All File Changes

v352_preview to v352_preview2 (2017-07-03 to 2017-07-10) v352

• confs/hgwdev.hg.conf
  • lines changed 1, context: html, text, full: html, text
    c76c8805e20a370bd1255687bd1a1cd9e26373d5 Sun Jul 9 01:11:42 2017 -0700
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 3, context: html, text, full: html, text
    c76c8805e20a370bd1255687bd1a1cd9e26373d5 Sun Jul 9 01:11:42 2017 -0700
    Installing updated hg.conf files from UCSC servers
• python/lib/ucscGb/qa/tables/checkGapOverlap.py
  • lines changed 5, context: html, text, full: html, text
    c6266a24ec2f94547db8ce8109a4180800d41dae Thu Jun 29 14:17:03 2017 -0700
    Renaming tableTypeUtils to trackUtils as it more accurate. Also more track-centered functions will be added to it soon. Changing references to tableTypeUtils to trackUtils. Inspired by CR, refs #19495
  • lines changed 87, context: html, text, full: html, text
    a97ba306c1d4392680e93bd87e5ca2a90df64c7f Wed Jul 5 15:12:48 2017 -0700
    Improving output from constructOutputUrls function to be aware of parents, both composites and superTracks. Also changed checkGapOverlap function to call makeBedFromTable for gap tables. Putting functions from checkGapOverlap.py and positionalQa.py into trackUtils.py to make them more accessible. The trackUtils.py should contain a pretty side selection of generally applicable functions that operate on tracks (and tables). Most functions were unchanged after their move (outside of changing references to what were once outside functions). Two functions were improved: makeBedFromTable and getLabels. I made getLabels work on correctly getting parent labels for both superTrack and composites and (hopefully) any combination of the two. The function makeBedFromTable now has a 'whereOpt' parameter that allows you to add a where filter to the hgsql command. Changed some references to 'table' to 'track' to be more consistent (e.g. a function named getTrackType that had table as one of its parameters). Lastly, changed the checkLabelLengths function in positonalQa.py to use new getLabels function. All inspired by Chris Lee in a Code Review, refs #19495
• python/lib/ucscGb/qa/tables/factory.py
  • lines changed 6, context: html, text, full: html, text
    c6266a24ec2f94547db8ce8109a4180800d41dae Thu Jun 29 14:17:03 2017 -0700
    Renaming tableTypeUtils to trackUtils as it more accurate. Also more track-centered functions will be added to it soon. Changing references to tableTypeUtils to trackUtils. Inspired by CR, refs #19495
• python/lib/ucscGb/qa/tables/positionalQa.py
  • lines changed 2, context: html, text, full: html, text
    c6266a24ec2f94547db8ce8109a4180800d41dae Thu Jun 29 14:17:03 2017 -0700
    Renaming tableTypeUtils to trackUtils as it more accurate. Also more track-centered functions will be added to it soon. Changing references to tableTypeUtils to trackUtils. Inspired by CR, refs #19495
  • lines changed 35, context: html, text, full: html, text
    a97ba306c1d4392680e93bd87e5ca2a90df64c7f Wed Jul 5 15:12:48 2017 -0700
    Improving output from constructOutputUrls function to be aware of parents, both composites and superTracks. Also changed checkGapOverlap function to call makeBedFromTable for gap tables. Putting functions from checkGapOverlap.py and positionalQa.py into trackUtils.py to make them more accessible. The trackUtils.py should contain a pretty side selection of generally applicable functions that operate on tracks (and tables). Most functions were unchanged after their move (outside of changing references to what were once outside functions). Two functions were improved: makeBedFromTable and getLabels. I made getLabels work on correctly getting parent labels for both superTrack and composites and (hopefully) any combination of the two. The function makeBedFromTable now has a 'whereOpt' parameter that allows you to add a where filter to the hgsql command. Changed some references to 'table' to 'track' to be more consistent (e.g. a function named getTrackType that had table as one of its parameters). Lastly, changed the checkLabelLengths function in positonalQa.py to use new getLabels function. All inspired by Chris Lee in a Code Review, refs #19495
