All File Changes

v351_preview to v351_preview2 (2017-06-12 to 2017-06-19) v351

• confs/hgwdev.hg.conf
  • lines changed 4, context: html, text, full: html, text
    ba82a59d8213b8105de79f7813dd4d7b82f78380 Sun Jun 18 01:11:51 2017 -0700
    Installing updated hg.conf files from UCSC servers
• src/browserbox/root/updateBrowser.sh
  • lines changed 1, context: html, text, full: html, text
    7c25764e7799be529d0d904a71082d30e7b46be8 Wed Jun 14 10:21:49 2017 -0700
    Fixing typo in table name so hgVai works on gbib. Fixes gbib update errors, refs #19565
• src/hca/fromArrayExpress/arrayExpressStormToHcaStorm/arrayExpressStormToHcaStorm.c
  • lines changed 5, context: html, text, full: html, text
    e3829b31e46f467d1efed0717d212866dff860d8 Sun Jun 11 13:30:56 2017 -0700
    Adding in sample.donor.id from one place it could appear. Adding in project.uuid.
  • lines changed 5, context: html, text, full: html, text
    5a74a4b4a4da39cb0b03cef3d6ad0561d20ee8c4 Tue Jun 13 16:50:19 2017 -0700
    Moving uuid generation to dedicated new program.
• src/hca/fromArrayExpress/arrayExpressStormToHcaStorm/makefile
  • lines changed 1, context: html, text, full: html, text
    5a74a4b4a4da39cb0b03cef3d6ad0561d20ee8c4 Tue Jun 13 16:50:19 2017 -0700
    Moving uuid generation to dedicated new program.
• src/hca/fromArrayExpress/arrayExpressToTagStorm/arrayExpressToTagStorm.c
  • lines changed 71, context: html, text, full: html, text
    c4b5aa62f38a281c0f78cd90f0e7444b9c9c0a72 Sat Jun 10 09:08:50 2017 -0700
    Adding logic to deal with paired end sets having two lines per read.
• src/hca/fromGeo/geoStormToHcaStorm/geoStormToHcaStorm.c
  • lines changed 46, context: html, text, full: html, text
    648839701eb8ba10b71f5d456f53a500e7803a2e Sun Jun 11 13:34:25 2017 -0700
    Generating uuids on sample.donor.id
  • lines changed 28, context: html, text, full: html, text
    5a74a4b4a4da39cb0b03cef3d6ad0561d20ee8c4 Tue Jun 13 16:50:19 2017 -0700
    Moving uuid generation to dedicated new program.
• src/hca/fromGeo/geoStormToHcaStorm/in.tags
  • lines changed 5, context: html, text, full: html, text
    648839701eb8ba10b71f5d456f53a500e7803a2e Sun Jun 11 13:34:25 2017 -0700
    Generating uuids on sample.donor.id
• src/hca/fromGeo/geoStormToHcaStorm/makefile
  • lines changed 1, context: html, text, full: html, text
    5a74a4b4a4da39cb0b03cef3d6ad0561d20ee8c4 Tue Jun 13 16:50:19 2017 -0700
    Moving uuid generation to dedicated new program.
• src/hca/fromGeo/geoToTagStorm/geoToTagStorm.c
  • lines changed 4, context: html, text, full: html, text
    2d15d70daa7bd690dc653169391f269bcb118f9b Mon Jun 12 10:04:33 2017 -0700
    Tolerating soft lines with nothing after symbol as they are common.
  • lines changed 2, context: html, text, full: html, text
    d07c9499caaab327d4104756436b37c021d8e7c4 Sun Jun 18 09:27:40 2017 -0700
    Changing '-' to '_' in field names.
• src/hca/fromGeo/hcaAddSrrFiles/hcaAddSrrFiles.c
  • lines changed 55, context: html, text, full: html, text
    35cd53e650da0fb23cf7ade0b78dc06d75f4d7b7 Mon Jun 12 10:06:32 2017 -0700
    Adding barcode info even if it is not on root stanza since have some submissions that are only partly barcoded.
• src/hca/oneShot/arrayExpressFetchProtocols/arrayExpressFetchProtocols.c
  • lines changed 84, context: html, text, full: html, text
    24e1ec0d7f5e51ab76208bda3a15a74e24d82e42 Fri Jun 9 20:22:14 2017 -0700
    We don't seem to need this utility. I didn't realize the protocols were actually in the idf.txt file.
• src/hca/oneShot/arrayExpressFetchProtocols/makefile
  • lines changed 3, context: html, text, full: html, text
    24e1ec0d7f5e51ab76208bda3a15a74e24d82e42 Fri Jun 9 20:22:14 2017 -0700
    We don't seem to need this utility. I didn't realize the protocols were actually in the idf.txt file.
• src/hca/toHca/hcaAddUuidToStorm/hcaAddUuidToStorm.c
  • lines changed 145, context: html, text, full: html, text
    9c9eab2cfea930f9a1a2e6ca74bac93345457ee1 Tue Jun 13 16:49:04 2017 -0700
    Moving the job of assigning uuids to this new program. It will avoid regenerating them if possible.
• src/hca/toHca/hcaAddUuidToStorm/makefile
  • lines changed 4, context: html, text, full: html, text
    9c9eab2cfea930f9a1a2e6ca74bac93345457ee1 Tue Jun 13 16:49:04 2017 -0700
    Moving the job of assigning uuids to this new program. It will avoid regenerating them if possible.
