All File Changes

v324_preview2 to v324_base (2015-10-19 to 2015-10-26) v324

• src/hg/cirm/cdw/wrangle/addMetaDataToJson/makefile
  • lines changed 2, context: html, text, full: html, text
    Changing the makefile so it is not cluster dependent. Refs #16182
    
• src/hg/cirm/cdw/wrangle/addToStepTables/addToStepTables
  • lines changed 164, context: html, text, full: html, text
    This program is also known as maniMani, were using it on CIRM. refs #16113
    
• src/hg/cirm/cdw/wrangle/addToStepTables/makefile
  • lines changed 6, context: html, text, full: html, text
    This program is also known as maniMani, were using it on CIRM. refs #16113
    
  • lines changed 2, context: html, text, full: html, text
    Changing the makefile so it is not cluster dependent. Refs #16113
    
• src/hg/cirm/cdw/wrangle/condenseMatrix/condenseMatrix
  • lines changed 80, context: html, text, full: html, text
    Finishing this program up, refs #16182
    
• src/hg/cirm/cdw/wrangle/condenseMatrix/makefile
  • lines changed 2, context: html, text, full: html, text
    Changing the makefile so it is not cluster dependent. Refs #16182
    
• src/hg/cirm/cdw/wrangle/kallistoOnFastqMani/kallisto
  • lines changed 0, context: html, text, full: html, text
    Finishing the program kallistoOnFastqMani and adding some dependencies. Refs #16244
    
• src/hg/cirm/cdw/wrangle/kallistoOnFastqMani/kallistoOnFastqMani
  • lines changed 114, context: html, text, full: html, text
    Finishing the program kallistoOnFastqMani and adding some dependencies. Refs #16244
    
• src/hg/cirm/cdw/wrangle/kallistoOnFastqMani/makefile
  • lines changed 6, context: html, text, full: html, text
    Changing the makefile so it is not cluster dependent. Refs #16244
    
• src/hg/cirm/cdw/wrangle/kallistoOnFastqMani/runKallisto.sh
  • lines changed 56, context: html, text, full: html, text
    Finishing the program kallistoOnFastqMani and adding some dependencies. Refs #16244
    
• src/hg/cirm/cdw/wrangle/makeExpMatrix/makeExpMatrix
  • lines changed 47, context: html, text, full: html, text
    Finishing up this program, refs #16182
    
  • lines changed 5, context: html, text, full: html, text
    Finishing this program and adding it to the pipeline, refs #16244
    
• src/hg/cirm/cdw/wrangle/makeExpMatrix/makefile
  • lines changed 2, context: html, text, full: html, text
    Changing the makefile so it is not cluster dependent. Refs #16182
    
• src/hg/cirm/cdw/wrangle/makefile
  • lines changed 22, context: html, text, full: html, text
    Adding a makefile for the cirm wrangle directory. Incorporates python and C flawlessly using the new python framework! No ref for this, general CIRM thing.
    
• src/hg/cirm/cdw/wrangle/rnaSeqToClustersPipeline/makefile
  • lines changed 6, context: html, text, full: html, text
    The first version of this program. Relatively complete still, refs #16244
    
  • lines changed 2, context: html, text, full: html, text
    Adding a check to the argparse module that causes the program to spit help with no arguments. This replicates the C code style. Refs #16156
    
• src/hg/cirm/cdw/wrangle/rnaSeqToClustersPipeline/rnaSeqToClustersPipeline
  • lines changed 176, context: html, text, full: html, text
    The first version of this program. Relatively complete still, refs #16244
    
  • lines changed 78, context: html, text, full: html, text
    Finishing up the pipeline and making it a bit more universal, refs #16244
    
• src/hg/expMatrixToJson/expMatrixToJson.c
  • lines changed 248, context: html, text, full: html, text
    Removed a bunch of cruft, two useless files and added some documentation. Refs #16216
    
• src/hg/expMatrixToJson/forceLayout.json
  • lines changed 247, context: html, text, full: html, text
    Removed a bunch of cruft, two useless files and added some documentation. Refs #16216
    
• src/hg/expMatrixToJson/radialDend.html
  • lines changed 109, context: html, text, full: html, text
    Removed a bunch of cruft, two useless files and added some documentation. Refs #16216
    
• src/hg/hgGtexApi/hgGtexApi.c
  • lines changed 78, context: html, text, full: html, text
    Checking in graph exploratory work (JS D3) to save it (in a branch) before whacking. refs #15645
    
• src/hg/hgGtexApi/makefile
  • lines changed 14, context: html, text, full: html, text
    Checking in graph exploratory work (JS D3) to save it (in a branch) before whacking. refs #15645
    
• src/hg/hgTables/hgTables.c
  • lines changed 1, context: html, text, full: html, text
    didn't test my previous fix, stupid typo, should be OK now.
    refs #16158
    
• src/hg/hgTables/maf.c
  • lines changed 10, context: html, text, full: html, text
    more work on bigMaf. Works in hgc and hgTables now. #15935
    
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 4, context: html, text, full: html, text
    Add support for GTEX tissue color scheme. refs #15645
    
• src/hg/hgTracks/bigBedTrack.c
  • lines changed 17, context: html, text, full: html, text
    more work on bigMaf. Works in hgc and hgTables now. #15935
    
• src/hg/hgTracks/gtexTracks.c
  • lines changed 177, context: html, text, full: html, text
    First cut GTEX gene track display. refs #13504
    
  • lines changed 58, context: html, text, full: html, text
    Add alternate displays for different zoom levels. refs #13504
    
  • lines changed 51, context: html, text, full: html, text
    Add support for GTEX tissue color scheme. refs #15645
    
  • lines changed 91, context: html, text, full: html, text
    Mouseover improvements. refs #15645
    
  • lines changed 116, context: html, text, full: html, text
    Add squished gene model under expression graph (address concern of SAB and others re anchoring to genome. refs #15645
    