• python/lib/ucscGb/qa/tables/tableTypeUtils.py
  • lines changed 89, context: html, text, full: html, text
    c6266a24ec2f94547db8ce8109a4180800d41dae Thu Jun 29 14:17:03 2017 -0700
    Renaming tableTypeUtils to trackUtils as it more accurate. Also more track-centered functions will be added to it soon. Changing references to tableTypeUtils to trackUtils. Inspired by CR, refs #19495
• python/lib/ucscGb/qa/tables/trackUtils.py
  • lines changed 89, context: html, text, full: html, text
    c6266a24ec2f94547db8ce8109a4180800d41dae Thu Jun 29 14:17:03 2017 -0700
    Renaming tableTypeUtils to trackUtils as it more accurate. Also more track-centered functions will be added to it soon. Changing references to tableTypeUtils to trackUtils. Inspired by CR, refs #19495
  • lines changed 114, context: html, text, full: html, text
    a97ba306c1d4392680e93bd87e5ca2a90df64c7f Wed Jul 5 15:12:48 2017 -0700
    Improving output from constructOutputUrls function to be aware of parents, both composites and superTracks. Also changed checkGapOverlap function to call makeBedFromTable for gap tables. Putting functions from checkGapOverlap.py and positionalQa.py into trackUtils.py to make them more accessible. The trackUtils.py should contain a pretty side selection of generally applicable functions that operate on tracks (and tables). Most functions were unchanged after their move (outside of changing references to what were once outside functions). Two functions were improved: makeBedFromTable and getLabels. I made getLabels work on correctly getting parent labels for both superTrack and composites and (hopefully) any combination of the two. The function makeBedFromTable now has a 'whereOpt' parameter that allows you to add a where filter to the hgsql command. Changed some references to 'table' to 'track' to be more consistent (e.g. a function named getTrackType that had table as one of its parameters). Lastly, changed the checkLabelLengths function in positonalQa.py to use new getLabels function. All inspired by Chris Lee in a Code Review, refs #19495
• src/gfServer/gfServer.c
  • lines changed 4, context: html, text, full: html, text
    4ac69dd9425c5437842f66d2034a8ba4867117fd Fri Jul 7 12:25:52 2017 -0700
    Making gfServer have a debugLog option.
• src/hg/cirm/cdw/cdwWebBrowse/cdwWebBrowse.c
  • lines changed 4, context: html, text, full: html, text
    5b2005f80b081f30319b3d51fee86083029c6417 Wed Jul 5 12:18:41 2017 -0700
    CIRM: fixing bug where one download option did not respect username/password, refs #19733
• src/hg/hgGeneGraph/hgGeneGraph
  • lines changed 1, context: html, text, full: html, text
    fd591cb7db465e8d30fb21b5672550cb93243c42 Thu Jul 6 12:33:25 2017 -0700
    Adding GBIB/GBIC support to hgGeneGraph, refs #13634
• src/hg/hgGtexTrackSettings/hgGtexTrackSettings.c
  • lines changed 56, context: html, text, full: html, text
    45c5e17075e31abf2735b09ca201d29ce6e0e1f4 Thu Jun 29 18:17:22 2017 -0700
    Add trackUi (body map and right-click versions) and implement filters in hgTracks. refs #15646
  • lines changed 2, context: html, text, full: html, text
    7c2d98b2096ecfe0c2a45c4a8b81a0fd41788879 Wed Jul 5 14:45:11 2017 -0700
    Cleanup before merge. refs #15646
• src/hg/hgTables/bigWig.c
  • lines changed 9, context: html, text, full: html, text
    904c1c8e951519488cf06099bfab3feb81abb3db Wed Jul 5 14:45:07 2017 -0700
    Fixing the table browser bug with bigWig files without tables, refs #19701
• src/hg/hgTables/hgTables.c
  • lines changed 2, context: html, text, full: html, text
    904c1c8e951519488cf06099bfab3feb81abb3db Wed Jul 5 14:45:07 2017 -0700