• src/hca/toHca/hcaStormToBundles/hcaStormToBundles.c
  • lines changed 151, context: html, text, full: html, text
    12dd2c658e0f18bc1060f644ae67acfe3f45d5af Mon Jun 12 10:07:43 2017 -0700
    Adding a manifest with file directory info instead of symbolically linking fastq files into submission dir.
  • lines changed 49, context: html, text, full: html, text
    66d8efb12fa1ec4d72a160c1ac3221ef42bbe1ee Mon Jun 12 13:27:38 2017 -0700
    Adding lane to assay.files.
  • lines changed 7, context: html, text, full: html, text
    0b149d763e8c04f7f84e321c4f7fe2f4f0b00370 Sun Jun 18 09:28:54 2017 -0700
    Moving uuid generation to a separate program.
• src/hca/toHca/hcaStormToBundles/testIt
  • lines changed 1, context: html, text, full: html, text
    12dd2c658e0f18bc1060f644ae67acfe3f45d5af Mon Jun 12 10:07:43 2017 -0700
    Adding a manifest with file directory info instead of symbolically linking fastq files into submission dir.
• src/hg/genePredToFakePsl/genePredToFakePsl.c
  • lines changed 21, context: html, text, full: html, text
    61917474c6c267cd21f007c1f2d5b5f243ee7d5f Mon Jun 19 09:25:58 2017 -0700
    Prevent unsigned int underflow when sum of blockSizes is greater than actual qSize. Collapse contiguous 'exons' that are split to represent internal frameshift (e.g. ribosomal frameshift) in genePredExt but need to be a single block to avoid pslCheck errors downstream. This prevents a few PSLs from being lost from ncbiRefSeqPsl.
• src/hg/hgCustom/hgCustom.c
  • lines changed 1, context: html, text, full: html, text
    c39806584d831c8a3a679e69658430aa6f9409f8 Fri Jun 16 12:57:24 2017 -0700
    Updating link to bigBarChart track format in hgCustom, refs #18736
• src/hg/hgGeneGraph/hgGeneGraph
  • lines changed 1, context: html, text, full: html, text
    e42cc09ffbb67d00c855ff96ad9aa6ff2aa98f14 Tue Jun 13 15:11:16 2017 -0700
    fixing small bug visible only in error log, refs #13634
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 707, context: html, text, full: html, text
    79e2e0421ffa1203d75e66351a2046085129528e Thu Jun 15 15:16:16 2017 -0700
    hgHubConnect now displays search details and indexes description content, refs #13625
  • lines changed 2, context: html, text, full: html, text
    a5cd114e4b68544136bf74576d7a249f91450beb Thu Jun 15 15:44:40 2017 -0700
    hgHubConnect needed to support an hg.conf-specified cache directory for search, refs #13625
• src/hg/hgLinkIn/handlerList.c
  • lines changed 214, context: html, text, full: html, text
    7de3069f4395af52d10e69722052094ff42268ce Fri Jun 16 20:05:58 2017 -0700
    Initial commit of hgLinkIn tool to translate external identifiers to genome positions, refs #16668
• src/hg/hgLinkIn/handlerList.h
  • lines changed 26, context: html, text, full: html, text
    7de3069f4395af52d10e69722052094ff42268ce Fri Jun 16 20:05:58 2017 -0700
    Initial commit of hgLinkIn tool to translate external identifiers to genome positions, refs #16668
• src/hg/hgLinkIn/hgLinkIn.c
  • lines changed 133, context: html, text, full: html, text
    7de3069f4395af52d10e69722052094ff42268ce Fri Jun 16 20:05:58 2017 -0700
    Initial commit of hgLinkIn tool to translate external identifiers to genome positions, refs #16668
• src/hg/hgLinkIn/linkInHandlers.c
  • lines changed 104, context: html, text, full: html, text
    7de3069f4395af52d10e69722052094ff42268ce Fri Jun 16 20:05:58 2017 -0700
    Initial commit of hgLinkIn tool to translate external identifiers to genome positions, refs #16668
• src/hg/hgLinkIn/linkInHandlers.h
  • lines changed 50, context: html, text, full: html, text
    7de3069f4395af52d10e69722052094ff42268ce Fri Jun 16 20:05:58 2017 -0700
    Initial commit of hgLinkIn tool to translate external identifiers to genome positions, refs #16668
• src/hg/hgLinkIn/makefile
  • lines changed 18, context: html, text, full: html, text
    7de3069f4395af52d10e69722052094ff42268ce Fri Jun 16 20:05:58 2017 -0700
    Initial commit of hgLinkIn tool to translate external identifiers to genome positions, refs #16668
• src/hg/hgLogin/hgLogin.c
  • lines changed 11, context: html, text, full: html, text
    731f609d40cd0b0d4a7bcd27ed79d3a04ff3c22a Thu Jun 15 10:04:23 2017 -0700
    making hgLogin create links as it was before my recent changes, so return to the status at commit 263daca0593f4d67610f2466cdcdb262f27d6a67. This code is only relevant when no returnto argument is specified (which shouldn't happen as long as people click around on our website). the relativeLink hg.conf option is only used on the CIRM server. refs #19630
  • lines changed 10, context: html, text, full: html, text
    090d4afcaf0482dfa3f5eaec25d915f1d4a9fa9e Thu Jun 15 13:34:32 2017 -0700
    Cleanup of hgSession to make the distinction between the login server and local server clearer in the code. Renaming and moving two functions from wikiLink to hdb, as at least one is not necessarily wikiLink-related and it's good to keep them together. Also adding a warning to hgSession.c (probably useless). refs #19632 and also see related tickets there.
