All File Changes

v367_base to v368_preview (2018-06-18 to 2018-06-25) v368

• src/hg/cirm/cdw/cdwMakeFileTags/cdwMakeFileTags.c
  • lines changed 12, context: html, text, full: html, text
    7d97e6dbbff81471ca8f8d49f1acd18798f6d302 Wed Jun 20 12:11:03 2018 -0700
    Adding new facet biosample_cell_type, and changing facet order as requested by Jim. Also adding hg.conf settings so that developers and testers can play with the facet order without recompiling.
  • lines changed 32, context: html, text, full: html, text
    6f31e05d176b35c1814734e253c3df5cee569a12 Wed Jun 20 15:36:22 2018 -0700
    drop with warning any facet fields requested which are not available in the file tags table.
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 92, context: html, text, full: html, text
    7d97e6dbbff81471ca8f8d49f1acd18798f6d302 Wed Jun 20 12:11:03 2018 -0700
    Adding new facet biosample_cell_type, and changing facet order as requested by Jim. Also adding hg.conf settings so that developers and testers can play with the facet order without recompiling.
  • lines changed 2, context: html, text, full: html, text
    b4b0d97c779bafaee1a934ea95a7580725e67bc4 Fri Jun 22 10:41:08 2018 -0700
    Fixes problem with oneTag
  • lines changed 50, context: html, text, full: html, text
    eb2d2d726825942e7438acabf7db1c6d0e071382 Fri Jun 22 17:54:32 2018 -0700
    Attempt to allow net.c code to process cdwGetFiles url by passing through the basic auth from the browser. However, even with this change, because cdwGetFiles does not support byte ranges, bigDataUrl customTracks in cirm that use cdwGetFiles will not work.
  • lines changed 50, context: html, text, full: html, text
    ed5e5f64aa184852647d79e66d73c285ff007d47 Mon Jun 25 02:51:36 2018 -0700
    Revert "Attempt to allow net.c code to process cdwGetFiles url by passing through the basic auth from the browser. However, even with this change, because cdwGetFiles does not support byte ranges, bigDataUrl customTracks in cirm that use cdwGetFiles will not work." This reverts commit eb2d2d726825942e7438acabf7db1c6d0e071382.
  • lines changed 3, context: html, text, full: html, text
    3e34aa4230c968e62f740c6242f3b522db5c6aa0 Mon Jun 25 03:12:22 2018 -0700
    CIRM: fixing genome browser links, refs #20679
• src/hg/hgLiftOver/hgLiftOver.c
  • lines changed 1, context: html, text, full: html, text
    5dd57ba4756985d35f8ca72756d963b77934fcf0 Thu Jun 7 16:08:53 2018 -0700
    Expand support for -multiple to BED 3 to 12 (instead of 4 to 6). refs #18853 Added a -noSerial option to prevent -multiple from forcing the score field to contain a serial number for BED without blocks. Also fixed a bug with the loop on chains overwriting args thickStart and thickEnd. Todo: genePred. Probably won't bother doing PSL because pslMap should be used for that. Also removed some very old #ifdef'd code.
• src/hg/hgTracks/hgTracks.c
  • lines changed 15, context: html, text, full: html, text
    082f118d6f5d17754c5fafd8d95f700c9397d99e Thu Jun 21 11:10:32 2018 -0700
    Update multi-region haplotype mode to work with _fix patch sequences in addition to _alt sequences. refs #18854
  • lines changed 1, context: html, text, full: html, text
    5dd57ba4756985d35f8ca72756d963b77934fcf0 Thu Jun 7 16:08:53 2018 -0700
    Expand support for -multiple to BED 3 to 12 (instead of 4 to 6). refs #18853 Added a -noSerial option to prevent -multiple from forcing the score field to contain a serial number for BED without blocks. Also fixed a bug with the loop on chains overwriting args thickStart and thickEnd. Todo: genePred. Probably won't bother doing PSL because pslMap should be used for that. Also removed some very old #ifdef'd code.
• src/hg/hgTracks/menu.c
  • lines changed 1, context: html, text, full: html, text
    5dd57ba4756985d35f8ca72756d963b77934fcf0 Thu Jun 7 16:08:53 2018 -0700
    Expand support for -multiple to BED 3 to 12 (instead of 4 to 6). refs #18853 Added a -noSerial option to prevent -multiple from forcing the score field to contain a serial number for BED without blocks. Also fixed a bug with the loop on chains overwriting args thickStart and thickEnd. Todo: genePred. Probably won't bother doing PSL because pslMap should be used for that. Also removed some very old #ifdef'd code.
• src/hg/hgTracks/simpleTracks.c
  • lines changed 1, context: html, text, full: html, text
    5dd57ba4756985d35f8ca72756d963b77934fcf0 Thu Jun 7 16:08:53 2018 -0700
    Expand support for -multiple to BED 3 to 12 (instead of 4 to 6). refs #18853 Added a -noSerial option to prevent -multiple from forcing the score field to contain a serial number for BED without blocks. Also fixed a bug with the loop on chains overwriting args thickStart and thickEnd. Todo: genePred. Probably won't bother doing PSL because pslMap should be used for that. Also removed some very old #ifdef'd code.