    Fixing the table browser bug with bigWig files without tables, refs #19701
• src/hg/hgTables/hgTables.h
  • lines changed 3, context: html, text, full: html, text
    904c1c8e951519488cf06099bfab3feb81abb3db Wed Jul 5 14:45:07 2017 -0700
    Fixing the table browser bug with bigWig files without tables, refs #19701
• src/hg/hgTables/schema.c
  • lines changed 3, context: html, text, full: html, text
    904c1c8e951519488cf06099bfab3feb81abb3db Wed Jul 5 14:45:07 2017 -0700
    Fixing the table browser bug with bigWig files without tables, refs #19701
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 2, context: html, text, full: html, text
    45c5e17075e31abf2735b09ca201d29ce6e0e1f4 Thu Jun 29 18:17:22 2017 -0700
    Add trackUi (body map and right-click versions) and implement filters in hgTracks. refs #15646
• src/hg/hgTracks/gtexEqtlClusterTrack.c
  • lines changed 71, context: html, text, full: html, text
    c5e7de3acfdc5a8290417df8161a23f5b02c92a7 Mon Jun 26 11:32:48 2017 -0700
    Add GTEx eQTL cluster track initial code support. refs #15646
  • lines changed 51, context: html, text, full: html, text
    6d65c7caa2da509639f5dba2fa2b30eab2d82c02 Mon Jun 26 14:35:27 2017 -0700
    Add mouseover with tissue names and effect sizes. Commented out code to show colors (not working). refs #15646
  • lines changed 2, context: html, text, full: html, text
    0846eb5a094ecf1f8400f5ea091f3e6727794477 Mon Jun 26 14:42:15 2017 -0700
    Remove debug stmts. refs #15646
  • lines changed 7, context: html, text, full: html, text
    1217988d31947663be0f94309c9e8dbc9867b06e Wed Jun 28 08:22:50 2017 -0700
    Fix problem with thresholding. refs #15646
  • lines changed 124, context: html, text, full: html, text
    45c5e17075e31abf2735b09ca201d29ce6e0e1f4 Thu Jun 29 18:17:22 2017 -0700
    Add trackUi (body map and right-click versions) and implement filters in hgTracks. refs #15646
  • lines changed 9, context: html, text, full: html, text
    7c2d98b2096ecfe0c2a45c4a8b81a0fd41788879 Wed Jul 5 14:45:11 2017 -0700
    Cleanup before merge. refs #15646
  • lines changed 44, context: html, text, full: html, text
    0301e7107474990ca5b3328ad5f622b018fb481c Thu Jul 6 13:14:00 2017 -0700
    Split label into left (gene) and right (tissues). refs #15646
• src/hg/hgTracks/gtexEqtlTracks.c
  • lines changed 26, context: html, text, full: html, text
    c5e7de3acfdc5a8290417df8161a23f5b02c92a7 Mon Jun 26 11:32:48 2017 -0700
    Add GTEx eQTL cluster track initial code support. refs #15646
  • lines changed 26, context: html, text, full: html, text
    7c2d98b2096ecfe0c2a45c4a8b81a0fd41788879 Wed Jul 5 14:45:11 2017 -0700
    Cleanup before merge. refs #15646
• src/hg/hgTracks/hgTracks.h
  • lines changed 6, context: html, text, full: html, text
    c5e7de3acfdc5a8290417df8161a23f5b02c92a7 Mon Jun 26 11:32:48 2017 -0700
    Add GTEx eQTL cluster track initial code support. refs #15646
  • lines changed 3, context: html, text, full: html, text
    7c2d98b2096ecfe0c2a45c4a8b81a0fd41788879 Wed Jul 5 14:45:11 2017 -0700
    Cleanup before merge. refs #15646
  • lines changed 5, context: html, text, full: html, text
    0301e7107474990ca5b3328ad5f622b018fb481c Thu Jul 6 13:14:00 2017 -0700
    Split label into left (gene) and right (tissues). refs #15646
• src/hg/hgTracks/makefile
  • lines changed 1, context: html, text, full: html, text
    c5e7de3acfdc5a8290417df8161a23f5b02c92a7 Mon Jun 26 11:32:48 2017 -0700
    Add GTEx eQTL cluster track initial code support. refs #15646
  • lines changed 1, context: html, text, full: html, text
    7c2d98b2096ecfe0c2a45c4a8b81a0fd41788879 Wed Jul 5 14:45:11 2017 -0700
    Cleanup before merge. refs #15646
• src/hg/hgTracks/simpleTracks.c
  • lines changed 5, context: html, text, full: html, text
    c5e7de3acfdc5a8290417df8161a23f5b02c92a7 Mon Jun 26 11:32:48 2017 -0700