  • lines changed 7, context: html, text, full: html, text
    8ae0ae3613df46ae3fffc6618e7e276ac679633c Thu Jun 15 13:45:35 2017 -0700
    some more cleanup of old code that I wrote, refs #19632
• src/hg/hgSession/hgSession.c
  • lines changed 20, context: html, text, full: html, text
    090d4afcaf0482dfa3f5eaec25d915f1d4a9fa9e Thu Jun 15 13:34:32 2017 -0700
    Cleanup of hgSession to make the distinction between the login server and local server clearer in the code. Renaming and moving two functions from wikiLink to hdb, as at least one is not necessarily wikiLink-related and it's good to keep them together. Also adding a warning to hgSession.c (probably useless). refs #19632 and also see related tickets there.
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 13, context: html, text, full: html, text
    c0deef868e9c63dcff1d23fba1d766f4cd8d3a8c Fri Jun 16 12:15:48 2017 -0700
    Adding references to barChart format page to other supplementary pages, refs #18736
  • lines changed 1, context: html, text, full: html, text
    516cd7f778553c7755b4c431c9b29d3d5d3ab1ef Fri Jun 16 12:24:15 2017 -0700
    Fixing broken link to gtex track
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 30, context: html, text, full: html, text
    ccdd079dd893919f4ff1758b848cb2f399fdd795 Mon Jun 12 14:11:26 2017 -0700
    Added a few missing links to TOC. Implemented center-alignment for first column in chromosome table (human genome).
• src/hg/htdocs/goldenPath/help/barChart.html
  • lines changed 1, context: html, text, full: html, text
    516cd7f778553c7755b4c431c9b29d3d5d3ab1ef Fri Jun 16 12:24:15 2017 -0700
    Fixing broken link to gtex track
• src/hg/htdocs/goldenPath/help/customTrackText.html
  • lines changed 2, context: html, text, full: html, text
    c0deef868e9c63dcff1d23fba1d766f4cd8d3a8c Fri Jun 16 12:15:48 2017 -0700
    Adding references to barChart format page to other supplementary pages, refs #18736
• src/hg/htdocs/goldenPath/help/hgGeneGraph.html
  • lines changed 37, context: html, text, full: html, text
    0cd6e7822a2a71cfa08a0d8ccc2f2298cd24e5e4 Tue Jun 13 13:49:23 2017 -0700
    Adding images to hgGeneGraph help doc, refs #13634
  • lines changed 13, context: html, text, full: html, text
    061aec2ab24cfb1d301b18f2c335d2d84ab92593 Tue Jun 13 14:38:50 2017 -0700
    minor changes to hgGeneGraph help doc to add image suggested by Brian Lee, refs #13634
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 24, context: html, text, full: html, text
    c0deef868e9c63dcff1d23fba1d766f4cd8d3a8c Fri Jun 16 12:15:48 2017 -0700
    Adding references to barChart format page to other supplementary pages, refs #18736
• src/hg/htdocs/goldenPath/help/mirror.html
  • lines changed 1, context: html, text, full: html, text
    d01977fdb90eeab36e47bd3346314723439b596b Mon Jun 12 13:27:49 2017 -0700
    fixing typo, refs #19602
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 1, context: html, text, full: html, text
    c4f23ba1cacb0c97d84be35dccc3bdcd4f24e575 Tue Jun 13 09:00:07 2017 -0700
    Link update in trackDbLibrary to new barChart.html refs #18736
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 29, context: html, text, full: html, text
    1691656503311eb8097d2bb33c6e782936aac7b8 Mon Jun 12 16:00:56 2017 -0700
    Staging barChart announcement for after cgi release, refs #18736
  • lines changed 8, context: html, text, full: html, text
    b8d6f1eb52b647675484c3f68677a0bb1b95c588 Tue Jun 13 07:38:14 2017 -0700
    Changing up barChart announcement as per #18736
  • lines changed 7, context: html, text, full: html, text
    29f94079c5ffdf979f36096d5e5001e829d75f93 Tue Jun 13 08:22:43 2017 -0700
    More edits to barChart announcement as per #18736
  • lines changed 2, context: html, text, full: html, text
    1d52142a0e896f24cf9a2e97ed7f4194f08162ef Tue Jun 13 14:31:32 2017 -0700
    uncommenting staged barChart announcement, refs #18736
  • lines changed 4, context: html, text, full: html, text
    b4bd5dc94a961f46b925c6d70d7d9c7100a8cb79 Fri Jun 16 10:20:04 2017 -0700
    edited newsarch.html per refs #19600
• src/hg/htdocs/images/hgGeneGraph.png
  • lines changed 0, context: html, text, full: html, text
    983dcbab4c71041966510648bf53e1d8f0b013c9 Tue Jun 13 14:08:40 2017 -0700
    Adding images for hgGeneGraph help doc, refs #13634
• src/hg/htdocs/images/hgGeneGraphAnnotateDemo.png
  • lines changed 0, context: html, text, full: html, text
    983dcbab4c71041966510648bf53e1d8f0b013c9 Tue Jun 13 14:08:40 2017 -0700
    Adding images for hgGeneGraph help doc, refs #13634
• src/hg/htdocs/images/hgGeneGraphExtraInteractionsTable.png
  • lines changed 0, context: html, text, full: html, text
    983dcbab4c71041966510648bf53e1d8f0b013c9 Tue Jun 13 14:08:40 2017 -0700
    Adding images for hgGeneGraph help doc, refs #13634