• src/hg/hgc/barChartClick.c
  • lines changed 39, context: html, text, full: html, text
    23ecc080ba35d0563c208e8ff96f9852475e34f6 Mon Jun 18 14:23:06 2018 -0700
    Adding url, urls, urlLabel and extraFields support to bigBarChart tracks
  • lines changed 2, context: html, text, full: html, text
    32216bfbd7b8ea04805cb96ec1ba4b3310b64aaf Tue Jun 19 07:17:25 2018 -0700
    Forget to initialize some variables that are used later, thanks Jonathan
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    23ecc080ba35d0563c208e8ff96f9852475e34f6 Mon Jun 18 14:23:06 2018 -0700
    Adding url, urls, urlLabel and extraFields support to bigBarChart tracks
• src/hg/hgc/hgc.h
  • lines changed 10, context: html, text, full: html, text
    23ecc080ba35d0563c208e8ff96f9852475e34f6 Mon Jun 18 14:23:06 2018 -0700
    Adding url, urls, urlLabel and extraFields support to bigBarChart tracks
• src/hg/hgc/hgcData/barChartBoxplot.R
  • lines changed 110, context: html, text, full: html, text
    77b271a7f4756ce33099089d347ea5134739c70f Mon Jun 18 15:03:59 2018 -0700
    Moving barplot and boxplot drawing code into separate functions after code review, refs #21626
• src/hg/hgc/peakClusters.c
  • lines changed 2, context: html, text, full: html, text
    2fd1f4e705f129be8654845b0ca452862706cd06 Fri Jun 15 17:13:32 2018 -0700
    corner case: hFreeConn was not called when a peakClusters input track table doesn't exist, leading to 'too many connections' error when none of the input tables exist
• src/hg/hgc/vcfClick.c
  • lines changed 1, context: html, text, full: html, text
    4d43519727301846829ed0fd8fc2f4060158ee70 Mon Jun 18 16:10:39 2018 -0700
    Re-adding links out to gnomAD, refs #18951
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 7, context: html, text, full: html, text
    c03fdf49e6d431bd8e0c8bf478df67b245620eef Fri Jun 22 15:34:53 2018 -0700
    add information about meta, metaDb, and metaTab tags to track hub documentation
• src/hg/htdocs/goldenPath/help/interact.html
  • lines changed 42, context: html, text, full: html, text
    1f91e2adaff458a9f370e2026cd60103e18a8601 Tue Jun 19 13:00:12 2018 -0700
    Improve examples. refs #21615
  • lines changed 32, context: html, text, full: html, text
    68c7bb84fb29f3a2f080d0105a4b927de88292a3 Thu Jun 21 15:17:50 2018 -0700
    Update examples. refs #21615
• src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
  • lines changed 8, context: html, text, full: html, text
    23ecc080ba35d0563c208e8ff96f9852475e34f6 Mon Jun 18 14:23:06 2018 -0700
    Adding url, urls, urlLabel and extraFields support to bigBarChart tracks
• src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v2.html
  • lines changed 3, context: html, text, full: html, text
    23ecc080ba35d0563c208e8ff96f9852475e34f6 Mon Jun 18 14:23:06 2018 -0700
    Adding url, urls, urlLabel and extraFields support to bigBarChart tracks
  • lines changed 3, context: html, text, full: html, text
    c03fdf49e6d431bd8e0c8bf478df67b245620eef Fri Jun 22 15:34:53 2018 -0700
    add information about meta, metaDb, and metaTab tags to track hub documentation
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 1, context: html, text, full: html, text
    23ecc080ba35d0563c208e8ff96f9852475e34f6 Mon Jun 18 14:23:06 2018 -0700
    Adding url, urls, urlLabel and extraFields support to bigBarChart tracks
  • lines changed 6, context: html, text, full: html, text
    c03fdf49e6d431bd8e0c8bf478df67b245620eef Fri Jun 22 15:34:53 2018 -0700
    add information about meta, metaDb, and metaTab tags to track hub documentation
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 22, context: html, text, full: html, text
    dfa0d27a55709e262434001788a9c116b3d47ee4 Mon Jun 25 10:22:52 2018 -0700
    Announcing gnomAD 2.0 tracks for hg19, refs #18951
• src/hg/htdocs/images/interactExample1.png
  • lines changed 0, context: html, text, full: html, text
    68c7bb84fb29f3a2f080d0105a4b927de88292a3 Thu Jun 21 15:17:50 2018 -0700
    Update examples. refs #21615
• src/hg/htdocs/images/interactExample2.png
  • lines changed 0, context: html, text, full: html, text
    68c7bb84fb29f3a2f080d0105a4b927de88292a3 Thu Jun 21 15:17:50 2018 -0700
    Update examples. refs #21615
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    dfa0d27a55709e262434001788a9c116b3d47ee4 Mon Jun 25 10:22:52 2018 -0700
    Announcing gnomAD 2.0 tracks for hg19, refs #18951
• src/hg/htdocs/training/index.html
  • lines changed 28, context: html, text, full: html, text
    b722f2853b71e0e8caadb89863510dcc0a880eb3 Thu Jun 21 09:32:34 2018 -0700
    dropping Italy workshops, adding Davis, Malaysia, link for KC later
• src/hg/inc/liftOver.h
  • lines changed 4, context: html, text, full: html, text
    5dd57ba4756985d35f8ca72756d963b77934fcf0 Thu Jun 7 16:08:53 2018 -0700
    Expand support for -multiple to BED 3 to 12 (instead of 4 to 6). refs #18853 Added a -noSerial option to prevent -multiple from forcing the score field to contain a serial number for BED without blocks. Also fixed a bug with the loop on chains overwriting args thickStart and thickEnd. Todo: genePred. Probably won't bother doing PSL because pslMap should be used for that. Also removed some very old #ifdef'd code.
• src/hg/inc/wikiLink.h
  • lines changed 11, context: html, text, full: html, text
    eb2d2d726825942e7438acabf7db1c6d0e071382 Fri Jun 22 17:54:32 2018 -0700
    Attempt to allow net.c code to process cdwGetFiles url by passing through the basic auth from the browser. However, even with this change, because cdwGetFiles does not support byte ranges, bigDataUrl customTracks in cirm that use cdwGetFiles will not work.
  • lines changed 11, context: html, text, full: html, text
    ed5e5f64aa184852647d79e66d73c285ff007d47 Mon Jun 25 02:51:36 2018 -0700
    Revert "Attempt to allow net.c code to process cdwGetFiles url by passing through the basic auth from the browser. However, even with this change, because cdwGetFiles does not support byte ranges, bigDataUrl customTracks in cirm that use cdwGetFiles will not work." This reverts commit eb2d2d726825942e7438acabf7db1c6d0e071382.