    Add GTEx eQTL cluster track initial code support. refs #15646
  • lines changed 3, context: html, text, full: html, text
    7c2d98b2096ecfe0c2a45c4a8b81a0fd41788879 Wed Jul 5 14:45:11 2017 -0700
    Cleanup before merge. refs #15646
  • lines changed 1, context: html, text, full: html, text
    0301e7107474990ca5b3328ad5f622b018fb481c Thu Jul 6 13:14:00 2017 -0700
    Split label into left (gene) and right (tissues). refs #15646
• src/hg/hgc/bigBedClick.c
  • lines changed 9, context: html, text, full: html, text
    ea4e0db808801644e3fa40916bc3b0a7216cebba Wed Jul 5 14:50:26 2017 -0700
    fixing a bug in the crisprTrack due to stupid memory management issues. No idea why this code ever worked on the RR. No redmine, email by Hiram
• src/hg/hgc/gtexClick.c
  • lines changed 1, context: html, text, full: html, text
    8d724c5b24b55e805c0f57542676a35f5dc30494 Thu Jun 29 18:18:40 2017 -0700
    Expand details page. refs #15646
• src/hg/hgc/gtexEqtlClusterClick.c
  • lines changed 72, context: html, text, full: html, text
    707bd9f05c4c104fb6a90a680aa72d38895b67a3 Mon Jun 26 18:32:29 2017 -0700
    Details page. refs #15646
  • lines changed 49, context: html, text, full: html, text
    8d724c5b24b55e805c0f57542676a35f5dc30494 Thu Jun 29 18:18:40 2017 -0700
    Expand details page. refs #15646
  • lines changed 17, context: html, text, full: html, text
    a3de0378c0ef6ffff6fd40e77407b2b8b80b5573 Wed Jul 5 12:00:34 2017 -0700
    Allow bin field for speedup. refs #15646
  • lines changed 8, context: html, text, full: html, text
    0a35a5aef108000ab4d18b84f0bdbb882e0d59e0 Wed Jul 5 14:20:15 2017 -0700
    Add flanking sequence to position link so border eQTL's show up in display. refs #15646
  • lines changed 1, context: html, text, full: html, text
    7c2d98b2096ecfe0c2a45c4a8b81a0fd41788879 Wed Jul 5 14:45:11 2017 -0700
    Cleanup before merge. refs #15646
• src/hg/hgc/hgc.c
  • lines changed 4, context: html, text, full: html, text
    707bd9f05c4c104fb6a90a680aa72d38895b67a3 Mon Jun 26 18:32:29 2017 -0700
    Details page. refs #15646
• src/hg/hgc/hgc.h
  • lines changed 3, context: html, text, full: html, text
    707bd9f05c4c104fb6a90a680aa72d38895b67a3 Mon Jun 26 18:32:29 2017 -0700
    Details page. refs #15646
• src/hg/hgc/makefile
  • lines changed 1, context: html, text, full: html, text
    707bd9f05c4c104fb6a90a680aa72d38895b67a3 Mon Jun 26 18:32:29 2017 -0700
    Details page. refs #15646
• src/hg/htdocs/inc/gbPageStartHardcoded.html
  • lines changed 8, context: html, text, full: html, text
    a6f02415c78b766a356fe8b7472b7a0c1e37723a Thu Jul 6 16:35:39 2017 -0700
    Adding a note for hgdownloads hardcoded blue bar about links going to genome.ucsc.edu ref# 19626
• src/hg/inc/gtexEqtlCluster.h
  • lines changed 87, context: html, text, full: html, text
    eae24c27fd543e049969915b3bb690980e15b7d0 Wed Jul 5 14:48:11 2017 -0700
    Cleanup before merge. refs #15646
• src/hg/inc/gtexUi.h
  • lines changed 48, context: html, text, full: html, text
    45c5e17075e31abf2735b09ca201d29ce6e0e1f4 Thu Jun 29 18:17:22 2017 -0700
    Add trackUi (body map and right-click versions) and implement filters in hgTracks. refs #15646
• src/hg/inc/hdb.h
  • lines changed 3, context: html, text, full: html, text
    904c1c8e951519488cf06099bfab3feb81abb3db Wed Jul 5 14:45:07 2017 -0700
    Fixing the table browser bug with bigWig files without tables, refs #19701
• src/hg/inc/hui.h
  • lines changed 20, context: html, text, full: html, text
    45c5e17075e31abf2735b09ca201d29ce6e0e1f4 Thu Jun 29 18:17:22 2017 -0700
    Add trackUi (body map and right-click versions) and implement filters in hgTracks. refs #15646
• src/hg/lib/cart.c
  • lines changed 5, context: html, text, full: html, text
    42cd42d52a9d964bf59af16964323dc9effe1bb9 Wed Jul 5 12:13:57 2017 -0700
    Removing confusing "ASH: " prefixes from some diagnostic warning messages.