• src/hg/htdocs/images/hgGeneGraphItemHover.png
  • lines changed 0, context: html, text, full: html, text
    983dcbab4c71041966510648bf53e1d8f0b013c9 Tue Jun 13 14:08:40 2017 -0700
    Adding images for hgGeneGraph help doc, refs #13634
• src/hg/htdocs/images/hgGeneGraphLineClickDemo.png
  • lines changed 0, context: html, text, full: html, text
    061aec2ab24cfb1d301b18f2c335d2d84ab92593 Tue Jun 13 14:38:50 2017 -0700
    minor changes to hgGeneGraph help doc to add image suggested by Brian Lee, refs #13634
• src/hg/htdocs/images/hgGeneGraphLineDemo.png
  • lines changed 0, context: html, text, full: html, text
    983dcbab4c71041966510648bf53e1d8f0b013c9 Tue Jun 13 14:08:40 2017 -0700
    Adding images for hgGeneGraph help doc, refs #13634
• src/hg/htdocs/images/hgGeneGraphLineHover.png
  • lines changed 0, context: html, text, full: html, text
    983dcbab4c71041966510648bf53e1d8f0b013c9 Tue Jun 13 14:08:40 2017 -0700
    Adding images for hgGeneGraph help doc, refs #13634
• src/hg/htdocs/indexNews.html
  • lines changed 6, context: html, text, full: html, text
    1d52142a0e896f24cf9a2e97ed7f4194f08162ef Tue Jun 13 14:31:32 2017 -0700
    uncommenting staged barChart announcement, refs #18736
• src/hg/htdocs/staticStyle/gbStatic.css
  • lines changed 12, context: html, text, full: html, text
    9da311c11f27d17b96d0b5f444cb56b287e9ae2a Mon Jun 12 13:58:45 2017 -0700
    Tweak indent spacing and support horizontal alignment classes in table cells, as per DK request.
  • lines changed 2, context: html, text, full: html, text
    cfe0b1467f975d15ad3ce8997a1851f510da8897 Mon Jun 12 14:05:55 2017 -0700
    Cleanup
  • lines changed 4, context: html, text, full: html, text
    e7bca28a23ef45f023358cd6b2e905b16ced9173 Mon Jun 12 15:40:18 2017 -0700
    Adjust margins so paragrah and div have same indent when used with collapse.
  • lines changed 3, context: html, text, full: html, text
    aa67e4f5b66d08281c1e8ef18037a58ff224e461 Mon Jun 12 16:06:54 2017 -0700
    Re-fix inconsistent idents.
• src/hg/htdocs/style/hgHubConnect.css
  • lines changed 3, context: html, text, full: html, text
    79e2e0421ffa1203d75e66351a2046085129528e Thu Jun 15 15:16:16 2017 -0700
    hgHubConnect now displays search details and indexes description content, refs #13625
• src/hg/inc/hdb.h
  • lines changed 29, context: html, text, full: html, text
    090d4afcaf0482dfa3f5eaec25d915f1d4a9fa9e Thu Jun 15 13:34:32 2017 -0700
    Cleanup of hgSession to make the distinction between the login server and local server clearer in the code. Renaming and moving two functions from wikiLink to hdb, as at least one is not necessarily wikiLink-related and it's good to keep them together. Also adding a warning to hgSession.c (probably useless). refs #19632 and also see related tickets there.
• src/hg/inc/hubConnect.h
  • lines changed 4, context: html, text, full: html, text
    79e2e0421ffa1203d75e66351a2046085129528e Thu Jun 15 15:16:16 2017 -0700
    hgHubConnect now displays search details and indexes description content, refs #13625
• src/hg/inc/hubSearchText.h
  • lines changed 79, context: html, text, full: html, text
    79e2e0421ffa1203d75e66351a2046085129528e Thu Jun 15 15:16:16 2017 -0700
    hgHubConnect now displays search details and indexes description content, refs #13625
• src/hg/inc/trackHub.h
  • lines changed 3, context: html, text, full: html, text
    79e2e0421ffa1203d75e66351a2046085129528e Thu Jun 15 15:16:16 2017 -0700
    hgHubConnect now displays search details and indexes description content, refs #13625
• src/hg/inc/wikiLink.h
  • lines changed 1, context: html, text, full: html, text
    090d4afcaf0482dfa3f5eaec25d915f1d4a9fa9e Thu Jun 15 13:34:32 2017 -0700
    Cleanup of hgSession to make the distinction between the login server and local server clearer in the code. Renaming and moving two functions from wikiLink to hdb, as at least one is not necessarily wikiLink-related and it's good to keep them together. Also adding a warning to hgSession.c (probably useless). refs #19632 and also see related tickets there.
• src/hg/js/hgHubConnect.js
  • lines changed 8, context: html, text, full: html, text
    79e2e0421ffa1203d75e66351a2046085129528e Thu Jun 15 15:16:16 2017 -0700
    hgHubConnect now displays search details and indexes description content, refs #13625
• src/hg/lib/hdb.c
  • lines changed 47, context: html, text, full: html, text
    090d4afcaf0482dfa3f5eaec25d915f1d4a9fa9e Thu Jun 15 13:34:32 2017 -0700
    Cleanup of hgSession to make the distinction between the login server and local server clearer in the code. Renaming and moving two functions from wikiLink to hdb, as at least one is not necessarily wikiLink-related and it's good to keep them together. Also adding a warning to hgSession.c (probably useless). refs #19632 and also see related tickets there.