  • lines changed 41, context: html, text, full: html, text
    Better placement of map boxes for mouseover. refs #15645
    
  • lines changed 33, context: html, text, full: html, text
    Add faint gray line under graph to show extent when bars are missing. refs #15645
    
  • lines changed 33, context: html, text, full: html, text
    1. Fix pack problem. 2. Fix map box in dense/squish. refs #15645
    
  • lines changed 129, context: html, text, full: html, text
    Add support for comparison graphs (2 graphs, one top and one below inverted, based on splitting samples by sex or age). First cut of display only. refs #15645
    
  • lines changed 43, context: html, text, full: html, text
    Scale wrt all genes, not just those in window. We now save the max tissue median score in the gtexInfo table. refs #15645
    
  • lines changed 2, context: html, text, full: html, text
    Allow comparison graphs when zoomed out (suppress only when this requires querying the sample db which would be too slow). refs #15645
    
  • lines changed 51, context: html, text, full: html, text
    1. Fix tissue ordering problem (hgGtex). 2. Add stats table (rename gtexTissueData to gtexTissueMedian and use gtexTissueData for stats. 3. Extend gtexInfo table.refs #15645
    
  • lines changed 40, context: html, text, full: html, text
    Fix a few bugs - connection handling, bin field in genePred, more color handling - introduced while messing with schemas (to extend features and improve perf). refs #15645
    
  • lines changed 181, context: html, text, full: html, text
    Major reorg of track load/draw, prep for computing medians (for filtering and comparison graphs. refs #15645
    
  • lines changed 36, context: html, text, full: html, text
    More prep moved to loader. Fix mapping problem in squish mode. refs #15645
    
  • lines changed 106, context: html, text, full: html, text
    Implement medians computed on sub-samples (initially for M/F comparison. refs #15645
    
  • lines changed 74, context: html, text, full: html, text
    Add labels (e.g. M/F) to comparison graphs. refs #15645
    
  • lines changed 190, context: html, text, full: html, text
    Ifdef'ed in Galt's support for multi-region display, so continuing development can consider it. refs #15645
    
  • lines changed 29, context: html, text, full: html, text
    Add log transform option to display config. refs #15645
    
  • lines changed 4, context: html, text, full: html, text
    Cleanup trackUi in prep for merging into main. refs #15645
    
  • lines changed 404, context: html, text, full: html, text
    Code cleanup, in preparation for branch merge. refs #15645
    
  • lines changed 146, context: html, text, full: html, text
    Add map box to comparison graph. Code cleanup. refs #15645
    
  • lines changed 43, context: html, text, full: html, text
    Improve display for non-log transformed by adding max view limit. refs #15645
    
  • lines changed 47, context: html, text, full: html, text
    Fix map boxes on non-log display. refs #15645
    
• src/hg/hgTracks/hgTracks.c
  • lines changed 10, context: html, text, full: html, text
    GTEX track display: Add hgc to show tissue color table. Add debug statements for hgTracks. Also doc. This is version demoed at SAB. refs #13504
    
  • lines changed 3, context: html, text, full: html, text
    Minor cleanup
    
  • lines changed 3, context: html, text, full: html, text
    Resolving merge
    
• src/hg/hgTracks/hgTracks.h
  • lines changed 3, context: html, text, full: html, text
    Some initial display work for GTEX gene expression track. refs #13504
    
  • lines changed 7, context: html, text, full: html, text
    more work on bigMaf. Works in hgc and hgTables now. #15935
    
• src/hg/hgTracks/imageV2.c
  • lines changed 2, context: html, text, full: html, text
    Label fix. Clarify imageV2 warning. refs #15645
    
• src/hg/hgTracks/makefile
  • lines changed 2, context: html, text, full: html, text
    Some initial display work for GTEX gene expression track. refs #13504
    
  • lines changed 4, context: html, text, full: html, text
    Conflict resolution
    
• src/hg/hgTracks/simpleTracks.c
  • lines changed 3, context: html, text, full: html, text
    Some initial display work for GTEX gene expression track. refs #13504
    
  • lines changed 1, context: html, text, full: html, text
    more work on bigMaf. Works in hgc and hgTables now. #15935
    
  • lines changed 11, context: html, text, full: html, text
    Adding colorblindness-friendly colors for upcoming release of new ORegAnno data, refs #15957
    
  • lines changed 3, context: html, text, full: html, text
    Fixed logic bug with oreganno filters, also made case-insensitive, refs #16257, #15957
    
• src/hg/hgTracks/wigMafTrack.c
  • lines changed 35, context: html, text, full: html, text
    more work on bigMaf. Works in hgc and hgTables now. #15935
    
  • lines changed 148, context: html, text, full: html, text
    get frames to work with bigMaf #15935
    
• src/hg/hgc/gtex/geneBoxplot.R
  • lines changed 31, context: html, text, full: html, text
    Initial code for R-based graph on GTEx details page. refs #15645
    
  • lines changed 35, context: html, text, full: html, text
    Add X axis labels, rotated 45 degrees. Adjust colors, line styles,e tc. refs #15645
    
  • lines changed 29, context: html, text, full: html, text
    Scale graph limits and place X axis labels appropriately for variously ranged graphs, and log transformed data. refs #15645
    
  • lines changed 11, context: html, text, full: html, text
    Colors and labels now reordered propertly. refs #15645
    
  • lines changed 2, context: html, text, full: html, text
    Fix label ordering. This is final check-in before ripping out alternate implementations (JS and C). Will keep this in a branch. refs #15645
    
  • lines changed 74, context: html, text, full: html, text
    Code cleanup in preparation for mergingin into main. refs #15645
    
• src/hg/hgc/gtex/tissueColors.R
  • lines changed 58, context: html, text, full: html, text
    Checking in graph exploratory work (JS D3) to save it (in a branch) before whacking. refs #15645
    
  • lines changed 58, context: html, text, full: html, text
    Code cleanup in preparation for mergingin into main. refs #15645
    
