All File Changes

v295_preview to v295_preview2 (2014-01-20 to 2014-01-27) v295

• src/hg/bedItemOverlapCount/tests/RunTest.sh
  • lines changed 3, context: html, text, full: html, text
    fix the bedItemOverlapCount test script to have the correct sums and toactually exit with bad status if the tests fail.
    
• src/hg/encode3/eap/README
  • lines changed 8, context: html, text, full: html, text
    Adding a paragraph of doc on EAP overall.
• src/hg/encode3/eap/eapAddSoftware/eapAddSoftware.c
  • lines changed 68, context: html, text, full: html, text
    Utility to help make it easier to add new software with version tracking etc now made.
• src/hg/encode3/eap/eapAddSoftware/makefile
  • lines changed 4, context: html, text, full: html, text
    Utility to help make it easier to add new software with version tracking etc now made.
• src/hg/encode3/eap/eapAddStep/eapAddStep.c
  • lines changed 230, context: html, text, full: html, text
    Somewhat awkard helper program to add steps to database.
• src/hg/encode3/eap/eapAddStep/makefile
  • lines changed 4, context: html, text, full: html, text
    Somewhat awkard helper program to add steps to database.
• src/hg/encode3/eap/eapAnalysisJson/eapAnalysisJson.c
  • lines changed 215, context: html, text, full: html, text
    Moving one more thing from edw to eap.
  • lines changed 4, context: html, text, full: html, text
    Adapting to new position in source tree.
  • lines changed 6, context: html, text, full: html, text
    Making self references consistent with new self name.
  • lines changed 82, context: html, text, full: html, text
    Adapting to new eapStep schema. Making inputs and outputs arrays.
  • lines changed 2, context: html, text, full: html, text
    Adding a null check
• src/hg/encode3/eap/eapAnalysisJson/makefile
  • lines changed 4, context: html, text, full: html, text
    Moving one more thing from edw to eap.
  • lines changed 2, context: html, text, full: html, text
    Adapting to new position in source tree.
  • lines changed 1, context: html, text, full: html, text
    Adding another library
• src/hg/encode3/eap/eapDaemon/eapDaemon.c
  • lines changed 14, context: html, text, full: html, text
    Adapting to name changes from edw->eap move.
• src/hg/encode3/eap/eapFinish/eapFinish.c
  • lines changed 54, context: html, text, full: html, text
    CHanging many symbols from edwAnalysis... to eap... Adapting to refactoring of eapStep and related tables.
• src/hg/encode3/eap/eapFinish/makefile
  • lines changed 1, context: html, text, full: html, text
    Adding more libraries.
• src/hg/encode3/eap/eapMonitor/eapMonitor.c
  • lines changed 21, context: html, text, full: html, text
    Adding count of waiting jobs to eapMonitor steps command. Making jobs scheduled not include jobs running in status command.
  • lines changed 31, context: html, text, full: html, text
    Improving sorting of eapMonitor steps.
  • lines changed 59, context: html, text, full: html, text
    Added doctor command, which resets counters on all sick batches we own.
  • lines changed 1, context: html, text, full: html, text
    Adding doctor to usage message.
  • lines changed 19, context: html, text, full: html, text
    Renaming edwAnalysis to eap on many symbols. Fixing some corner case crashes.
• src/hg/encode3/eap/eapSchedule/eapSchedule.c
  • lines changed 8, context: html, text, full: html, text
    Adding -step option to limit which steps are taken. Fixing old bug in usage.
  • lines changed 138, context: html, text, full: html, text
    Refactoring for new eapStep and related tables. Killing sneaky up option since now have a separate update utility. Adding inFormat option.
  • lines changed 33, context: html, text, full: html, text
    Changing handling of mixed read length files so eapSchedule warns on them in the hotspot section, and declines to schedule, rather than by aborting with an error message.
• src/hg/encode3/eap/eapSchedule/makefile
  • lines changed 1, context: html, text, full: html, text
    Adding new library.