• src/hg/lib/gtexGeneBed.c
  • lines changed 3, context: html, text, full: html, text
    51bd7d1443d629518ab0f9beed9b2c223a6342ae Mon Jun 18 14:19:44 2018 -0700
    gtexGeneBed.sql used PRIMARY KEY(geneId), which excluded nearly all mappings to chr*_alt. Change it to (chrom,geneId) to allow mapping to multiple sequences. refs #18853
• src/hg/lib/gtexGeneBed.sql
  • lines changed 2, context: html, text, full: html, text
    51bd7d1443d629518ab0f9beed9b2c223a6342ae Mon Jun 18 14:19:44 2018 -0700
    gtexGeneBed.sql used PRIMARY KEY(geneId), which excluded nearly all mappings to chr*_alt. Change it to (chrom,geneId) to allow mapping to multiple sequences. refs #18853
• src/hg/lib/liftOver.c
  • lines changed 306, context: html, text, full: html, text
    5dd57ba4756985d35f8ca72756d963b77934fcf0 Thu Jun 7 16:08:53 2018 -0700
    Expand support for -multiple to BED 3 to 12 (instead of 4 to 6). refs #18853 Added a -noSerial option to prevent -multiple from forcing the score field to contain a serial number for BED without blocks. Also fixed a bug with the loop on chains overwriting args thickStart and thickEnd. Todo: genePred. Probably won't bother doing PSL because pslMap should be used for that. Also removed some very old #ifdef'd code.
• src/hg/lib/web.c
  • lines changed 1, context: html, text, full: html, text
    c43ca83298c70d2cd0bd58e04328fc09b1ee4883 Tue Jun 19 11:00:50 2018 -0700
    Initialize track for Table Browser. refs #21633
• src/hg/lib/wikiLink.c
  • lines changed 15, context: html, text, full: html, text
    eb2d2d726825942e7438acabf7db1c6d0e071382 Fri Jun 22 17:54:32 2018 -0700
    Attempt to allow net.c code to process cdwGetFiles url by passing through the basic auth from the browser. However, even with this change, because cdwGetFiles does not support byte ranges, bigDataUrl customTracks in cirm that use cdwGetFiles will not work.
  • lines changed 6, context: html, text, full: html, text
    92caf6b44d2a66bf52d2e41961355a325d9d16fb Mon Jun 25 02:49:37 2018 -0700
    making http auth mandatory, after a link wait
  • lines changed 15, context: html, text, full: html, text
    ed5e5f64aa184852647d79e66d73c285ff007d47 Mon Jun 25 02:51:36 2018 -0700
    Revert "Attempt to allow net.c code to process cdwGetFiles url by passing through the basic auth from the browser. However, even with this change, because cdwGetFiles does not support byte ranges, bigDataUrl customTracks in cirm that use cdwGetFiles will not work." This reverts commit eb2d2d726825942e7438acabf7db1c6d0e071382.
• src/hg/liftOver/liftOver.c
  • lines changed 11, context: html, text, full: html, text
    5dd57ba4756985d35f8ca72756d963b77934fcf0 Thu Jun 7 16:08:53 2018 -0700
    Expand support for -multiple to BED 3 to 12 (instead of 4 to 6). refs #18853 Added a -noSerial option to prevent -multiple from forcing the score field to contain a serial number for BED without blocks. Also fixed a bug with the loop on chains overwriting args thickStart and thickEnd. Todo: genePred. Probably won't bother doing PSL because pslMap should be used for that. Also removed some very old #ifdef'd code.
• src/hg/makeDb/doc/grcHhh38/grcH38P11.lastzRuns.txt
  • lines changed 11191, context: html, text, full: html, text
    0bf6af3ae38aea8ce09f24d41a75e0cae189ad95 Mon Jun 25 08:51:37 2018 -0700
    Experimental work in preparation for adding patch sequences to an existing database: not-for-release databases grcHhh38 and grcH38P11. refs #18853 grcHhh38 initialBuild used hg38 sequences and added a few basic tracks, mostly copied from hg38. grcH38P11 is a patches-only build of GRCh38.p11, similar to Hiram's hg38Patch11, but with a couple extra steps to make it a full browsable database with the usual directory structure for building tracks such as chain/net. patchUpdate.11.txt is the process for adding patch sequences (from grcH38P11) to an existing database (grcHhh38) and adding annotations on patch sequences to existing annotation tracks.
• src/hg/makeDb/doc/grcHhh38/grcH38P11.txt
  • lines changed 475, context: html, text, full: html, text
    0bf6af3ae38aea8ce09f24d41a75e0cae189ad95 Mon Jun 25 08:51:37 2018 -0700
    Experimental work in preparation for adding patch sequences to an existing database: not-for-release databases grcHhh38 and grcH38P11. refs #18853 grcHhh38 initialBuild used hg38 sequences and added a few basic tracks, mostly copied from hg38. grcH38P11 is a patches-only build of GRCh38.p11, similar to Hiram's hg38Patch11, but with a couple extra steps to make it a full browsable database with the usual directory structure for building tracks such as chain/net. patchUpdate.11.txt is the process for adding patch sequences (from grcH38P11) to an existing database (grcHhh38) and adding annotations on patch sequences to existing annotation tracks.
