All File Changes
v352_preview to v352_preview2 (2017-07-03 to 2017-07-10) v352
Show details
- 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