• src/hg/encode3/eap/eapUpdateSoftware/eapUpdateSoftware.c
  • lines changed 79, context: html, text, full: html, text
    Utility to make it easier to update analysis software and version tables with a new software version seems to work.
• src/hg/encode3/eap/eapUpdateSoftware/makefile
  • lines changed 4, context: html, text, full: html, text
    Utility to make it easier to update analysis software and version tables with a new software version seems to work.
• src/hg/encode3/eap/inc/eapDb.h
  • lines changed 713, context: html, text, full: html, text
    First draft of eap tables as distinct from edw ones. Decided to share a db though with edw, but tables will have different prefix for the eap. As part of this switch I'm refactoring the design on the tables so that you can always do SQL searches of inputs and outputs.
  • lines changed 49, context: html, text, full: html, text
    Polishing schema a bit more. First working draft. Still want to rename eapAnalysis table, but it's working for the first time in 48 hours, so time to take a snapshot.
• src/hg/encode3/eap/inc/eapLib.h
  • lines changed 47, context: html, text, full: html, text
    Moving in a bunch of stuff from edwLib, refactoring as needed.
• src/hg/encode3/eap/lib/eapDb.as
  • lines changed 106, context: html, text, full: html, text
    First draft of eap tables as distinct from edw ones. Decided to share a db though with edw, but tables will have different prefix for the eap. As part of this switch I'm refactoring the design on the tables so that you can always do SQL searches of inputs and outputs.
  • lines changed 15, context: html, text, full: html, text
    Polishing schema a bit more. First working draft. Still want to rename eapAnalysis table, but it's working for the first time in 48 hours, so time to take a snapshot.
• src/hg/encode3/eap/lib/eapDb.c
  • lines changed 1776, context: html, text, full: html, text
    First draft of eap tables as distinct from edw ones. Decided to share a db though with edw, but tables will have different prefix for the eap. As part of this switch I'm refactoring the design on the tables so that you can always do SQL searches of inputs and outputs.
  • lines changed 151, context: html, text, full: html, text
    Polishing schema a bit more. First working draft. Still want to rename eapAnalysis table, but it's working for the first time in 48 hours, so time to take a snapshot.
• src/hg/encode3/eap/lib/eapDb.sql
  • lines changed 130, context: html, text, full: html, text
    First draft of eap tables as distinct from edw ones. Decided to share a db though with edw, but tables will have different prefix for the eap. As part of this switch I'm refactoring the design on the tables so that you can always do SQL searches of inputs and outputs.
  • lines changed 19, context: html, text, full: html, text
    Polishing schema a bit more. First working draft. Still want to rename eapAnalysis table, but it's working for the first time in 48 hours, so time to take a snapshot.
• src/hg/encode3/eap/lib/eapLib.c
  • lines changed 229, context: html, text, full: html, text
    Moving in a bunch of stuff from edwLib, refactoring as needed.
  • lines changed 12, context: html, text, full: html, text
    Adapting to schema changes in edw->eap transition.
• src/hg/encode3/eap/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Moving some of encodeDataWarehouse.as output to eapDb.as
• src/hg/encode3/eap/lib/redoSchema
  • lines changed 4, context: html, text, full: html, text
    First draft of eap tables as distinct from edw ones. Decided to share a db though with edw, but tables will have different prefix for the eap. As part of this switch I'm refactoring the design on the tables so that you can always do SQL searches of inputs and outputs.
  • lines changed 1, context: html, text, full: html, text
    Making resetDb properly build up software and step tables.
• src/hg/encode3/eap/lib/resetDb
  • lines changed 8, context: html, text, full: html, text
    First draft of eap tables as distinct from edw ones. Decided to share a db though with edw, but tables will have different prefix for the eap. As part of this switch I'm refactoring the design on the tables so that you can always do SQL searches of inputs and outputs.
