
• src/utils/rowsToCols/test/expected/spaced
  • lines changed 5, context: html, text, full: html, text
    ba2e7617497f87ccc700f53802a7b7ed28bec07f Fri Jan 6 11:51:22 2017 -0800
    renaming test directory to tests no redmine
• src/utils/rowsToCols/test/expected/spacedVarious
  • lines changed 5, context: html, text, full: html, text
    ba2e7617497f87ccc700f53802a7b7ed28bec07f Fri Jan 6 11:51:22 2017 -0800
    renaming test directory to tests no redmine
• src/utils/rowsToCols/test/expected/tab
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