• src/hg/makeDb/doc/grcHhh38/initialBuild.txt
  • lines changed 512, context: html, text, full: html, text
    0bf6af3ae38aea8ce09f24d41a75e0cae189ad95 Mon Jun 25 08:51:37 2018 -0700
    Experimental work in preparation for adding patch sequences to an existing database: not-for-release databases grcHhh38 and grcH38P11. refs #18853 grcHhh38 initialBuild used hg38 sequences and added a few basic tracks, mostly copied from hg38. grcH38P11 is a patches-only build of GRCh38.p11, similar to Hiram's hg38Patch11, but with a couple extra steps to make it a full browsable database with the usual directory structure for building tracks such as chain/net. patchUpdate.11.txt is the process for adding patch sequences (from grcH38P11) to an existing database (grcHhh38) and adding annotations on patch sequences to existing annotation tracks.
• src/hg/makeDb/doc/grcHhh38/patchUpdate.11.txt
  • lines changed 591, context: html, text, full: html, text
    0bf6af3ae38aea8ce09f24d41a75e0cae189ad95 Mon Jun 25 08:51:37 2018 -0700
    Experimental work in preparation for adding patch sequences to an existing database: not-for-release databases grcHhh38 and grcH38P11. refs #18853 grcHhh38 initialBuild used hg38 sequences and added a few basic tracks, mostly copied from hg38. grcH38P11 is a patches-only build of GRCh38.p11, similar to Hiram's hg38Patch11, but with a couple extra steps to make it a full browsable database with the usual directory structure for building tracks such as chain/net. patchUpdate.11.txt is the process for adding patch sequences (from grcH38P11) to an existing database (grcHhh38) and adding annotations on patch sequences to existing annotation tracks.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 14, context: html, text, full: html, text
    79b4b0c9b07ec4bad8687b6c0f63bbd6b1805655 Fri May 11 09:15:40 2018 -0700
    Ran same-species liftOver with chainBridge through net stage for comparison with existing hg19ToHg38.over.chain. refs #21651
• src/hg/makeDb/doc/hg38/miRnaAtlas.txt
  • lines changed 36, context: html, text, full: html, text
    ab0857e8086bf3955be436c8b33df2467f5effec Thu Jun 21 14:02:34 2018 -0700
    miRna tissue atlas QA ready, refs #18508
• src/hg/makeDb/trackDb/anopheles/anoGam3/description.html
  • lines changed 1, context: html, text, full: html, text
    dcf5654d2a9a8eab66935f1d7edd1b45807c2b26 Fri Jun 22 09:03:54 2018 -0700
    The assembly name is NOT an NCBI assembly name refs #20970
• src/hg/makeDb/trackDb/baboon/papAnu3/description.html
  • lines changed 1, context: html, text, full: html, text
    dcf5654d2a9a8eab66935f1d7edd1b45807c2b26 Fri Jun 22 09:03:54 2018 -0700
    The assembly name is NOT an NCBI assembly name refs #20970
• src/hg/makeDb/trackDb/baboon/papAnu4/description.html
  • lines changed 1, context: html, text, full: html, text
    dcf5654d2a9a8eab66935f1d7edd1b45807c2b26 Fri Jun 22 09:03:54 2018 -0700
    The assembly name is NOT an NCBI assembly name refs #20970
• src/hg/makeDb/trackDb/bacteria/staAur1/description.html
  • lines changed 1, context: html, text, full: html, text
    dcf5654d2a9a8eab66935f1d7edd1b45807c2b26 Fri Jun 22 09:03:54 2018 -0700
    The assembly name is NOT an NCBI assembly name refs #20970
• src/hg/makeDb/trackDb/birds/ficAlb1/description.html
  • lines changed 1, context: html, text, full: html, text
    dcf5654d2a9a8eab66935f1d7edd1b45807c2b26 Fri Jun 22 09:03:54 2018 -0700
    The assembly name is NOT an NCBI assembly name refs #20970
• src/hg/makeDb/trackDb/cat/felCat9/description.html
  • lines changed 1, context: html, text, full: html, text
    dcf5654d2a9a8eab66935f1d7edd1b45807c2b26 Fri Jun 22 09:03:54 2018 -0700
    The assembly name is NOT an NCBI assembly name refs #20970
• src/hg/makeDb/trackDb/chicken/galGal2/ecoresTetraodon.html
  • lines changed 3, context: html, text, full: html, text
    e550505e01095f14d081fc5fa5c18ac4b4f415fd Mon Jun 25 10:26:50 2018 -0700
    Updating redirected links for galGal2, uiLinks cronjob.
• src/hg/makeDb/trackDb/chicken/galGal2/isochore.html
  • lines changed 1, context: html, text, full: html, text
    e550505e01095f14d081fc5fa5c18ac4b4f415fd Mon Jun 25 10:26:50 2018 -0700
    Updating redirected links for galGal2, uiLinks cronjob.
• src/hg/makeDb/trackDb/chicken/galGal2/multiz7way.html
  • lines changed 7, context: html, text, full: html, text
    e550505e01095f14d081fc5fa5c18ac4b4f415fd Mon Jun 25 10:26:50 2018 -0700
    Updating redirected links for galGal2, uiLinks cronjob.
• src/hg/makeDb/trackDb/chicken/galGal2/phastConsElements7way.html
  • lines changed 5, context: html, text, full: html, text
    e550505e01095f14d081fc5fa5c18ac4b4f415fd Mon Jun 25 10:26:50 2018 -0700
    Updating redirected links for galGal2, uiLinks cronjob.
• src/hg/makeDb/trackDb/chicken/galGal2/rnaGene.html
  • lines changed 4, context: html, text, full: html, text
    e550505e01095f14d081fc5fa5c18ac4b4f415fd Mon Jun 25 10:26:50 2018 -0700
    Updating redirected links for galGal2, uiLinks cronjob.
• src/hg/makeDb/trackDb/chicken/galGal2/uniGene_gg.html
  • lines changed 1, context: html, text, full: html, text
    e550505e01095f14d081fc5fa5c18ac4b4f415fd Mon Jun 25 10:26:50 2018 -0700
    Updating redirected links for galGal2, uiLinks cronjob.