  • lines changed 34, context: html, text, full: html, text
    Making resetDb properly build up software and step tables.
• src/hg/encode3/eap/makefile
  • lines changed 9, context: html, text, full: html, text
    Fixed typo, added eapAnalysisJson, and fixed it so high level make builds everything instead of just lib
• src/hg/encode3/encodeDataWarehouse/edwAddAssembly/edwAddAssembly.c
  • lines changed 6, context: html, text, full: html, text
    Including seqCount in edwAssembly
• src/hg/encode3/encodeDataWarehouse/edwAnalysisAddJson/edwAnalysisAddJson.c
  • lines changed 215, context: html, text, full: html, text
    Moving one more thing from edw to eap.
• src/hg/encode3/encodeDataWarehouse/edwAnalysisAddJson/makefile
  • lines changed 4, context: html, text, full: html, text
    Moving one more thing from edw to eap.
• src/hg/encode3/encodeDataWarehouse/edwMakeValidFile/sorted.bed
  • lines changed 331449, context: html, text, full: html, text
    Didn't mean to commit this, oops.
• src/hg/encode3/encodeDataWarehouse/inc/edwLib.h
  • lines changed 19, context: html, text, full: html, text
    Moving a bunch of stuff from edwLib to eapLib.
• src/hg/encode3/encodeDataWarehouse/inc/encodeDataWarehouse.h
  • lines changed 290, context: html, text, full: html, text
    Moving a bunch of stuff from edw tables to eap ones, reformatting tables a bit in the process.
• src/hg/encode3/encodeDataWarehouse/lib/edwLib.c
  • lines changed 99, context: html, text, full: html, text
    Moving a bunch of stuff from edwLib to eapLib.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.as
  • lines changed 58, context: html, text, full: html, text
    Moving a bunch of stuff from edw tables to eap ones, reformatting tables a bit in the process.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.c
  • lines changed 928, context: html, text, full: html, text
    Moving a bunch of stuff from edw tables to eap ones, reformatting tables a bit in the process.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.sql
  • lines changed 67, context: html, text, full: html, text
    Moving a bunch of stuff from edw tables to eap ones, reformatting tables a bit in the process.
• src/hg/encode3/encodeDataWarehouse/lib/resetEdw
  • lines changed 37, context: html, text, full: html, text
    Adding admin privs to some users, X and Y chroms to enrichment targets, resyncing with Stanford.
• src/hg/encode3/encodeDataWarehouse/lib/restartDaemons
  • lines changed 2, context: html, text, full: html, text
    Taking out analysis daemon. Wanting to start that separately.
• src/hg/encode3/encodeDataWarehouse/makefile
  • lines changed 1, context: html, text, full: html, text
    Moving edwAnalysisAddJob to eap side of the world.
• src/hg/encode3/encodeDataWarehouse/oneShot/edwFakeBiosample/edwFakeBiosample.c
  • lines changed 2, context: html, text, full: html, text
    Adding in a NULL check on response from Stanford
• src/hg/encode3/encodeDataWarehouse/oneShot/edwToEap1/edwToEap1.c
  • lines changed 386, context: html, text, full: html, text
    Tool to convert analysis tables from edw to eap format seems to work.
  • lines changed 1, context: html, text, full: html, text
    Oops, forgot return code!
• src/hg/encode3/encodeDataWarehouse/oneShot/edwToEap1/makefile
  • lines changed 4, context: html, text, full: html, text
    Tool to convert analysis tables from edw to eap format seems to work.