• src/hg/lib/hubSearchText.as
  • lines changed 10, context: html, text, full: html, text
    79e2e0421ffa1203d75e66351a2046085129528e Thu Jun 15 15:16:16 2017 -0700
    hgHubConnect now displays search details and indexes description content, refs #13625
• src/hg/lib/hubSearchText.c
  • lines changed 236, context: html, text, full: html, text
    79e2e0421ffa1203d75e66351a2046085129528e Thu Jun 15 15:16:16 2017 -0700
    hgHubConnect now displays search details and indexes description content, refs #13625
• src/hg/lib/hubSearchText.sql
  • lines changed 17, context: html, text, full: html, text
    79e2e0421ffa1203d75e66351a2046085129528e Thu Jun 15 15:16:16 2017 -0700
    hgHubConnect now displays search details and indexes description content, refs #13625
• src/hg/lib/hui.c
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    349dc938fdeb4ed133dc6bc6710e9c9505c22170 Wed Jun 14 14:56:25 2017 -0700
    take out "add" and "subtract" as options for overlay mode in custom composites
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    79e2e0421ffa1203d75e66351a2046085129528e Thu Jun 15 15:16:16 2017 -0700
    hgHubConnect now displays search details and indexes description content, refs #13625
• src/hg/lib/trackHub.c
  • lines changed 3, context: html, text, full: html, text
    79e2e0421ffa1203d75e66351a2046085129528e Thu Jun 15 15:16:16 2017 -0700
    hgHubConnect now displays search details and indexes description content, refs #13625
• src/hg/lib/wikiLink.c
  • lines changed 1, context: html, text, full: html, text
    69b7826e8b8ac5071b038120ab340c8d8e625987 Wed Jun 14 11:49:03 2017 -0700
    fixing hgSession session links on genome-euro not going to genome euro, refs #19623
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    090d4afcaf0482dfa3f5eaec25d915f1d4a9fa9e Thu Jun 15 13:34:32 2017 -0700
    Cleanup of hgSession to make the distinction between the login server and local server clearer in the code. Renaming and moving two functions from wikiLink to hdb, as at least one is not necessarily wikiLink-related and it's good to keep them together. Also adding a warning to hgSession.c (probably useless). refs #19632 and also see related tickets there.
• src/hg/makeDb/doc/danRer11/initialBuild.txt
  • lines changed 107, context: html, text, full: html, text
    d7e8c0fea645b8ce3b444eb5213003b666e092c8 Mon Jun 12 12:13:54 2017 -0700
    Working through the danRer11 build, refs #19459
  • lines changed 21, context: html, text, full: html, text
    1347ee43dce04a7400e9a235a056de32b6e79a34 Wed Jun 14 11:08:30 2017 -0700
    Working through initial build, refs #19459
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    6441808caaf8c3c66246b88be0b83fa4e31eebcd Thu Jun 15 09:38:42 2017 -0700
    Lastz documentation for danRer11, refs #19459
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    6fd655fc113267c360d55919e7d1abcb21b49c1f Fri Jun 16 13:03:06 2017 -0700
    Blat servers, refs #19459
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    a5b32408c12c2c46a7c22aa3df740e4bf8ea5a6d Tue Jun 13 13:58:19 2017 -0700
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    a5b32408c12c2c46a7c22aa3df740e4bf8ea5a6d Tue Jun 13 13:58:19 2017 -0700
    hbv1 browser build and 185 way alignment refs #19533
• src/hg/makeDb/doc/hg38/hg38.txt
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    6441808caaf8c3c66246b88be0b83fa4e31eebcd Thu Jun 15 09:38:42 2017 -0700
    Lastz documentation for danRer11, refs #19459
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    7c683e8fc23cca0fe7817b4615dfdd59ad8cbefd Wed Jun 14 12:17:54 2017 -0700
    Adding the lastz from mm10 to danRer11, refs #19459
• src/hg/makeDb/doc/mouseStrains/GCA_001624185.1_129S1_SvImJ_v1/html/GCA_001624185.1_129S1_SvImJ_v1.augustus.html
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    5cc38ed906decd4ec230b17e834112ead03e63ea Mon Jun 12 14:58:03 2017 -0700
    Fixing broken links on the Augustus gene page, refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624185.1_129S1_SvImJ_v1/html/GCA_001624185.1_129S1_SvImJ_v1.ensGene.html
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    dd71ccba720aa2509bcce4e4ad0746f071278aec Wed Jun 14 10:12:31 2017 -0700
    Updating the Ensembl track description page with the correct information from Ian, refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624215.1_A_J_v1/html/GCA_001624215.1_A_J_v1.augustus.html
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    5cc38ed906decd4ec230b17e834112ead03e63ea Mon Jun 12 14:58:03 2017 -0700
    Fixing broken links on the Augustus gene page, refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624215.1_A_J_v1/html/GCA_001624215.1_A_J_v1.ensGene.html
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    dd71ccba720aa2509bcce4e4ad0746f071278aec Wed Jun 14 10:12:31 2017 -0700
    Updating the Ensembl track description page with the correct information from Ian, refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624295.1_AKR_J_v1/html/GCA_001624295.1_AKR_J_v1.augustus.html
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    5cc38ed906decd4ec230b17e834112ead03e63ea Mon Jun 12 14:58:03 2017 -0700
    Fixing broken links on the Augustus gene page, refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624295.1_AKR_J_v1/html/GCA_001624295.1_AKR_J_v1.ensGene.html
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    dd71ccba720aa2509bcce4e4ad0746f071278aec Wed Jun 14 10:12:31 2017 -0700
    Updating the Ensembl track description page with the correct information from Ian, refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624445.1_CAST_EiJ_v1/html/GCA_001624445.1_CAST_EiJ_v1.augustus.html
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    5cc38ed906decd4ec230b17e834112ead03e63ea Mon Jun 12 14:58:03 2017 -0700
    Fixing broken links on the Augustus gene page, refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624445.1_CAST_EiJ_v1/html/GCA_001624445.1_CAST_EiJ_v1.ensGene.html