• src/hg/hgc/gtexClick.c
  • lines changed 88, context: html, text, full: html, text
    Move GTEx track details into separate file. refs #13504
    
  • lines changed 229, context: html, text, full: html, text
    First cut gene expression boxplot image for GTEx details page. refs #15645
    
  • lines changed 24, context: html, text, full: html, text
    1. Graph aesthetics (colors, etc.). 2. Change ordering to median descending. refs #15645
    
  • lines changed 34, context: html, text, full: html, text
    A stab at adding axes and title to graph for GTEx details page. refs #15645
    
  • lines changed 49, context: html, text, full: html, text
    Preliminary work to add tick marks and sanity check Y axis label (max value) on GTEx expression graph. refs #15645
    
  • lines changed 252, context: html, text, full: html, text
    Exploratory use of D3 JS for boxplot on GTEX gene track details page. refs #15645
    
  • lines changed 47, context: html, text, full: html, text
    Initial code for R-based graph on GTEx details page. refs #15645
    
  • lines changed 7, context: html, text, full: html, text
    Add X axis labels, rotated 45 degrees. Adjust colors, line styles,e tc. refs #15645
    
  • lines changed 7, context: html, text, full: html, text
    Scale graph limits and place X axis labels appropriately for variously ranged graphs, and log transformed data. refs #15645
    
  • lines changed 6, context: html, text, full: html, text
    Make R graphics default. refs #15645
    
  • lines changed 218, context: html, text, full: html, text
    Code cleanup in preparation for mergingin into main. refs #15645
    
• src/hg/hgc/hgc.c
  • lines changed 75, context: html, text, full: html, text
    GTEX track display: Add hgc to show tissue color table. Add debug statements for hgTracks. Also doc. This is version demoed at SAB. refs #13504
    
  • lines changed 5, context: html, text, full: html, text
    Conflict resolution
    
  • lines changed 18, context: html, text, full: html, text
    Minor work on GTEX details during meeting (much more needed). refs #13504
    
  • lines changed 87, context: html, text, full: html, text
    Merge branch 'master' into gtex
    
  • lines changed 77, context: html, text, full: html, text
    Move GTEx track details into separate file. refs #13504
    
  • lines changed 2, context: html, text, full: html, text
    more work on bigMaf. Works in hgc and hgTables now. #15935
    
• src/hg/hgc/hgc.h
  • lines changed 3, context: html, text, full: html, text
    GTEX track display: Add hgc to show tissue color table. Add debug statements for hgTracks. Also doc. This is version demoed at SAB. refs #13504
    
• src/hg/hgc/hgcData/gtexBoxplot.R
  • lines changed 72, context: html, text, full: html, text
    Code cleanup in preparation for mergingin into main. refs #15645
    
• src/hg/hgc/hgcData/gtexColorsV4.R
  • lines changed 58, context: html, text, full: html, text
    Code cleanup in preparation for mergingin into main. refs #15645
    
• src/hg/hgc/mafClick.c
  • lines changed 13, context: html, text, full: html, text
    more work on bigMaf. Works in hgc and hgTables now. #15935
    
• src/hg/hgc/makefile
  • lines changed 1, context: html, text, full: html, text
    Move GTEx track details into separate file. refs #13504
    
  • lines changed 9, context: html, text, full: html, text
    Checking in graph exploratory work (JS D3) to save it (in a branch) before whacking. refs #15645
    
  • lines changed 9, context: html, text, full: html, text
    Code cleanup in preparation for mergingin into main. refs #15645
    
• src/hg/htdocs/indexNews.html
  • lines changed 11, context: html, text, full: html, text
    Adding a temporary note to indexNews about Custom Tracks server issue
    
  • lines changed 11, context: html, text, full: html, text
    Removing temporary note about Custom Track Service from indexNews
    
• src/hg/htdocs/training/index.html
  • lines changed 6, context: html, text, full: html, text
    added city of hope workshop
    
• src/hg/inc/gtexInfo.h
  • lines changed 71, context: html, text, full: html, text
    Scale wrt all genes, not just those in window. We now save the max tissue median score in the gtexInfo table. refs #15645
    
  • lines changed 23, context: html, text, full: html, text
    1. Fix tissue ordering problem (hgGtex). 2. Add stats table (rename gtexTissueData to gtexTissueMedian and use gtexTissueData for stats. 3. Extend gtexInfo table.refs #15645
    
• src/hg/inc/gtexSample.h
  • lines changed 17, context: html, text, full: html, text
    Expand GTEx sample table. Now includes all fields except RNA-seqC metrics, which if we decide to include them, will likley be in an auxiliary table. refs #13504
    
• src/hg/inc/gtexTissue.h
  • lines changed 5, context: html, text, full: html, text
    Get new GTEX data and the color scheme, from GTEX portal. Follow-up from 2015 GTEX meeting. refs #13504
    
  • lines changed 15, context: html, text, full: html, text
    Add support for GTEX tissue color scheme. refs #15645
    
  • lines changed 3, context: html, text, full: html, text
    Restore a bit of lost code.
    
  • lines changed 7, context: html, text, full: html, text
    Fix a few bugs - connection handling, bin field in genePred, more color handling - introduced while messing with schemas (to extend features and improve perf). refs #15645
    
• src/hg/inc/gtexTissueData.h
  • lines changed 30, context: html, text, full: html, text
    1. Fix tissue ordering problem (hgGtex). 2. Add stats table (rename gtexTissueData to gtexTissueMedian and use gtexTissueData for stats. 3. Extend gtexInfo table.refs #15645
    
• src/hg/inc/gtexTissueMedian.h
  • lines changed 64, context: html, text, full: html, text
    1. Fix tissue ordering problem (hgGtex). 2. Add stats table (rename gtexTissueData to gtexTissueMedian and use gtexTissueData for stats. 3. Extend gtexInfo table.refs #15645
    
• src/hg/inc/gtexUi.h
  • lines changed 19, context: html, text, full: html, text
    Add support for GTEX tissue color scheme. refs #15645
    