• src/hg/encode3/validateFiles/tests/goodMaleHg19.bed7
  • lines changed 141882, context: html, text, full: html, text
    cleaning up bloat in validateFiles
  • lines changed 1000, context: html, text, full: html, text
    cleaning up bloat in validateFiles, part 2
• src/hg/encode3/validateFiles/tests/goodMaleHg19.bed8
  • lines changed 141883, context: html, text, full: html, text
    cleaning up bloat in validateFiles
  • lines changed 1000, context: html, text, full: html, text
    cleaning up bloat in validateFiles, part 2
• src/hg/encode3/validateFiles/tests/goodMaleHg19.bed9
  • lines changed 141884, context: html, text, full: html, text
    cleaning up bloat in validateFiles
  • lines changed 1000, context: html, text, full: html, text
    cleaning up bloat in validateFiles, part 2
• src/hg/encode3/validateFiles/tests/goodMaleHg19.bedRrbs
  • lines changed 141883, context: html, text, full: html, text
    cleaning up bloat in validateFiles
  • lines changed 1000, context: html, text, full: html, text
    cleaning up bloat in validateFiles, part 2
• src/hg/encode3/validateFiles/tests/goodMalehg19.bedRnaElements
  • lines changed 624500, context: html, text, full: html, text
    cleaning up bloat in validateFiles
  • lines changed 100, context: html, text, full: html, text
    cleaning up bloat in validateFiles, part 2
• src/hg/featureBits/featureBits.c
  • lines changed 2, context: html, text, full: html, text
    correctly recognize _alt as a haplotype for hg38 refs #11681
  • lines changed 2, context: html, text, full: html, text
    clarify the backslash argument usage refs #11681
  • lines changed 4, context: html, text, full: html, text
    gather in the diaspora of haplotype check routines and add hg38 haplotype recognition refs #11681
• src/hg/hgChroms/hgChroms.c
  • lines changed 2, context: html, text, full: html, text
    gather in the diaspora of haplotype check routines and add hg38 haplotype recognition refs #11681
• src/hg/hgLogin/hgLogin.c
  • lines changed 38, context: html, text, full: html, text
    change hgLogin to allow deactivating the email confirmation email viahg.conf refs #11957
    
• src/hg/hgMirror/hgMirror
  • lines changed 65, context: html, text, full: html, text
    suppress sudo when running on hgwdev, Erich watches the sudo log andcomplained
    
• src/hg/hgSelect/hgSelect.c
  • lines changed 2, context: html, text, full: html, text
    gather in the diaspora of haplotype check routines and add hg38 haplotype recognition refs #11681
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 14, context: html, text, full: html, text
    Add trackDb setting, 'motifDrawDefault', and UI checkbox to alter whether motifs are highlighted. refs #9092
• src/hg/hgTracks/config.c
  • lines changed 7, context: html, text, full: html, text
    Checking in new feature 'drag-select highlight', which was originally coded by Larry. Redmine #709 (been on the shelf for awhile).
  • lines changed 25, context: html, text, full: html, text
    Cleaned up the hgTracks configure group tables at Donna's request. All groups are combined into a single table divided by empty data rows. Redmine #12546
• src/hg/hgTracks/factorSource.c
  • lines changed 56, context: html, text, full: html, text
    Fix dense mode display of motifs by splitting drawItems into two phases (items, and then motifs)
  • lines changed 13, context: html, text, full: html, text
    1. Correct bad test for no canonical motif in table (thanks Hiram!). 2. Lose an indent for readability
  • lines changed 14, context: html, text, full: html, text
    Suppress overwrite of factor item labels with motif highlight color. refs #9092.
  • lines changed 5, context: html, text, full: html, text
    Add trackDbsetting 'motifMaxWindow' to suppress display of motifs in large windows
  • lines changed 5, context: html, text, full: html, text
    Add trackDb setting, 'motifDrawDefault', and UI checkbox to alter whether motifs are highlighted. refs #9092
  • lines changed 59, context: html, text, full: html, text
    Replace per-item SQL query for motifs with single query at load time (trims 500msec from 30K window timing). refs #9092
• src/hg/hgTracks/hgTracks.c
  • lines changed 63, context: html, text, full: html, text
    Checking in new feature 'drag-select highlight', which was originally coded by Larry. Redmine #709 (been on the shelf for awhile).