• src/hg/lib/cosmicNew.as
  • lines changed 2, context: html, text, full: html, text
    fd20884e51fe0cd5708f971a94ea0a10e06503c8 Wed Jul 5 12:16:09 2017 -0700
    Adding a mouse over field and new label field as suggested by Chris Lee refs #14461
• src/hg/lib/gtexEqtlCluster.as
  • lines changed 14, context: html, text, full: html, text
    108d2fdf0aa57ebca7e2a62a028ce2c30cbe8049 Wed Jul 5 14:51:47 2017 -0700
    Cleanup before merge. refs #15646
• src/hg/lib/gtexEqtlCluster.c
  • lines changed 272, context: html, text, full: html, text
    f822a574e460d88df6c5c7d841cd2052374a4896 Mon Jun 26 18:04:31 2017 -0700
    Adding lib file. refs #15646
• src/hg/lib/gtexEqtlCluster.sql
  • lines changed 22, context: html, text, full: html, text
    108d2fdf0aa57ebca7e2a62a028ce2c30cbe8049 Wed Jul 5 14:51:47 2017 -0700
    Cleanup before merge. refs #15646
• src/hg/lib/gtexUi.c
  • lines changed 110, context: html, text, full: html, text
    64d9809600ba9cf12c331e053533886817523405 Thu Jun 29 18:19:09 2017 -0700
    Add trackUi (body map and right-click versions) and implement filters in hgTracks. refs #15646
• src/hg/lib/hdb.c
  • lines changed 1, context: html, text, full: html, text
    42cd42d52a9d964bf59af16964323dc9effe1bb9 Wed Jul 5 12:13:57 2017 -0700
    Removing confusing "ASH: " prefixes from some diagnostic warning messages.
  • lines changed 31, context: html, text, full: html, text
    904c1c8e951519488cf06099bfab3feb81abb3db Wed Jul 5 14:45:07 2017 -0700
    Fixing the table browser bug with bigWig files without tables, refs #19701
• src/hg/lib/hui.c
  • lines changed 2, context: html, text, full: html, text
    c5e7de3acfdc5a8290417df8161a23f5b02c92a7 Mon Jun 26 11:32:48 2017 -0700
    Add GTEx eQTL cluster track initial code support. refs #15646
  • lines changed 3, context: html, text, full: html, text
    45c5e17075e31abf2735b09ca201d29ce6e0e1f4 Thu Jun 29 18:17:22 2017 -0700
    Add trackUi (body map and right-click versions) and implement filters in hgTracks. refs #15646
• src/hg/lib/jksql.c
  • lines changed 1, context: html, text, full: html, text
    42cd42d52a9d964bf59af16964323dc9effe1bb9 Wed Jul 5 12:13:57 2017 -0700
    Removing confusing "ASH: " prefixes from some diagnostic warning messages.
• src/hg/lib/makefile
  • lines changed 2, context: html, text, full: html, text
    c5e7de3acfdc5a8290417df8161a23f5b02c92a7 Mon Jun 26 11:32:48 2017 -0700
    Add GTEx eQTL cluster track initial code support. refs #15646
  • lines changed 3, context: html, text, full: html, text
    5078b92cebab8e340d4c0d68e6d9e02f49c8db45 Wed Jul 5 14:23:36 2017 -0700
    Resolving merge conflict
• src/hg/makeDb/doc/hg19.txt
  • lines changed 84, context: html, text, full: html, text
    24890e3d3c4f23994e5b6cdb00d57141269162dc Wed Apr 12 13:02:05 2017 -0700
    snp150* tracks (dbSNP b150) for hg19 and hg38. refs #19202
• src/hg/makeDb/doc/hg38/variation.txt
  • lines changed 95, context: html, text, full: html, text
    24890e3d3c4f23994e5b6cdb00d57141269162dc Wed Apr 12 13:02:05 2017 -0700
    snp150* tracks (dbSNP b150) for hg19 and hg38. refs #19202
• src/hg/makeDb/doc/mouseStrains/GCA_001632615.1_LP_J_v1/GCA_001632615.1_LP_J_v1.trackDb.txt
  • lines changed 9, context: html, text, full: html, text
    6e1e19d9d9ce8ac59446e4be55e27e862a8785e2 Thu Jul 6 10:44:17 2017 -0700