• src/hg/makeDb/trackDb/chimp/panTro6/description.html
  • lines changed 1, context: html, text, full: html, text
    dcf5654d2a9a8eab66935f1d7edd1b45807c2b26 Fri Jun 22 09:03:54 2018 -0700
    The assembly name is NOT an NCBI assembly name refs #20970
• src/hg/makeDb/trackDb/criGri/criGri1/crispr.html
  • lines changed 12, context: html, text, full: html, text
    56ca2c13aebd823ace9d6aa7b5aa3506a434a53c Wed Jun 20 09:08:24 2018 -0700
    Updating redirected links for criGri1, uiLinks cronjob.
• src/hg/makeDb/trackDb/criGri/criGriChoV2/description.html
  • lines changed 1, context: html, text, full: html, text
    dcf5654d2a9a8eab66935f1d7edd1b45807c2b26 Fri Jun 22 09:03:54 2018 -0700
    The assembly name is NOT an NCBI assembly name refs #20970
• src/hg/makeDb/trackDb/dog/canFam1/bacEndPairs.html
  • lines changed 1, context: html, text, full: html, text
    bc72ff69a124746b94dcc803c963210babc9cf97 Thu Jun 21 08:28:51 2018 -0700
    Updating redirected links for canFam1, uiLinks cronjob.
• src/hg/makeDb/trackDb/dog/canFam1/mzHg17Mm5_phast.html
  • lines changed 7, context: html, text, full: html, text
    bc72ff69a124746b94dcc803c963210babc9cf97 Thu Jun 21 08:28:51 2018 -0700
    Updating redirected links for canFam1, uiLinks cronjob.
• src/hg/makeDb/trackDb/dog/canFam1/snp125.html
  • lines changed 1, context: html, text, full: html, text
    bc72ff69a124746b94dcc803c963210babc9cf97 Thu Jun 21 08:28:51 2018 -0700
    Updating redirected links for canFam1, uiLinks cronjob.
• src/hg/makeDb/trackDb/dog/canFam1/twinscan.html
  • lines changed 1, context: html, text, full: html, text
    bc72ff69a124746b94dcc803c963210babc9cf97 Thu Jun 21 08:28:51 2018 -0700
    Updating redirected links for canFam1, uiLinks cronjob.
• src/hg/makeDb/trackDb/guineaPig/cavApe1/description.html
  • lines changed 1, context: html, text, full: html, text
    dcf5654d2a9a8eab66935f1d7edd1b45807c2b26 Fri Jun 22 09:03:54 2018 -0700
    The assembly name is NOT an NCBI assembly name refs #20970
• src/hg/makeDb/trackDb/horse/equCab3/description.html
  • lines changed 1, context: html, text, full: html, text
    903c811f4e4deebf950c145958c23b6fcd97aa4e Fri Jun 22 08:50:52 2018 -0700
    the assembly name is NOT an NCBI assembly name refs #20970
• src/hg/makeDb/trackDb/human/hg19/trackDb.gnomad.ra
  • lines changed 271, context: html, text, full: html, text
    061b274149a36812984562914f13603ee34b5c9c Tue Jun 19 11:59:29 2018 -0700
    Reorganizing the trackDb structure so that the release tags can be managed from one include statement rather than from the various stanzas, refs #18951
  • lines changed 1, context: html, text, full: html, text
    08c76607d36aa80707a4d0ff287da0ba34dccb06 Thu Jun 21 09:00:23 2018 -0700
    Adding the pennantIcon for the new gnomAD 2.0 tracks for hg19, refs #18951
  • lines changed 1, context: html, text, full: html, text
    e900603c6af71da8a68f7b5ae4e7ed8d7bda1090 Thu Jun 21 10:06:42 2018 -0700
    Forgot to add the New pennantIcon for the gnomAD Coverage supertrack, refs #18951
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 301, context: html, text, full: html, text
    061b274149a36812984562914f13603ee34b5c9c Tue Jun 19 11:59:29 2018 -0700
    Reorganizing the trackDb structure so that the release tags can be managed from one include statement rather than from the various stanzas, refs #18951
  • lines changed 1, context: html, text, full: html, text
    07ed8a6c9f81e4ccba2f56b7a77a0516c92fff7d Tue Jun 19 13:22:21 2018 -0700
    Adding beta release tag for the gnomAD 2.0 tracks for hg19, refs #18951
  • lines changed 1, context: html, text, full: html, text
    0359e152bb765f4da6b222fcb2c7d30e68a8a85e Wed Jun 20 12:23:16 2018 -0700
    Removing alpha and beta release tags for release, refs #18951
• src/hg/makeDb/trackDb/human/hg38/miRnaAtlas.html
  • lines changed 95, context: html, text, full: html, text
    ab0857e8086bf3955be436c8b33df2467f5effec Thu Jun 21 14:02:34 2018 -0700
    miRna tissue atlas QA ready, refs #18508
  • lines changed 3, context: html, text, full: html, text
    79f6490a63155bcb0eb9f0c3094b9fcba7f9d41f Thu Jun 21 14:26:25 2018 -0700
    Woops forgot to mention that miRna atlas coordinates come from mirbase v21 and forgot to link to mirbase, refs #18508
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 22, context: html, text, full: html, text
    ab0857e8086bf3955be436c8b33df2467f5effec Thu Jun 21 14:02:34 2018 -0700
    miRna tissue atlas QA ready, refs #18508
  • lines changed 4, context: html, text, full: html, text
    79f6490a63155bcb0eb9f0c3094b9fcba7f9d41f Thu Jun 21 14:26:25 2018 -0700
    Woops forgot to mention that miRna atlas coordinates come from mirbase v21 and forgot to link to mirbase, refs #18508
• src/hg/makeDb/trackDb/kangarooRat/dipOrd2/description.html
  • lines changed 1, context: html, text, full: html, text
    dcf5654d2a9a8eab66935f1d7edd1b45807c2b26 Fri Jun 22 09:03:54 2018 -0700
    The assembly name is NOT an NCBI assembly name refs #20970
• src/hg/makeDb/trackDb/macaca/macNem1/description.html
  • lines changed 1, context: html, text, full: html, text