• src/hg/hgTracks/snakeTrack.c
  • lines changed 2, context: html, text, full: html, text
    a little update to a new HAL api
• src/hg/hgTracks/wigTrack.c
  • lines changed 4, context: html, text, full: html, text
    corrections after code review refs #12524. These changes probably don'tneed to reviewed anymore, as Angie has already seen them, I copied them into
    the ticket #12524.
    
• src/hg/hgVai/hgVai.c
  • lines changed 3, context: html, text, full: html, text
    corrections after code review refs #12524. These changes probably don'tneed to reviewed anymore, as Angie has already seen them, I copied them into
    the ticket #12524.
    
• src/hg/hgc/peakClusters.c
  • lines changed 103, context: html, text, full: html, text
    1. Split out motif display code for better modularization. Clean up motif details info (add Name, remove max score for perf reasons)
  • lines changed 10, context: html, text, full: html, text
    Make cell abbrev table into a collapsible section to reduce clutter on details page
• src/hg/htdocs/ENCODE/aboutScaleup.html
  • lines changed 2, context: html, text, full: html, text
    Replace ENCODE portal summary graphic with newer version from Mike Pazin, processed with ImageMagick (tnx Hiram) to trim whitespace and convert format:convert -quality 100 -trim -border 30x30 -bordercolor white ENCODEDatatypes2013v6.jpg EncodeDatatypes2013.png
• src/hg/htdocs/ENCODE/index.html
  • lines changed 2, context: html, text, full: html, text
    Replace ENCODE portal summary graphic with newer version from Mike Pazin, processed with ImageMagick (tnx Hiram) to trim whitespace and convert format:convert -quality 100 -trim -border 30x30 -bordercolor white ENCODEDatatypes2013v6.jpg EncodeDatatypes2013.png
• src/hg/htdocs/FAQ/FAQlink.html
  • lines changed 11, context: html, text, full: html, text
    Added example of link to hgGenes page. refs #2372
  • lines changed 40, context: html, text, full: html, text
    More edits to this file. Fixed broken table formatting, updated some assembly references to more recent versions, and did some rewording in last section to hopefully improve readability.
• src/hg/htdocs/contacts.html
  • lines changed 1, context: html, text, full: html, text
    Removed <P> tag from image block for alignment purposes, per Matt review.
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 19, context: html, text, full: html, text
    Add trackDb setting, 'motifDrawDefault', and UI checkbox to alter whether motifs are highlighted. refs #9092
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 23, context: html, text, full: html, text
    Adding Web sequences track announcement, refs #12212
  • lines changed 1, context: html, text, full: html, text
    Correcting typo in Max Haeussler's name in Web Sequences announcement
  • lines changed 1, context: html, text, full: html, text
    Changing title for Web Sequences track announcement, refs #12212
• src/hg/htdocs/images/1.jpg
  • lines changed 0, context: html, text, full: html, text
    adding some missing number balls for liftover tracks
• src/hg/htdocs/images/10.jpg
  • lines changed 0, context: html, text, full: html, text
    adding some missing number balls for liftover tracks
• src/hg/htdocs/images/16.jpg
  • lines changed 0, context: html, text, full: html, text
    added a 16-ball for ultraConsereved liftover. refs #12158
• src/hg/htdocs/images/17.jpg
  • lines changed 0, context: html, text, full: html, text
    changing 4,5,617.jpg so they are the same size as the other number balls
• src/hg/htdocs/images/3.jpg
  • lines changed 0, context: html, text, full: html, text
    adding some missing number balls for liftover tracks
• src/hg/htdocs/images/4.jpg
  • lines changed 0, context: html, text, full: html, text
    changing 4,5,617.jpg so they are the same size as the other number balls
• src/hg/htdocs/images/5.jpg
  • lines changed 0, context: html, text, full: html, text
    changing 4,5,617.jpg so they are the same size as the other number balls
• src/hg/htdocs/images/6.jpg
  • lines changed 0, context: html, text, full: html, text
    changing 4,5,617.jpg so they are the same size as the other number balls
• src/hg/htdocs/images/7.jpg
  • lines changed 0, context: html, text, full: html, text
    adding some missing number balls for liftover tracks
• src/hg/htdocs/images/8.jpg
  • lines changed 0, context: html, text, full: html, text
    adding some missing number balls for liftover tracks
• src/hg/htdocs/images/EncodeDatatypes2013.png
  • lines changed 0, context: html, text, full: html, text
    Replace ENCODE portal summary graphic with newer version from Mike Pazin, processed with ImageMagick (tnx Hiram) to trim whitespace and convert format:convert -quality 100 -trim -border 30x30 -bordercolor white ENCODEDatatypes2013v6.jpg EncodeDatatypes2013.png
• src/hg/htdocs/images/highlight.png
  • lines changed 0, context: html, text, full: html, text
    Checking in new feature 'drag-select highlight', which was originally coded by Larry. Redmine #709 (been on the shelf for awhile).