  • lines changed 15, context: html, text, full: html, text
    Add support for comparison graphs (2 graphs, one top and one below inverted, based on splitting samples by sex or age). First cut of display only. refs #15645
    
  • lines changed 4, context: html, text, full: html, text
    Add log transform option to display config. refs #15645
    
  • lines changed 28, context: html, text, full: html, text
    Cleanup trackUi in prep for merging into main. refs #15645
    
  • lines changed 2, context: html, text, full: html, text
    Improve display for non-log transformed by adding max view limit. refs #15645
    
  • lines changed 1, context: html, text, full: html, text
    Fix map boxes on non-log display. refs #15645
    
• src/hg/inc/hgMaf.h
  • lines changed 4, context: html, text, full: html, text
    more work on bigMaf. Works in hgc and hgTables now. #15935
    
• src/hg/inc/hui.h
  • lines changed 3, context: html, text, full: html, text
    Add support for GTEX tissue color scheme. refs #15645
    
• src/hg/inc/trackDb.h
  • lines changed 1, context: html, text, full: html, text
    more work on bigMaf. Works in hgc and hgTables now. #15935
    
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v324
    
• src/hg/js/d3.min.js
  • lines changed 5, context: html, text, full: html, text
    Checking in graph exploratory work (JS D3) to save it (in a branch) before whacking. refs #15645
    
  • lines changed 5, context: html, text, full: html, text
    Code cleanup in preparation for mergingin into main. refs #15645
    
• src/hg/js/d3plus.gtex.js
  • lines changed 33973, context: html, text, full: html, text
    Checking in graph exploratory work (JS D3) to save it (in a branch) before whacking. refs #15645
    
  • lines changed 33973, context: html, text, full: html, text
    Code cleanup in preparation for mergingin into main. refs #15645
    
• src/hg/js/gtex.js
  • lines changed 18, context: html, text, full: html, text
    Checking in graph exploratory work (JS D3) to save it (in a branch) before whacking. refs #15645
    
  • lines changed 18, context: html, text, full: html, text
    Code cleanup in preparation for mergingin into main. refs #15645
    
• src/hg/js/makefile
  • lines changed 4, context: html, text, full: html, text
    Exploratory use of D3 JS for boxplot on GTEX gene track details page. refs #15645
    
  • lines changed 2, context: html, text, full: html, text
    Code cleanup in preparation for mergingin into main. refs #15645
    
  • lines changed 2, context: html, text, full: html, text
    Backing out JS details page for GTEx
    
• src/hg/lib/bed6FloatVal.as
  • lines changed 12, context: html, text, full: html, text
    Schemas for GTEX exon and gene tracks. Likely interim. refs #15648
    
• src/hg/lib/bed6FloatVal.sql
  • lines changed 20, context: html, text, full: html, text
    Schemas for GTEX exon and gene tracks. Likely interim. refs #15648
    
• src/hg/lib/gtexGeneBed.sql
  • lines changed 21, context: html, text, full: html, text
    Schemas for GTEX exon and gene tracks. Likely interim. refs #15648
    
• src/hg/lib/gtexInfo.as
  • lines changed 7, context: html, text, full: html, text
    Scale wrt all genes, not just those in window. We now save the max tissue median score in the gtexInfo table. refs #15645
    
  • lines changed 1, context: html, text, full: html, text
    1. Fix tissue ordering problem (hgGtex). 2. Add stats table (rename gtexTissueData to gtexTissueMedian and use gtexTissueData for stats. 3. Extend gtexInfo table.refs #15645
    
• src/hg/lib/gtexInfo.c
  • lines changed 162, context: html, text, full: html, text
    Scale wrt all genes, not just those in window. We now save the max tissue median score in the gtexInfo table. refs #15645
    
  • lines changed 49, context: html, text, full: html, text
    1. Fix tissue ordering problem (hgGtex). 2. Add stats table (rename gtexTissueData to gtexTissueMedian and use gtexTissueData for stats. 3. Extend gtexInfo table.refs #15645
    
  • lines changed 3, context: html, text, full: html, text
    Fix a few bugs - connection handling, bin field in genePred, more color handling - introduced while messing with schemas (to extend features and improve perf). refs #15645
    
• src/hg/lib/gtexInfo.sql
  • lines changed 13, context: html, text, full: html, text
    Scale wrt all genes, not just those in window. We now save the max tissue median score in the gtexInfo table. refs #15645
    
  • lines changed 1, context: html, text, full: html, text
    1. Fix tissue ordering problem (hgGtex). 2. Add stats table (rename gtexTissueData to gtexTissueMedian and use gtexTissueData for stats. 3. Extend gtexInfo table.refs #15645
    
• src/hg/lib/gtexSample.as
  • lines changed 11, context: html, text, full: html, text
    Expand GTEx sample table. Now includes all fields except RNA-seqC metrics, which if we decide to include them, will likley be in an auxiliary table. refs #13504
    
• src/hg/lib/gtexSample.c
  • lines changed 77, context: html, text, full: html, text
    Expand GTEx sample table. Now includes all fields except RNA-seqC metrics, which if we decide to include them, will likley be in an auxiliary table. refs #13504
    
• src/hg/lib/gtexSample.sql
  • lines changed 12, context: html, text, full: html, text
    Expand GTEx sample table. Now includes all fields except RNA-seqC metrics, which if we decide to include them, will likley be in an auxiliary table. refs #13504
    
• src/hg/lib/gtexSampleData.sql
  • lines changed 2, context: html, text, full: html, text
    1. Fix tissue ordering problem (hgGtex). 2. Add stats table (rename gtexTissueData to gtexTissueMedian and use gtexTissueData for stats. 3. Extend gtexInfo table.refs #15645
    
• src/hg/lib/gtexTissue.as
  • lines changed 1, context: html, text, full: html, text
    Get new GTEX data and the color scheme, from GTEX portal. Follow-up from 2015 GTEX meeting. refs #13504
    
• src/hg/lib/gtexTissue.c
  • lines changed 24, context: html, text, full: html, text
    Get new GTEX data and the color scheme, from GTEX portal. Follow-up from 2015 GTEX meeting. refs #13504
    
  • lines changed 36, context: html, text, full: html, text
    Add support for GTEX tissue color scheme. refs #15645
    
  • lines changed 18, context: html, text, full: html, text
    Restore a bit of lost code.
    