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    dd71ccba720aa2509bcce4e4ad0746f071278aec Wed Jun 14 10:12:31 2017 -0700
    Updating the Ensembl track description page with the correct information from Ian, refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624475.1_CBA_J_v1/html/GCA_001624475.1_CBA_J_v1.augustus.html
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    5cc38ed906decd4ec230b17e834112ead03e63ea Mon Jun 12 14:58:03 2017 -0700
    Fixing broken links on the Augustus gene page, refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624475.1_CBA_J_v1/html/GCA_001624475.1_CBA_J_v1.ensGene.html
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    dd71ccba720aa2509bcce4e4ad0746f071278aec Wed Jun 14 10:12:31 2017 -0700
    Updating the Ensembl track description page with the correct information from Ian, refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624505.1_DBA_2J_v1/html/GCA_001624505.1_DBA_2J_v1.augustus.html
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    5cc38ed906decd4ec230b17e834112ead03e63ea Mon Jun 12 14:58:03 2017 -0700
    Fixing broken links on the Augustus gene page, refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624505.1_DBA_2J_v1/html/GCA_001624505.1_DBA_2J_v1.ensGene.html
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    dd71ccba720aa2509bcce4e4ad0746f071278aec Wed Jun 14 10:12:31 2017 -0700
    Updating the Ensembl track description page with the correct information from Ian, refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624535.1_FVB_NJ_v1/html/GCA_001624535.1_FVB_NJ_v1.augustus.html
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    5cc38ed906decd4ec230b17e834112ead03e63ea Mon Jun 12 14:58:03 2017 -0700
    Fixing broken links on the Augustus gene page, refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624535.1_FVB_NJ_v1/html/GCA_001624535.1_FVB_NJ_v1.ensGene.html
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    dd71ccba720aa2509bcce4e4ad0746f071278aec Wed Jun 14 10:12:31 2017 -0700
    Updating the Ensembl track description page with the correct information from Ian, refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624675.1_NOD_ShiLtJ_v1/html/GCA_001624675.1_NOD_ShiLtJ_v1.augustus.html
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    5cc38ed906decd4ec230b17e834112ead03e63ea Mon Jun 12 14:58:03 2017 -0700
    Fixing broken links on the Augustus gene page, refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624675.1_NOD_ShiLtJ_v1/html/GCA_001624675.1_NOD_ShiLtJ_v1.ensGene.html
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    dd71ccba720aa2509bcce4e4ad0746f071278aec Wed Jun 14 10:12:31 2017 -0700
    Updating the Ensembl track description page with the correct information from Ian, refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624745.1_NZO_HlLtJ_v1/html/GCA_001624745.1_NZO_HlLtJ_v1.augustus.html
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    5cc38ed906decd4ec230b17e834112ead03e63ea Mon Jun 12 14:58:03 2017 -0700
    Fixing broken links on the Augustus gene page, refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624745.1_NZO_HlLtJ_v1/html/GCA_001624745.1_NZO_HlLtJ_v1.ensGene.html
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    dd71ccba720aa2509bcce4e4ad0746f071278aec Wed Jun 14 10:12:31 2017 -0700
    Updating the Ensembl track description page with the correct information from Ian, refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624775.1_PWK_PhJ_v1/html/GCA_001624775.1_PWK_PhJ_v1.augustus.html
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    5cc38ed906decd4ec230b17e834112ead03e63ea Mon Jun 12 14:58:03 2017 -0700
    Fixing broken links on the Augustus gene page, refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624775.1_PWK_PhJ_v1/html/GCA_001624775.1_PWK_PhJ_v1.ensGene.html
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    dd71ccba720aa2509bcce4e4ad0746f071278aec Wed Jun 14 10:12:31 2017 -0700
    Updating the Ensembl track description page with the correct information from Ian, refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624835.1_WSB_EiJ_v1/html/GCA_001624835.1_WSB_EiJ_v1.augustus.html
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    5cc38ed906decd4ec230b17e834112ead03e63ea Mon Jun 12 14:58:03 2017 -0700
    Fixing broken links on the Augustus gene page, refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624835.1_WSB_EiJ_v1/html/GCA_001624835.1_WSB_EiJ_v1.ensGene.html
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    dd71ccba720aa2509bcce4e4ad0746f071278aec Wed Jun 14 10:12:31 2017 -0700
    Updating the Ensembl track description page with the correct information from Ian, refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624865.1_SPRET_EiJ_v1/GCA_001624865.1_SPRET_EiJ_v1.trackDb.txt
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    5e1064d67624b34a6e4081a31dc4b2d0a4c4d25a Wed Jun 14 15:58:51 2017 -0700
    adding augustus gene track refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001624865.1_SPRET_EiJ_v1/html/GCA_001624865.1_SPRET_EiJ_v1.ensGene.html
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    dd71ccba720aa2509bcce4e4ad0746f071278aec Wed Jun 14 10:12:31 2017 -0700
    Updating the Ensembl track description page with the correct information from Ian, refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001632525.1_BALB_cJ_v1/html/GCA_001632525.1_BALB_cJ_v1.augustus.html
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    5cc38ed906decd4ec230b17e834112ead03e63ea Mon Jun 12 14:58:03 2017 -0700
    Fixing broken links on the Augustus gene page, refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001632525.1_BALB_cJ_v1/html/GCA_001632525.1_BALB_cJ_v1.ensGene.html
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    dd71ccba720aa2509bcce4e4ad0746f071278aec Wed Jun 14 10:12:31 2017 -0700
    Updating the Ensembl track description page with the correct information from Ian, refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001632555.1_C57BL_6NJ_v1/html/GCA_001632555.1_C57BL_6NJ_v1.augustus.html