    dcf5654d2a9a8eab66935f1d7edd1b45807c2b26 Fri Jun 22 09:03:54 2018 -0700
    The assembly name is NOT an NCBI assembly name refs #20970
• src/hg/makeDb/trackDb/mammal/casCan1/description.html
  • lines changed 1, context: html, text, full: html, text
    dcf5654d2a9a8eab66935f1d7edd1b45807c2b26 Fri Jun 22 09:03:54 2018 -0700
    The assembly name is NOT an NCBI assembly name refs #20970
• src/hg/makeDb/trackDb/mammal/fukDam1/description.html
  • lines changed 1, context: html, text, full: html, text
    dcf5654d2a9a8eab66935f1d7edd1b45807c2b26 Fri Jun 22 09:03:54 2018 -0700
    The assembly name is NOT an NCBI assembly name refs #20970
• src/hg/makeDb/trackDb/micOch/micOch1/description.html
  • lines changed 1, context: html, text, full: html, text
    dcf5654d2a9a8eab66935f1d7edd1b45807c2b26 Fri Jun 22 09:03:54 2018 -0700
    The assembly name is NOT an NCBI assembly name refs #20970
• src/hg/makeDb/trackDb/mouseLemur/micMur3/description.html
  • lines changed 1, context: html, text, full: html, text
    dcf5654d2a9a8eab66935f1d7edd1b45807c2b26 Fri Jun 22 09:03:54 2018 -0700
    The assembly name is NOT an NCBI assembly name refs #20970
• src/hg/makeDb/trackDb/oldWorldMonkeys/colAng1/description.html
  • lines changed 1, context: html, text, full: html, text
    dcf5654d2a9a8eab66935f1d7edd1b45807c2b26 Fri Jun 22 09:03:54 2018 -0700
    The assembly name is NOT an NCBI assembly name refs #20970
• src/hg/makeDb/trackDb/orangutan/ponAbe3/description.html
  • lines changed 1, context: html, text, full: html, text
    dcf5654d2a9a8eab66935f1d7edd1b45807c2b26 Fri Jun 22 09:03:54 2018 -0700
    The assembly name is NOT an NCBI assembly name refs #20970
• src/hg/makeDb/trackDb/oreNil/oreNil3/description.html
  • lines changed 1, context: html, text, full: html, text
    dcf5654d2a9a8eab66935f1d7edd1b45807c2b26 Fri Jun 22 09:03:54 2018 -0700
    The assembly name is NOT an NCBI assembly name refs #20970
• src/hg/makeDb/trackDb/platypus/ornAna1/gold.html
  • lines changed 2, context: html, text, full: html, text
    997c01a2282ae7104e495c59688fabbea2713435 Tue Jun 19 08:37:47 2018 -0700
    Updating redirected links for ornAna1, uiLinks cronjob.
• src/hg/makeDb/trackDb/platypus/ornAna1/multiz6way.html
  • lines changed 7, context: html, text, full: html, text
    997c01a2282ae7104e495c59688fabbea2713435 Tue Jun 19 08:37:47 2018 -0700
    Updating redirected links for ornAna1, uiLinks cronjob.
• src/hg/makeDb/trackDb/platypus/ornAna1/phastConsElements6way.html
  • lines changed 5, context: html, text, full: html, text
    997c01a2282ae7104e495c59688fabbea2713435 Tue Jun 19 08:37:47 2018 -0700
    Updating redirected links for ornAna1, uiLinks cronjob.
• src/hg/makeDb/trackDb/platypus/ornAna1/wssdCoverage.html
  • lines changed 3, context: html, text, full: html, text
    997c01a2282ae7104e495c59688fabbea2713435 Tue Jun 19 08:37:47 2018 -0700
    Updating redirected links for ornAna1, uiLinks cronjob.
• src/hg/makeDb/trackDb/primate/aotNan1/description.html
  • lines changed 1, context: html, text, full: html, text
    dcf5654d2a9a8eab66935f1d7edd1b45807c2b26 Fri Jun 22 09:03:54 2018 -0700
    The assembly name is NOT an NCBI assembly name refs #20970
• src/hg/makeDb/trackDb/primate/cebCap1/description.html
  • lines changed 1, context: html, text, full: html, text
    dcf5654d2a9a8eab66935f1d7edd1b45807c2b26 Fri Jun 22 09:03:54 2018 -0700
    The assembly name is NOT an NCBI assembly name refs #20970
• src/hg/makeDb/trackDb/primate/cerAty1/description.html
  • lines changed 1, context: html, text, full: html, text
    dcf5654d2a9a8eab66935f1d7edd1b45807c2b26 Fri Jun 22 09:03:54 2018 -0700
    The assembly name is NOT an NCBI assembly name refs #20970
• src/hg/makeDb/trackDb/primate/eulFla1/description.html
  • lines changed 1, context: html, text, full: html, text
    dcf5654d2a9a8eab66935f1d7edd1b45807c2b26 Fri Jun 22 09:03:54 2018 -0700
    The assembly name is NOT an NCBI assembly name refs #20970
• src/hg/makeDb/trackDb/primate/eulMac1/description.html
  • lines changed 1, context: html, text, full: html, text
    dcf5654d2a9a8eab66935f1d7edd1b45807c2b26 Fri Jun 22 09:03:54 2018 -0700
    The assembly name is NOT an NCBI assembly name refs #20970
• src/hg/makeDb/trackDb/primate/manLeu1/description.html
  • lines changed 1, context: html, text, full: html, text
    dcf5654d2a9a8eab66935f1d7edd1b45807c2b26 Fri Jun 22 09:03:54 2018 -0700
    The assembly name is NOT an NCBI assembly name refs #20970
• src/hg/makeDb/trackDb/primate/proCoq1/description.html
  • lines changed 1, context: html, text, full: html, text
    dcf5654d2a9a8eab66935f1d7edd1b45807c2b26 Fri Jun 22 09:03:54 2018 -0700
    The assembly name is NOT an NCBI assembly name refs #20970
• src/hg/makeDb/trackDb/reptiles/thaSir1/description.html
  • lines changed 1, context: html, text, full: html, text
    dcf5654d2a9a8eab66935f1d7edd1b45807c2b26 Fri Jun 22 09:03:54 2018 -0700
    The assembly name is NOT an NCBI assembly name refs #20970
• src/hg/makeDb/trackDb/rhinopithecus/rhiBie1/description.html
  • lines changed 1, context: html, text, full: html, text
    dcf5654d2a9a8eab66935f1d7edd1b45807c2b26 Fri Jun 22 09:03:54 2018 -0700