    Removing the duplicated gapOverlap track that appears more than once in genome LP_J, refs #13553
• src/hg/makeDb/doc/mouseStrains/hubIndex.html
  • lines changed 4, context: html, text, full: html, text
    d8be9af7a81d59389cc424783f68f90008ba18bf Wed Jul 5 13:22:32 2017 -0700
    Minor edit as per code review, CR #19729
• src/hg/makeDb/doc/mouseStrains/mm10/mm10.bigMaf.trackDb.txt
  • lines changed 1, context: html, text, full: html, text
    93185c656e7597bee35d7fac664f09c874e3f987 Wed Jul 5 15:43:13 2017 -0700
    Including the catcus alignments (mice strains track) html page to mm10 and rn6, refs #13553
• src/hg/makeDb/doc/mouseStrains/rn6/rn6.bigMaf.trackDb.txt
  • lines changed 1, context: html, text, full: html, text
    93185c656e7597bee35d7fac664f09c874e3f987 Wed Jul 5 15:43:13 2017 -0700
    Including the catcus alignments (mice strains track) html page to mm10 and rn6, refs #13553
• src/hg/makeDb/schema/all.joiner
  • lines changed 19, context: html, text, full: html, text
    24890e3d3c4f23994e5b6cdb00d57141269162dc Wed Apr 12 13:02:05 2017 -0700
    snp150* tracks (dbSNP b150) for hg19 and hg38. refs #19202
• src/hg/makeDb/trackDb/human/hg19/cons100way.html
  • lines changed 1, context: html, text, full: html, text
    bca0f1688cce89b22754a21b312aaf755cfb9f82 Thu Jul 6 17:06:49 2017 -0700
    changed a comma to a period
• src/hg/makeDb/trackDb/human/hg19/gtexEqtl.ra
  • lines changed 552, context: html, text, full: html, text
    c5e7de3acfdc5a8290417df8161a23f5b02c92a7 Mon Jun 26 11:32:48 2017 -0700
    Add GTEx eQTL cluster track initial code support. refs #15646
  • lines changed 1, context: html, text, full: html, text
    45c5e17075e31abf2735b09ca201d29ce6e0e1f4 Thu Jun 29 18:17:22 2017 -0700
    Add trackUi (body map and right-click versions) and implement filters in hgTracks. refs #15646
  • lines changed 19, context: html, text, full: html, text
    7c2d98b2096ecfe0c2a45c4a8b81a0fd41788879 Wed Jul 5 14:45:11 2017 -0700
    Cleanup before merge. refs #15646
  • lines changed 3, context: html, text, full: html, text
    c025d190ec42127ad2d702b0ea47a1216566e85a Thu Jul 6 07:11:05 2017 -0700
    Fix dupe.
  • lines changed 7, context: html, text, full: html, text
    5408748cccb1dd36573de163b9eed0b4a72cd59a Thu Jul 6 07:17:44 2017 -0700
    Fix dupe.
• src/hg/makeDb/trackDb/human/hg19/gtexEqtlCluster.html
  • lines changed 41, context: html, text, full: html, text
    707bd9f05c4c104fb6a90a680aa72d38895b67a3 Mon Jun 26 18:32:29 2017 -0700
    Details page. refs #15646
  • lines changed 3, context: html, text, full: html, text
    45c5e17075e31abf2735b09ca201d29ce6e0e1f4 Thu Jun 29 18:17:22 2017 -0700
    Add trackUi (body map and right-click versions) and implement filters in hgTracks. refs #15646
  • lines changed 5, context: html, text, full: html, text
    5078b92cebab8e340d4c0d68e6d9e02f49c8db45 Wed Jul 5 14:23:36 2017 -0700
    Resolving merge conflict
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    c5e7de3acfdc5a8290417df8161a23f5b02c92a7 Mon Jun 26 11:32:48 2017 -0700
    Add GTEx eQTL cluster track initial code support. refs #15646
  • lines changed 6, context: html, text, full: html, text
    c025d190ec42127ad2d702b0ea47a1216566e85a Thu Jul 6 07:11:05 2017 -0700
    Fix dupe.
  • lines changed 7, context: html, text, full: html, text
    5408748cccb1dd36573de163b9eed0b4a72cd59a Thu Jul 6 07:17:44 2017 -0700
    Fix dupe.