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    5cc38ed906decd4ec230b17e834112ead03e63ea Mon Jun 12 14:58:03 2017 -0700
    Fixing broken links on the Augustus gene page, refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001632555.1_C57BL_6NJ_v1/html/GCA_001632555.1_C57BL_6NJ_v1.ensGene.html
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    dd71ccba720aa2509bcce4e4ad0746f071278aec Wed Jun 14 10:12:31 2017 -0700
    Updating the Ensembl track description page with the correct information from Ian, refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001632575.1_C3H_HeJ_v1/html/GCA_001632575.1_C3H_HeJ_v1.augustus.html
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    5cc38ed906decd4ec230b17e834112ead03e63ea Mon Jun 12 14:58:03 2017 -0700
    Fixing broken links on the Augustus gene page, refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001632575.1_C3H_HeJ_v1/html/GCA_001632575.1_C3H_HeJ_v1.ensGene.html
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    dd71ccba720aa2509bcce4e4ad0746f071278aec Wed Jun 14 10:12:31 2017 -0700
    Updating the Ensembl track description page with the correct information from Ian, refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001632615.1_LP_J_v1/html/GCA_001632615.1_LP_J_v1.augustus.html
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    5cc38ed906decd4ec230b17e834112ead03e63ea Mon Jun 12 14:58:03 2017 -0700
    Fixing broken links on the Augustus gene page, refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_001632615.1_LP_J_v1/html/GCA_001632615.1_LP_J_v1.ensGene.html
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    dd71ccba720aa2509bcce4e4ad0746f071278aec Wed Jun 14 10:12:31 2017 -0700
    Updating the Ensembl track description page with the correct information from Ian, refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_900094665.1_CAROLI_EIJ_v1/html/GCA_900094665.1_CAROLI_EIJ_v1.augustus.html
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    5cc38ed906decd4ec230b17e834112ead03e63ea Mon Jun 12 14:58:03 2017 -0700
    Fixing broken links on the Augustus gene page, refs #13553
• src/hg/makeDb/doc/mouseStrains/GCA_900095145.1_PAHARI_EIJ_v1/html/GCA_900095145.1_PAHARI_EIJ_v1.augustus.html
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    5cc38ed906decd4ec230b17e834112ead03e63ea Mon Jun 12 14:58:03 2017 -0700
    Fixing broken links on the Augustus gene page, refs #13553
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    064f871acff9227152247a1f49ae730ec6ccd257 Wed Jun 14 11:07:18 2017 -0700
    Added danRer11 - zebrafish refs #19459
• src/hg/makeDb/genbank/etc/hgwdev.dbs
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    064f871acff9227152247a1f49ae730ec6ccd257 Wed Jun 14 11:07:18 2017 -0700
    Added danRer11 - zebrafish refs #19459
• src/hg/makeDb/trackDb/HPV/hpv1/trackDb.47way.ra
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    3fd0616178ef4a17d745d2671910aadf03fbeeeb Tue Jun 13 14:09:53 2017 -0700
    adding ncbiRefGene and 47-way alignment refs #18971
• src/hg/makeDb/trackDb/HPV/hpv1/trackDb.ra
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    3fd0616178ef4a17d745d2671910aadf03fbeeeb Tue Jun 13 14:09:53 2017 -0700
    adding ncbiRefGene and 47-way alignment refs #18971
• src/hg/makeDb/trackDb/human/clinvar.html
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    7a2e5569d47f4767d849a093fd2c6c589e242651 Fri Jun 16 10:59:48 2017 -0700
    adding link to exac clinvar converter to clinvar desc page
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    5e23b18b23d285d36a34807e7599b0d8e340d0db Tue Jun 13 14:51:14 2017 -0700
    Commenting out release tag line so that track can show up everywhere, refs #13634
• src/hg/makeDb/trackDb/makefile
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    1376f6e1aabfc7aadd3df6a4649a190c139c9090 Tue Jun 13 09:53:44 2017 -0700
    leave hbv1 off the list for six months refs #19533
• src/hg/makefile
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    Adding hgLinkIn to list of CGIs build by hg/makefile, refs #16668
• src/hg/utils/automation/asmHubAugustusGene.pl
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    b0abcc96a4fca8df235c1d0f4e1fa2bd69458180 Fri Jun 16 17:19:22 2017 -0700
    fixup URL reference to Stanke lab refs #13553
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    068849c63a0e4fd892cd8b524149db0b60bc949b Thu Jun 15 23:07:13 2017 -0700
    beginning script for crispr procedure refs #19514
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    d392aee67e5722e8e7b225ebe4f15f884dc69fda Fri Jun 16 09:23:15 2017 -0700
    now with guides step refs #19514
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    ee6770c1552c2088ef47c49814e1dc48615070cc Mon Jun 19 10:17:21 2017 -0700
    working on load step refs #19514
• src/hg/utils/hubCrawl/hubCrawl.c
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    79e2e0421ffa1203d75e66351a2046085129528e Thu Jun 15 15:16:16 2017 -0700
    hgHubConnect now displays search details and indexes description content, refs #13625
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    2808b4a94a11470034ec69a6c79ede4db24f5b89 Wed Jun 14 12:08:09 2017 -0700
    fixing LOVD otto, no redmine
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    2808b4a94a11470034ec69a6c79ede4db24f5b89 Wed Jun 14 12:08:09 2017 -0700
    fixing LOVD otto, no redmine
• src/hg/utils/trashLoad/trashLoad.c
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    8c869125963768a70bd3e5020131ee584759fc9f Tue Jun 13 14:02:14 2017 -0700
    add mysql table write stress test for trash Apocalypse test no redmine
• src/inc/tagStorm.h
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    9c9eab2cfea930f9a1a2e6ca74bac93345457ee1 Tue Jun 13 16:49:04 2017 -0700
    Moving the job of assigning uuids to this new program. It will avoid regenerating them if possible.