    The assembly name is NOT an NCBI assembly name refs #20970
• src/hg/makeDb/trackDb/seal/neoSch1/description.html
  • lines changed 1, context: html, text, full: html, text
    dcf5654d2a9a8eab66935f1d7edd1b45807c2b26 Fri Jun 22 09:03:54 2018 -0700
    The assembly name is NOT an NCBI assembly name refs #20970
• src/hg/makeDb/trackDb/sheep/oviAri4/description.html
  • lines changed 1, context: html, text, full: html, text
    dcf5654d2a9a8eab66935f1d7edd1b45807c2b26 Fri Jun 22 09:03:54 2018 -0700
    The assembly name is NOT an NCBI assembly name refs #20970
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 3, context: html, text, full: html, text
    23ecc080ba35d0563c208e8ff96f9852475e34f6 Mon Jun 18 14:23:06 2018 -0700
    Adding url, urls, urlLabel and extraFields support to bigBarChart tracks
• src/hg/makeDb/trackDb/treeShrew/tupChi1/description.html
  • lines changed 1, context: html, text, full: html, text
    dcf5654d2a9a8eab66935f1d7edd1b45807c2b26 Fri Jun 22 09:03:54 2018 -0700
    The assembly name is NOT an NCBI assembly name refs #20970
• src/hg/makeDb/trackDb/turtle/chrPic2/description.html
  • lines changed 1, context: html, text, full: html, text
    dcf5654d2a9a8eab66935f1d7edd1b45807c2b26 Fri Jun 22 09:03:54 2018 -0700
    The assembly name is NOT an NCBI assembly name refs #20970
• src/hg/makeDb/trackDb/whale/orcOrc1/description.html
  • lines changed 1, context: html, text, full: html, text
    dcf5654d2a9a8eab66935f1d7edd1b45807c2b26 Fri Jun 22 09:03:54 2018 -0700
    The assembly name is NOT an NCBI assembly name refs #20970
• src/hg/mouseStuff/chainBridge/chainBridge.c
  • lines changed 397, context: html, text, full: html, text
    fdd9aae7db69e2c910f0a2cb0dc1fea0fc00f3cd Thu May 31 12:35:34 2018 -0700
    New program chainBridge (refs #21651): try to bridge double-sided gaps in chains, first by trivially extending over perfect matches if possible, then by banded S-W alignment if gap sizes are similar on t and q and not too large. This is useful for fixing up some double-sided gaps that skip identical or nearly identical sequences found in some of our liftOver chain files. In doSameSpeciesLiftOver.pl, pipe axtChain to chainBridge.
• src/hg/mouseStuff/chainBridge/makefile
  • lines changed 4, context: html, text, full: html, text
    fdd9aae7db69e2c910f0a2cb0dc1fea0fc00f3cd Thu May 31 12:35:34 2018 -0700
    New program chainBridge (refs #21651): try to bridge double-sided gaps in chains, first by trivially extending over perfect matches if possible, then by banded S-W alignment if gap sizes are similar on t and q and not too large. This is useful for fixing up some double-sided gaps that skip identical or nearly identical sequences found in some of our liftOver chain files. In doSameSpeciesLiftOver.pl, pipe axtChain to chainBridge.
• src/hg/mouseStuff/makefile
  • lines changed 1, context: html, text, full: html, text
    fdd9aae7db69e2c910f0a2cb0dc1fea0fc00f3cd Thu May 31 12:35:34 2018 -0700
    New program chainBridge (refs #21651): try to bridge double-sided gaps in chains, first by trivially extending over perfect matches if possible, then by banded S-W alignment if gap sizes are similar on t and q and not too large. This is useful for fixing up some double-sided gaps that skip identical or nearly identical sequences found in some of our liftOver chain files. In doSameSpeciesLiftOver.pl, pipe axtChain to chainBridge.
• src/hg/utils/agpAlign/agpAlign.c
  • lines changed 240, context: html, text, full: html, text
    1e47ca9f2acedf205f065ca259bef14f2b5bf6cc Mon May 14 17:03:49 2018 -0700
    New program agpAlign.c (not yet in top-level build) finds common contigs between assemblies. refs #21650
• src/hg/utils/agpAlign/makefile
  • lines changed 3, context: html, text, full: html, text
    1e47ca9f2acedf205f065ca259bef14f2b5bf6cc Mon May 14 17:03:49 2018 -0700
    New program agpAlign.c (not yet in top-level build) finds common contigs between assemblies. refs #21650
• src/hg/utils/automation/altScaffoldPlacementToBed.pl
  • lines changed 33, context: html, text, full: html, text
    ed8466aff18192993a02770c43028f77e211130f Fri Jun 15 17:18:39 2018 -0700
    Convert NCBI assembly's alt_scaffold_placement.txt file format to altLocations.bed format. refs #18853
• src/hg/utils/automation/doBlastzChainNet.pl
  • lines changed 2, context: html, text, full: html, text
    7f802759855f5b0e0bb868d761620ade936d9562 Wed Jun 13 13:39:04 2018 -0700
    Allow doBlastzChainNet.pl to run on patch-only databases. refs #18853
• src/hg/utils/automation/doSameSpeciesLiftOver.pl
  • lines changed 3, context: html, text, full: html, text
    fdd9aae7db69e2c910f0a2cb0dc1fea0fc00f3cd Thu May 31 12:35:34 2018 -0700
    New program chainBridge (refs #21651): try to bridge double-sided gaps in chains, first by trivially extending over perfect matches if possible, then by banded S-W alignment if gap sizes are similar on t and q and not too large. This is useful for fixing up some double-sided gaps that skip identical or nearly identical sequences found in some of our liftOver chain files. In doSameSpeciesLiftOver.pl, pipe axtChain to chainBridge.