• src/hg/makeDb/trackDb/human/hg38/hoffMap.ra
  • lines changed 20, context: html, text, full: html, text
    b25a010ff1f2a9de98da734f1ad04333b030368d Mon Jul 3 10:33:23 2017 -0700
    removing the priority from these tracks, refs #19154
• src/hg/makeDb/trackDb/human/snp150.html
  • lines changed 38, context: html, text, full: html, text
    24890e3d3c4f23994e5b6cdb00d57141269162dc Wed Apr 12 13:02:05 2017 -0700
    snp150* tracks (dbSNP b150) for hg19 and hg38. refs #19202
• src/hg/makeDb/trackDb/human/snp150.shared.html
  • lines changed 480, context: html, text, full: html, text
    24890e3d3c4f23994e5b6cdb00d57141269162dc Wed Apr 12 13:02:05 2017 -0700
    snp150* tracks (dbSNP b150) for hg19 and hg38. refs #19202
• src/hg/makeDb/trackDb/human/snp150Common.html
  • lines changed 28, context: html, text, full: html, text
    24890e3d3c4f23994e5b6cdb00d57141269162dc Wed Apr 12 13:02:05 2017 -0700
    snp150* tracks (dbSNP b150) for hg19 and hg38. refs #19202
• src/hg/makeDb/trackDb/human/snp150Flagged.html
  • lines changed 29, context: html, text, full: html, text
    24890e3d3c4f23994e5b6cdb00d57141269162dc Wed Apr 12 13:02:05 2017 -0700
    snp150* tracks (dbSNP b150) for hg19 and hg38. refs #19202
• src/hg/makeDb/trackDb/human/snp150Mult.html
  • lines changed 29, context: html, text, full: html, text
    24890e3d3c4f23994e5b6cdb00d57141269162dc Wed Apr 12 13:02:05 2017 -0700
    snp150* tracks (dbSNP b150) for hg19 and hg38. refs #19202
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 125, context: html, text, full: html, text
    24890e3d3c4f23994e5b6cdb00d57141269162dc Wed Apr 12 13:02:05 2017 -0700
    snp150* tracks (dbSNP b150) for hg19 and hg38. refs #19202
  • lines changed 8, context: html, text, full: html, text
    81d3bc4c2d557e6a957a6f3d9375e3a91c9938e8 Thu Jul 6 09:34:17 2017 -0700
    Oops, I made a duplicate searchTable stanza for snp150; removed.
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    d1c0d74e9d2f58a7d86659e6de5e4a1ddee3eeb4 Wed Jul 5 15:31:20 2017 -0700
    Turning off haplotype sorting by default, refs #18305
  • lines changed 1, context: html, text, full: html, text
    a671b7254cdafd51f0ed8a98c7129a4a0b634543 Thu Jul 6 14:32:01 2017 -0700
    Adding the Mouse SNPs track in alphabetical order for the Variation and Repeats section on hgTracks, refs #18305
• src/hg/makeDb/trackDb/oreNil/oreNil2/description.html
  • lines changed 1, context: html, text, full: html, text
    8909a83af03c81ee3cab74bc2ff781b8516c9225 Wed Jul 5 10:34:55 2017 -0700
    Removing an extra ) character that didn't get deleted, CR #19728
• src/hg/makeDb/trackDb/patSeq.html
  • lines changed 1, context: html, text, full: html, text
    498f1cc2e121d5feba4701074c424b33e5e63e31 Wed Jul 5 13:48:34 2017 -0700
    changed gratefully to graciously. we are grateful, they were gratious
• src/hg/pyLib/README.txt
  • lines changed 19, context: html, text, full: html, text
    fd591cb7db465e8d30fb21b5672550cb93243c42 Thu Jul 6 12:33:25 2017 -0700
    Adding GBIB/GBIC support to hgGeneGraph, refs #13634
• src/hg/pyLib/hgLib.py
  • lines changed 76, context: html, text, full: html, text
    fd591cb7db465e8d30fb21b5672550cb93243c42 Thu Jul 6 12:33:25 2017 -0700
    Adding GBIB/GBIC support to hgGeneGraph, refs #13634
• src/hg/utils/automation/doDbSnpOrthoAlleles.pl
  • lines changed 2, context: html, text, full: html, text
    33761f65e3b811035af2360f0e01f0844972882c Mon May 1 10:46:52 2017 -0700
    Updated ortho chimp assembly panTro4 -> panTro5 and macaque rheMac3 -> rheMac8. Really should make those into command line params for better doc!