• src/lib/bamFile.c
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    c086f66e9a26b985f97f473166189ed70301fc10 Tue Jun 13 11:42:10 2017 -0700
    fix a bug where unaligned sequences were causing a crash
• src/lib/htmshell.c
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    79e2e0421ffa1203d75e66351a2046085129528e Thu Jun 15 15:16:16 2017 -0700
    hgHubConnect now displays search details and indexes description content, refs #13625
• src/lib/linefile.c
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    3250ccef57e0a9c28c586d67fc5facec46cb4449 Sun Jun 11 16:36:22 2017 -0700
    Making it so that lineFileUdcMayOpen will work with stdin in a pipe.
• src/lib/tagStorm.c
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    9c9eab2cfea930f9a1a2e6ca74bac93345457ee1 Tue Jun 13 16:49:04 2017 -0700
    Moving the job of assigning uuids to this new program. It will avoid regenerating them if possible.
• src/makefile
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    e777dc616c08872dfe6cd9fd10b69c5eb81abbd3 Wed Jun 14 09:55:38 2017 -0700
    Adding optLib to libs target so that 'make libs' is sufficient to build CGIs. This does not affect userApps because userApps does not depend on libs.
• src/optimalLeaf/SimMat.cc
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    3588a32896eff48854b2e16d813f5693a4fbf045 Tue Jun 13 15:35:58 2017 -0700
    remove unneeded error message from optimalLeaf library
• src/product/README.txt
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    1c2f24349222726c33589796dd71b915d02cffb7 Mon Jun 12 16:04:24 2017 -0700
    fixing typo again, stupid me
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    hgHubConnect needed to support an hg.conf-specified cache directory for search, refs #13625
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    a22997cd9aee71c8bd6a3791a43f1dba822f02c5 Mon Jun 12 11:13:03 2017 -0700
    adding a 64bit check to GBIC after discussion with ChrisL, thx, no redmine
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    d156dc9e9c0f2cf8971bfa4d8ab777d43f743e7a Mon Jun 12 10:03:01 2017 -0700
    Adding tabToHtml to build.
• src/tabFile/tabQuery/tabQuery.c
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    2462760a02e47839b89ec632d331f78b894deef2 Wed Jun 14 09:47:00 2017 -0700
    Respecting limit clause.
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    Respecting limit clause.
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    82f2f54a85ec37827f6dbf2a1b4a863db5260288 Sun Jun 11 23:52:46 2017 -0700
    A quick table maker.
• src/tabFile/tabToHtml/tabToHtml.c
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    82f2f54a85ec37827f6dbf2a1b4a863db5260288 Sun Jun 11 23:52:46 2017 -0700
    A quick table maker.
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    076d54726c175d8fab099e10b8e83e3e89ef4eea Mon Jun 12 10:02:30 2017 -0700
    Adding title option
• src/tabFile/tabToHtml/test.in
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    82f2f54a85ec37827f6dbf2a1b4a863db5260288 Sun Jun 11 23:52:46 2017 -0700
    A quick table maker.
• src/tagStorm/tagStormQuery/tagStormQuery.c
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    7fc011d226f55f9ad88f3b455b5b9a26aeb67567 Wed Jun 14 09:42:49 2017 -0700
    Respecting limit clause.
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    Respecting limit clause.
• src/userApps/Makefile
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    3eb96eff8e5eac717baa74c70a42a7a8cff239d0 Wed Jun 14 15:29:25 2017 -0700
    do not need the make libs step and it does not work with optimumLib no redmine
• src/utils/bedToBigBed/bedToBigBed.c
  • lines changed 2, context: html, text, full: html, text
    8536a8841be90d46c8f6116307d5b56e4da86d42 Fri Jun 16 09:19:51 2017 -0700
    add an error message to bedToBigBed to catch submission of an illegal AS file
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    2417b6a5a369e4b6474e519caa56be79363c5445 Mon Jun 19 10:18:41 2017 -0700
    v351 preview2 refs #19641

• lines changed: 5782
• files changed: 159