• src/hg/utils/automation/makeGenomeDb.pl
  • lines changed 6, context: html, text, full: html, text
    54c270d9c0feb39dba83f4ab8c4d55115c545d63 Fri Jun 22 08:48:33 2018 -0700
    the assembly name is NOT an NCBI assembly name refs #20970
• src/hg/utils/liftOverBigWig
  • lines changed 34, context: html, text, full: html, text
    a87327b5ef28209e7a809728fb3bc8fb476dfdb8 Fri Jun 15 15:17:01 2018 -0700
    Adding liftOverBigWig for lifting from one assembly to another, and liftOverBigWigToPatches for lifting main chromosome scores to patch sequences and concatenating the results onto the original annotations. refs #18853
• src/hg/utils/liftOverBigWigToPatches
  • lines changed 40, context: html, text, full: html, text
    a87327b5ef28209e7a809728fb3bc8fb476dfdb8 Fri Jun 15 15:17:01 2018 -0700
    Adding liftOverBigWig for lifting from one assembly to another, and liftOverBigWigToPatches for lifting main chromosome scores to patch sequences and concatenating the results onto the original annotations. refs #18853
• src/oneShot/testBandExt/testBandExt.c
  • lines changed 2, context: html, text, full: html, text
    4bdf667d97956ba22278152ffff7eeff7a095a11 Tue May 15 11:08:26 2018 -0700
    Fix compiler warning about printf too few args -- doesn't affect top-level build.
• src/test/buildTableDescriptions.pl
  • lines changed 1, context: html, text, full: html, text
    ccbcc084780401ca9e070e3ce2e6da99a56db615 Wed Jun 20 12:03:19 2018 -0700
    changes to expMatrixToBarchartBed after code review, refs #21626
  • lines changed 2, context: html, text, full: html, text
    693da22cbcf223255b22c8ac835bc9dbb51fa4c2 Thu Jun 21 10:08:09 2018 -0700
    fixing buildTableDescriptions duplicate warnings for expMatrixToBarchartBed tests, refs #21626
• src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed
  • lines changed 14, context: html, text, full: html, text
    ccbcc084780401ca9e070e3ce2e6da99a56db615 Wed Jun 20 12:03:19 2018 -0700
    changes to expMatrixToBarchartBed after code review, refs #21626
• src/utils/expMatrixToBarchartBed/tests/allOptions2.output
  • lines changed 11, context: html, text, full: html, text
    ccbcc084780401ca9e070e3ce2e6da99a56db615 Wed Jun 20 12:03:19 2018 -0700
    changes to expMatrixToBarchartBed after code review, refs #21626
• src/utils/expMatrixToBarchartBed/tests/makefile
  • lines changed 9, context: html, text, full: html, text
    ccbcc084780401ca9e070e3ce2e6da99a56db615 Wed Jun 20 12:03:19 2018 -0700
    changes to expMatrixToBarchartBed after code review, refs #21626
  • lines changed 1, context: html, text, full: html, text
    693da22cbcf223255b22c8ac835bc9dbb51fa4c2 Thu Jun 21 10:08:09 2018 -0700
    fixing buildTableDescriptions duplicate warnings for expMatrixToBarchartBed tests, refs #21626
• src/utils/expMatrixToBarchartBed/tests/noExtraFields.coords
  • lines changed 10, context: html, text, full: html, text
    ccbcc084780401ca9e070e3ce2e6da99a56db615 Wed Jun 20 12:03:19 2018 -0700
    changes to expMatrixToBarchartBed after code review, refs #21626
• src/utils/expMatrixToBarchartBed/tests/test.as
  • lines changed 1, context: html, text, full: html, text
    693da22cbcf223255b22c8ac835bc9dbb51fa4c2 Thu Jun 21 10:08:09 2018 -0700
    fixing buildTableDescriptions duplicate warnings for expMatrixToBarchartBed tests, refs #21626
• src/utils/expMatrixToBarchartBed/tests/test2.as
  • lines changed 15, context: html, text, full: html, text
    ccbcc084780401ca9e070e3ce2e6da99a56db615 Wed Jun 20 12:03:19 2018 -0700
    changes to expMatrixToBarchartBed after code review, refs #21626
  • lines changed 15, context: html, text, full: html, text
    693da22cbcf223255b22c8ac835bc9dbb51fa4c2 Thu Jun 21 10:08:09 2018 -0700
    fixing buildTableDescriptions duplicate warnings for expMatrixToBarchartBed tests, refs #21626
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    3c36f5bb7630fefaa113ba8f98fd79ab87c760f2 Mon Jun 25 10:37:38 2018 -0700
    v368 preview1, refs #21564
• src/utils/userApps/fetchChromSizes
  • lines changed 27, context: html, text, full: html, text
    4a03df77a2dac2278e4e8e80a05037edd8daaca9 Wed Jun 20 10:45:45 2018 -0700
    Adding a curl option to fetchChromSizes, and fixing 'type' message difference by using the '-p' option after user request, refs #21637

• lines changed: 15462
• files changed: 132