• src/hg/utils/otto/omim/checkOmim.sh
  • lines changed 1, context: html, text, full: html, text
    6d0b8670d7b703b378ff6f07c5da7de8a170345f Wed Jul 5 10:50:28 2017 -0700
    Fixing OMIM script to not do an update when the only change was in a comment, refs #18151
• src/product/installer/browserSetup.sh
  • lines changed 9, context: html, text, full: html, text
    30e7a5f6293a5dcb4f00a5c06e517f70616f09af Mon Jul 3 13:26:31 2017 -0700
    Removing -z rsync option in gbic script. This option was causing major slowdown on hgdownload, refs #19587
• src/utils/crisprKmers/crisprKmers.c
  • lines changed 146, context: html, text, full: html, text
    47205c92c3cffc5a7db8835b772e32b8717bd253 Wed Jul 5 10:31:25 2017 -0700
    now counting bits with intrinsics builtin popcnt instruction and better representation of the base bit values refs #18969
  • lines changed 300, context: html, text, full: html, text
    4068e4c5ce3d0b375d570f651539b0709adba981 Wed Jul 5 15:58:19 2017 -0700
    beginning to use a ranges specification to limit the comparisons refs #18969
  • lines changed 234, context: html, text, full: html, text
    e20e93ca2a36c232d2fe3b2d918d03674f89d5d4 Fri Jul 7 08:56:14 2017 -0700
    the linked lists are too slow, maybe try arrays refs #18969
  • lines changed 344, context: html, text, full: html, text
    f8b37f0a0b7ac9bbd5529692fa61b921a6a2b67f Fri Jul 7 23:57:27 2017 -0700
    check in before removing all the garbage, appears to be working with arrays much faster refs #18969
  • lines changed 341, context: html, text, full: html, text
    458277a2bb9ff317669cd0e19e1cd1c1b29e2bff Sat Jul 8 00:41:33 2017 -0700
    removed all the garbage, see if it still works refs #18969
  • lines changed 75, context: html, text, full: html, text
    47a02857acb0e52455455f577dbe801d9b2b0a66 Sat Jul 8 23:04:40 2017 -0700
    now recording off-target data and discovered that (a > 1) is dramatically different from (a >> 1) with no warning of course, refs #18969
  • lines changed 82, context: html, text, full: html, text
    95a4ab24a874500faece4f5e71815b950697afb3 Mon Jul 10 00:16:59 2017 -0700
    adding some fake color to the bed output to test runtime on some larger ranges refs #18969
• src/utils/crisprKmers/makefile
  • lines changed 1, context: html, text, full: html, text
    ee4f9523a021f9ea6c4ba9c0695975024936a03f Wed Jul 5 10:32:00 2017 -0700
    need CFLAGS with -mpopcnt to use intrinsic builtin function refs #18969
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    a9ba05c24c4d3ed2806bb6be67c2295ed3531b64 Mon Jul 10 10:02:34 2017 -0700
    v352 preview2 refs #19715
• src/utils/qa/weeklybld/doNewBranch.csh
  • lines changed 1, context: html, text, full: html, text
    06c77dae09aa4152ecd65ae128f222bba6e0695a Mon Jul 3 10:43:42 2017 -0700
    remove Matt email add Chris Lee and Jairo refs #19715
  • lines changed 1, context: html, text, full: html, text
    47a2243d25c47d9cf3ebba86d65a42075afed829 Mon Jul 3 13:32:14 2017 -0700
    remove donnak email and fix chmalee to ucsc.edu refs #19715
• src/utils/qa/weeklybld/doNewReview.csh
  • lines changed 1, context: html, text, full: html, text
    06c77dae09aa4152ecd65ae128f222bba6e0695a Mon Jul 3 10:43:42 2017 -0700
    remove Matt email add Chris Lee and Jairo refs #19715
  • lines changed 1, context: html, text, full: html, text
    47a2243d25c47d9cf3ebba86d65a42075afed829 Mon Jul 3 13:32:14 2017 -0700
    remove donnak email and fix chmalee to ucsc.edu refs #19715
• src/utils/qa/weeklybld/doNewReview2.csh
  • lines changed 1, context: html, text, full: html, text
    06c77dae09aa4152ecd65ae128f222bba6e0695a Mon Jul 3 10:43:42 2017 -0700
    remove Matt email add Chris Lee and Jairo refs #19715
  • lines changed 1, context: html, text, full: html, text
    47a2243d25c47d9cf3ebba86d65a42075afed829 Mon Jul 3 13:32:14 2017 -0700
    remove donnak email and fix chmalee to ucsc.edu refs #19715

• lines changed: 4960
• files changed: 116