  • lines changed 19, context: html, text, full: html, text
    Fix a few bugs - connection handling, bin field in genePred, more color handling - introduced while messing with schemas (to extend features and improve perf). refs #15645
    
• src/hg/lib/gtexTissue.sql
  • lines changed 1, context: html, text, full: html, text
    Get new GTEX data and the color scheme, from GTEX portal. Follow-up from 2015 GTEX meeting. refs #13504
    
• src/hg/lib/gtexTissueData.as
  • lines changed 7, context: html, text, full: html, text
    1. Fix tissue ordering problem (hgGtex). 2. Add stats table (rename gtexTissueData to gtexTissueMedian and use gtexTissueData for stats. 3. Extend gtexInfo table.refs #15645
    
• src/hg/lib/gtexTissueData.c
  • lines changed 102, context: html, text, full: html, text
    1. Fix tissue ordering problem (hgGtex). 2. Add stats table (rename gtexTissueData to gtexTissueMedian and use gtexTissueData for stats. 3. Extend gtexInfo table.refs #15645
    
• src/hg/lib/gtexTissueData.sql
  • lines changed 9, context: html, text, full: html, text
    1. Fix tissue ordering problem (hgGtex). 2. Add stats table (rename gtexTissueData to gtexTissueMedian and use gtexTissueData for stats. 3. Extend gtexInfo table.refs #15645
    
• src/hg/lib/gtexTissueMedian.as
  • lines changed 7, context: html, text, full: html, text
    1. Fix tissue ordering problem (hgGtex). 2. Add stats table (rename gtexTissueData to gtexTissueMedian and use gtexTissueData for stats. 3. Extend gtexInfo table.refs #15645
    
• src/hg/lib/gtexTissueMedian.c
  • lines changed 158, context: html, text, full: html, text
    1. Fix tissue ordering problem (hgGtex). 2. Add stats table (rename gtexTissueData to gtexTissueMedian and use gtexTissueData for stats. 3. Extend gtexInfo table.refs #15645
    
• src/hg/lib/gtexTissueMedian.sql
  • lines changed 13, context: html, text, full: html, text
    1. Fix tissue ordering problem (hgGtex). 2. Add stats table (rename gtexTissueData to gtexTissueMedian and use gtexTissueData for stats. 3. Extend gtexInfo table.refs #15645
    
• src/hg/lib/gtexUi.c
  • lines changed 56, context: html, text, full: html, text
    Cleanup trackUi in prep for merging into main. refs #15645
    
  • lines changed 2, context: html, text, full: html, text
    Improve display for non-log transformed by adding max view limit. refs #15645
    
• src/hg/lib/hdb.c
  • lines changed 2, context: html, text, full: html, text
    more work on bigMaf. Works in hgc and hgTables now. #15935
    
• src/hg/lib/hgMaf.c
  • lines changed 20, context: html, text, full: html, text
    more work on bigMaf. Works in hgc and hgTables now. #15935
    
• src/hg/lib/hui.c
  • lines changed 20, context: html, text, full: html, text
    Mouseover display of tissues now works a bit better. Still fragile & messy (don't bother reviewing this commit). refs #15645
    
  • lines changed 34, context: html, text, full: html, text
    Add support for comparison graphs (2 graphs, one top and one below inverted, based on splitting samples by sex or age). First cut of display only. refs #15645
    
  • lines changed 10, context: html, text, full: html, text
    Add log transform option to display config. refs #15645
    
  • lines changed 59, context: html, text, full: html, text
    Cleanup trackUi in prep for merging into main. refs #15645
    
• src/hg/lib/makefile
  • lines changed 2, context: html, text, full: html, text
    Scale wrt all genes, not just those in window. We now save the max tissue median score in the gtexInfo table. refs #15645
    
  • lines changed 1, context: html, text, full: html, text
    1. Fix tissue ordering problem (hgGtex). 2. Add stats table (rename gtexTissueData to gtexTissueMedian and use gtexTissueData for stats. 3. Extend gtexInfo table.refs #15645
    
  • lines changed 1, context: html, text, full: html, text
    Cleanup trackUi in prep for merging into main. refs #15645
    
• src/hg/lib/oregannoUi.c
  • lines changed 9, context: html, text, full: html, text
    Adding support for two additional regulatory classes, refs #15957
    
• src/hg/lib/trackDbCustom.c
  • lines changed 2, context: html, text, full: html, text
    more work on bigMaf. Works in hgc and hgTables now. #15935
    
• src/hg/lib/trackHub.c
  • lines changed 19, context: html, text, full: html, text
    get frames to work with bigMaf #15935
    
• src/hg/lib/web.c
  • lines changed 1, context: html, text, full: html, text
    Adding base tag to CGI output, refs #16124
    
• src/hg/makeDb/doc/gtex/2014-jan.txt
  • lines changed 6, context: html, text, full: html, text
    GTEX track display: Add hgc to show tissue color table. Add debug statements for hgTracks. Also doc. This is version demoed at SAB. refs #13504
    
  • lines changed 9, context: html, text, full: html, text
    Download recent eQTL data. refs #13504
    
  • lines changed 3, context: html, text, full: html, text
    Get new GTEX data and the color scheme, from GTEX portal. Follow-up from 2015 GTEX meeting. refs #13504
    
  • lines changed 9, context: html, text, full: html, text
    Mouseover display of tissues now works a bit better. Still fragile & messy (don't bother reviewing this commit). refs #15645
    
  • lines changed 21, context: html, text, full: html, text
    Loaded gene models from GTEX portal. refs #15645
    
  • lines changed 14, context: html, text, full: html, text
    Scale wrt all genes, not just those in window. We now save the max tissue median score in the gtexInfo table. refs #15645
    
  • lines changed 3, context: html, text, full: html, text
    1. Fix tissue ordering problem (hgGtex). 2. Add stats table (rename gtexTissueData to gtexTissueMedian and use gtexTissueData for stats. 3. Extend gtexInfo table.refs #15645
    
  • lines changed 52, context: html, text, full: html, text
    Create build tool and build tracks of GTEX exon expression. refs #15648
    
  • lines changed 50, context: html, text, full: html, text
    Fix chrM entries in exon files. refs #15648
    
  • lines changed 49, context: html, text, full: html, text
    Resolving conflict
    
  • lines changed 19, context: html, text, full: html, text
    Expand GTEx sample table. Now includes all fields except RNA-seqC metrics, which if we decide to include them, will likley be in an auxiliary table. refs #13504
    
  • lines changed 61, context: html, text, full: html, text
    1. Add eQTL and variants tracks. 2. Modify loader to exclude expression table rows with zero-valued scores (shrinks table by half). 3. Prep a data frame for R (make a few plots to explore the data). refs #1350
    
  • lines changed 9, context: html, text, full: html, text
    Reload tissue median table to fix ordering problem in exp list. refs #15645
    
  • lines changed 15, context: html, text, full: html, text
    Fix label ordering. This is final check-in before ripping out alternate implementations (JS and C). Will keep this in a branch. refs #15645
    
• src/hg/makeDb/doc/hg19.txt
  • lines changed 37, context: html, text, full: html, text
    GTEX track display: Add hgc to show tissue color table. Add debug statements for hgTracks. Also doc. This is version demoed at SAB. refs #13504
    
  • lines changed 122, context: html, text, full: html, text
    Conflict resolution
    
  • lines changed 4, context: html, text, full: html, text
    1. Fix tissue ordering problem (hgGtex). 2. Add stats table (rename gtexTissueData to gtexTissueMedian and use gtexTissueData for stats. 3. Extend gtexInfo table.refs #15645
    
  • lines changed 48, context: html, text, full: html, text
    Fix chrM entries in exon files. refs #15648
    
  • lines changed 1, context: html, text, full: html, text
    Reload tissue median table to fix ordering problem in exp list. refs #15645
    
  • lines changed 8, context: html, text, full: html, text
    Reloaded 1000 Genomes Phase 3 Variants with updated VCF's and added description pages for variants and Phase 3 Accessible Regions.
    
• src/hg/makeDb/hgLoadSeq/hgLoadSeq.c
  • lines changed 11, context: html, text, full: html, text
    fixing a bug that causes the extTbl and seq tables to get out of sync, refs #16034
    
• src/hg/makeDb/outside/hgGtex/hgGtex.c
  • lines changed 37, context: html, text, full: html, text
    Scale wrt all genes, not just those in window. We now save the max tissue median score in the gtexInfo table. refs #15645
    
  • lines changed 80, context: html, text, full: html, text
    1. Fix tissue ordering problem (hgGtex). 2. Add stats table (rename gtexTissueData to gtexTissueMedian and use gtexTissueData for stats. 3. Extend gtexInfo table.refs #15645
    
  • lines changed 68, context: html, text, full: html, text
    Create build tool and build tracks of GTEX exon expression. refs #15648
    
  • lines changed 60, context: html, text, full: html, text
    Expand GTEx sample table. Now includes all fields except RNA-seqC metrics, which if we decide to include them, will likley be in an auxiliary table. refs #13504
    
  • lines changed 11, context: html, text, full: html, text
    1. Add eQTL and variants tracks. 2. Modify loader to exclude expression table rows with zero-valued scores (shrinks table by half). 3. Prep a data frame for R (make a few plots to explore the data). refs #1350
    
• src/hg/makeDb/outside/hgGtexExonBed/hgGtexExonBed.c
  • lines changed 199, context: html, text, full: html, text
    Create build tool and build tracks of GTEX exon expression. refs #15648
    
• src/hg/makeDb/outside/hgGtexExonBed/makefile
  • lines changed 4, context: html, text, full: html, text
    Create build tool and build tracks of GTEX exon expression. refs #15648
    
• src/hg/makeDb/outside/hgGtexGeneBed/hgGtexGeneBed.c
  • lines changed 2, context: html, text, full: html, text
    Fix options syntax
    
  • lines changed 9, context: html, text, full: html, text
    1. Fix tissue ordering problem (hgGtex). 2. Add stats table (rename gtexTissueData to gtexTissueMedian and use gtexTissueData for stats. 3. Extend gtexInfo table.refs #15645
    
• src/hg/makeDb/outside/makefile
  • lines changed 2, context: html, text, full: html, text
    Create build tool and build tracks of GTEX exon expression. refs #15648
    
• src/hg/makeDb/trackDb/drosophila/dm2/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    trackDb changes to support new regulatory categories in updated oreganno tracks while preserving documentation for old tracks refs #15957
    
  • lines changed 1, context: html, text, full: html, text
    Adjusting oreganno trackDb settings - no tracks will be left on the old version after release of the new version. refs #15957
    
• src/hg/makeDb/trackDb/drosophila/dm3/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    trackDb changes to support new regulatory categories in updated oreganno tracks while preserving documentation for old tracks refs #15957
    
  • lines changed 1, context: html, text, full: html, text
    Adjusting oreganno trackDb settings - no tracks will be left on the old version after release of the new version. refs #15957
    
• src/hg/makeDb/trackDb/gorilla/gorGor4/description.html
  • lines changed 63, context: html, text, full: html, text
    Adding gorGor4 assembly, refs #16220
    
• src/hg/makeDb/trackDb/gorilla/gorGor4/gap.html
  • lines changed 31, context: html, text, full: html, text
    Adding gorGor4 assembly, refs #16220
    
• src/hg/makeDb/trackDb/gorilla/gorGor4/gold.html
  • lines changed 33, context: html, text, full: html, text
    Adding gorGor4 assembly, refs #16220
    
• src/hg/makeDb/trackDb/gorilla/gorGor4/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    Adding gorGor4 assembly, refs #16220
    
• src/hg/makeDb/trackDb/human/gtexGeneExpr.html
  • lines changed 34, context: html, text, full: html, text
    Label fix. Clarify imageV2 warning. refs #15645
    
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    trackDb changes to support new regulatory categories in updated oreganno tracks while preserving documentation for old tracks refs #15957
    
  • lines changed 1, context: html, text, full: html, text
    Adjusting oreganno trackDb settings - no tracks will be left on the old version after release of the new version. refs #15957
    
• src/hg/makeDb/trackDb/human/hg19/tgpPhase3.html
  • lines changed 102, context: html, text, full: html, text
    Reloaded 1000 Genomes Phase 3 Variants with updated VCF's and added description pages for variants and Phase 3 Accessible Regions.
    
• src/hg/makeDb/trackDb/human/hg19/tgpPhase3Accessibility.html
  • lines changed 88, context: html, text, full: html, text
    Reloaded 1000 Genomes Phase 3 Variants with updated VCF's and added description pages for variants and Phase 3 Accessible Regions.
    
  • lines changed 12, context: html, text, full: html, text
    Updates to credits for 1000 Genomes Phase 3 Accessible Regions.
    
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    trackDb changes to support new regulatory categories in updated oreganno tracks while preserving documentation for old tracks refs #15957
    
• src/hg/makeDb/trackDb/human/hg38/trackDb.100way.ra
  • lines changed 2, context: html, text, full: html, text
    making an effort to standardize the naming of the Conservation tracks (at least for hg38). Trying to standardize on: Cons NNN [Primate|Vert|-way] etc.
    
• src/hg/makeDb/trackDb/human/hg38/trackDb.17way.ra
  • lines changed 3, context: html, text, full: html, text
    making an effort to standardize the naming of the Conservation tracks (at least for hg38). Trying to standardize on: Cons NNN [Primate|Vert|-way] etc.
    
• src/hg/makeDb/trackDb/human/hg38/trackDb.20way.ra
  • lines changed 3, context: html, text, full: html, text
    making an effort to standardize the naming of the Conservation tracks (at least for hg38). Trying to standardize on: Cons NNN [Primate|Vert|-way] etc.
    
• src/hg/makeDb/trackDb/human/hg38/trackDb.7way.ra
  • lines changed 3, context: html, text, full: html, text
    making an effort to standardize the naming of the Conservation tracks (at least for hg38). Trying to standardize on: Cons NNN [Primate|Vert|-way] etc.
    
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Forgot the 4-way. Still making an effort to standardize the naming of the Conservation tracks (at least for hg38). Trying to standardize on: Cons NNN [Primate|Vert|-way] etc.
    
• src/hg/makeDb/trackDb/human/trackDb.gtex.ra
  • lines changed 495, context: html, text, full: html, text
    Create build tool and build tracks of GTEX exon expression. refs #15648
    
  • lines changed 54, context: html, text, full: html, text
    Tweak labels. refs #15645
    
  • lines changed 2, context: html, text, full: html, text
    Correct donor count. Just use donors in sample table. refs #13504
    
  • lines changed 16, context: html, text, full: html, text
    1. Add eQTL and variants tracks. 2. Modify loader to exclude expression table rows with zero-valued scores (shrinks table by half). 3. Prep a data frame for R (make a few plots to explore the data). refs #1350
    
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 6, context: html, text, full: html, text
    Some initial display work for GTEX gene expression track. refs #13504
    
  • lines changed 2, context: html, text, full: html, text
    GTEX track display: Add hgc to show tissue color table. Add debug statements for hgTracks. Also doc. This is version demoed at SAB. refs #13504
    
  • lines changed 2, context: html, text, full: html, text
    Correct sample and tissue counts in track label. refs #13504
    
  • lines changed 1, context: html, text, full: html, text
    Label fix. Clarify imageV2 warning. refs #15645
    
  • lines changed 16, context: html, text, full: html, text
    Create build tool and build tracks of GTEX exon expression. refs #15648
    
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    Adding gorGor4 assembly, refs #16220
    
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
  • lines changed 4, context: html, text, full: html, text
    trackDb changes to support new regulatory categories in updated oreganno tracks while preserving documentation for old tracks refs #15957
    
• src/hg/makeDb/trackDb/oreganno.html
  • lines changed 5, context: html, text, full: html, text
    trackDb changes to support new regulatory categories in updated oreganno tracks while preserving documentation for old tracks refs #15957
    
• src/hg/makeDb/trackDb/oregannoOld.html
  • lines changed 102, context: html, text, full: html, text
    trackDb changes to support new regulatory categories in updated oreganno tracks while preserving documentation for old tracks refs #15957
    
• src/hg/makeDb/trackDb/sacCer/sacCer1/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    trackDb changes to support new regulatory categories in updated oreganno tracks while preserving documentation for old tracks refs #15957
    
  • lines changed 1, context: html, text, full: html, text
    Adjusting oreganno trackDb settings - no tracks will be left on the old version after release of the new version. refs #15957
    
• src/hg/makeDb/trackDb/sacCer/sacCer2/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    trackDb changes to support new regulatory categories in updated oreganno tracks while preserving documentation for old tracks refs #15957
    
  • lines changed 1, context: html, text, full: html, text
    Adjusting oreganno trackDb settings - no tracks will be left on the old version after release of the new version. refs #15957
    
• src/hg/utils/automation/genbank/agpNameTranslate.pl
  • lines changed 41, context: html, text, full: html, text
    now running up all tracks for both NCBI and UCSC naming schemes and with indexes on assembly and gene tracks refs #16078
    
• src/hg/utils/automation/genbank/agpToBbi.sh
  • lines changed 14, context: html, text, full: html, text
    now running up all tracks for both NCBI and UCSC naming schemes and with indexes on assembly and gene tracks refs #16078
    
• src/hg/utils/automation/genbank/alternatesAgp.pl
  • lines changed 3, context: html, text, full: html, text
    now running up all tracks for both NCBI and UCSC naming schemes and with indexes on assembly and gene tracks refs #16078
    
• src/hg/utils/automation/genbank/assemblyDescription.pl
  • lines changed 6, context: html, text, full: html, text
    now running up all tracks for both NCBI and UCSC naming schemes and with indexes on assembly and gene tracks refs #16078
    
• src/hg/utils/automation/genbank/compositeAgp.pl
  • lines changed 8, context: html, text, full: html, text
    now running up all tracks for both NCBI and UCSC naming schemes and with indexes on assembly and gene tracks refs #16078
    
• src/hg/utils/automation/genbank/compositeFasta.pl
  • lines changed 6, context: html, text, full: html, text
    now running up all tracks for both NCBI and UCSC naming schemes and with indexes on assembly and gene tracks refs #16078
    
• src/hg/utils/automation/genbank/gapDescription.pl
  • lines changed 2, context: html, text, full: html, text
    now running up all tracks for both NCBI and UCSC naming schemes and with indexes on assembly and gene tracks refs #16078
    
• src/hg/utils/automation/genbank/gc5Description.pl
  • lines changed 2, context: html, text, full: html, text
    now running up all tracks for both NCBI and UCSC naming schemes and with indexes on assembly and gene tracks refs #16078
    
• src/hg/utils/automation/genbank/gpToIx.pl
  • lines changed 14, context: html, text, full: html, text
    now running up all tracks for both NCBI and UCSC naming schemes and with indexes on assembly and gene tracks refs #16078
    
• src/hg/utils/automation/genbank/nameToIx.pl
  • lines changed 33, context: html, text, full: html, text
    now running up all tracks for both NCBI and UCSC naming schemes and with indexes on assembly and gene tracks refs #16078
    
• src/hg/utils/automation/genbank/ncbiGene.sh
  • lines changed 53, context: html, text, full: html, text
    now running up all tracks for both NCBI and UCSC naming schemes and with indexes on assembly and gene tracks refs #16078
    
• src/hg/utils/automation/genbank/ncbiGeneDescription.pl
  • lines changed 2, context: html, text, full: html, text
    now running up all tracks for both NCBI and UCSC naming schemes and with indexes on assembly and gene tracks refs #16078
    
• src/hg/utils/automation/genbank/ncbiToUcsc.sh
  • lines changed 185, context: html, text, full: html, text
    now running up all tracks for both NCBI and UCSC naming schemes and with indexes on assembly and gene tracks refs #16078
    
• src/hg/utils/automation/genbank/rmsk.sh
  • lines changed 38, context: html, text, full: html, text
    now running up all tracks for both NCBI and UCSC naming schemes and with indexes on assembly and gene tracks refs #16078
    
• src/hg/utils/automation/genbank/trackDb.sh
  • lines changed 71, context: html, text, full: html, text
    now running up all tracks for both NCBI and UCSC naming schemes and with indexes on assembly and gene tracks refs #16078
    
• src/hg/utils/automation/genbank/ucscAltNames.sh
  • lines changed 20, context: html, text, full: html, text
    now running up all tracks for both NCBI and UCSC naming schemes and with indexes on assembly and gene tracks refs #16078
    
• src/hg/utils/automation/genbank/ucscPatchAltsFa.sh
  • lines changed 61, context: html, text, full: html, text
    now running up all tracks for both NCBI and UCSC naming schemes and with indexes on assembly and gene tracks refs #16078
    
• src/hg/utils/automation/genbank/ucscPatchNames.sh
  • lines changed 21, context: html, text, full: html, text
    now running up all tracks for both NCBI and UCSC naming schemes and with indexes on assembly and gene tracks refs #16078
    
• src/hg/utils/automation/genbank/unlocalizedAgp.pl
  • lines changed 8, context: html, text, full: html, text
    now running up all tracks for both NCBI and UCSC naming schemes and with indexes on assembly and gene tracks refs #16078
    
• src/hg/utils/automation/genbank/unplacedAgp.pl
  • lines changed 10, context: html, text, full: html, text
    now running up all tracks for both NCBI and UCSC naming schemes and with indexes on assembly and gene tracks refs #16078
    
• src/inc/memgfx.h
  • lines changed 5, context: html, text, full: html, text
    Add support for GTEX tissue color scheme. refs #15645
    
  • lines changed 4, context: html, text, full: html, text
    Merge branch 'master' into gtex
    
  • lines changed 12, context: html, text, full: html, text
    Resolving merge
    
• src/inc/rainbow.h
  • lines changed 3, context: html, text, full: html, text
    Add support for GTEX tissue color scheme. refs #15645
    
  • lines changed 7, context: html, text, full: html, text
    Resolving merge
    
• src/lib/common.c
  • lines changed 1, context: html, text, full: html, text
    Verbosify a debug statement.
    
• src/lib/rainbow.c
  • lines changed 16, context: html, text, full: html, text
    Add support for GTEX tissue color scheme. refs #15645
    
  • lines changed 23, context: html, text, full: html, text
    Resolving merge
    
• src/pyLib/common.py
  • lines changed 37, context: html, text, full: html, text
    adding hg.conf parsing functions to Chris's common.py. Not
    using yet, as I don't want to break his code.
    
• src/utils/newPythonProg/newPythonProg.c
  • lines changed 1, context: html, text, full: html, text
    Changing the makefile produced to not be cluster dependent. Refs #16156
    
  • lines changed 2, context: html, text, full: html, text
    Adding a check to the argparse module that causes the program to spit help with no arguments. This replicates the C code style. Refs #16156
    
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v324 final build
    

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