• src/hg/htdocs/images/highlightRemove.png
  • lines changed 0, context: html, text, full: html, text
    Checking in new feature 'drag-select highlight', which was originally coded by Larry. Redmine #709 (been on the shelf for awhile).
• src/hg/htdocs/images/highlightZoom.png
  • lines changed 0, context: html, text, full: html, text
    Checking in new feature 'drag-select highlight', which was originally coded by Larry. Redmine #709 (been on the shelf for awhile).
• src/hg/htdocs/indexNews.html
  • lines changed 65, context: html, text, full: html, text
    Adding Web sequences track announcement, refs #12212
  • lines changed 2, context: html, text, full: html, text
    Adding Read more link to end of 100 way announcement
  • lines changed 1, context: html, text, full: html, text
    Correcting typo in Max Haeussler's name in Web Sequences announcement
  • lines changed 4, context: html, text, full: html, text
    Changing title for Web Sequences track announcement, refs #12212
• src/hg/htdocs/license/index.html
  • lines changed 4, context: html, text, full: html, text
    Encoded whale email address, per Matt.
• src/hg/htdocs/style/HGStyle.css
  • lines changed 4, context: html, text, full: html, text
    Checking in new feature 'drag-select highlight', which was originally coded by Larry. Redmine #709 (been on the shelf for awhile).
  • lines changed 4, context: html, text, full: html, text
    Cleaned up the hgTracks configure group tables at Donna's request. All groups are combined into a single table divided by empty data rows. Redmine #12546
• src/hg/inc/hdb.h
  • lines changed 2, context: html, text, full: html, text
    corrections after code review refs #12524. These changes probably don'tneed to reviewed anymore, as Angie has already seen them, I copied them into
    the ticket #12524.
    
• src/hg/inc/jksql.h
  • lines changed 4, context: html, text, full: html, text
    Exporting sqlExcapeTabFileString and improving it's opening comment.
• src/hg/inc/jsHelper.h
  • lines changed 6, context: html, text, full: html, text
    Make cell abbrev table into a collapsible section to reduce clutter on details page
• src/hg/inc/lav.h
  • lines changed 33, context: html, text, full: html, text
    move common lav reading business into the library and fixup more lavToPsl bugs and add to lav testing refs #12502
• src/hg/inc/trackHub.h
  • lines changed 1, context: html, text, full: html, text
    Fixing .h to match .c.
• src/hg/inc/web.h
  • lines changed 7, context: html, text, full: html, text
    Make cell abbrev table into a collapsible section to reduce clutter on details page
• src/hg/js/hgTracks.js
  • lines changed 311, context: html, text, full: html, text
    Checking in new feature 'drag-select highlight', which was originally coded by Larry. Redmine #709 (been on the shelf for awhile).
  • lines changed 1, context: html, text, full: html, text
    Scrool the page back to the top on 'refresh' as requested by Bob during #709 review.
  • lines changed 28, context: html, text, full: html, text
    Adding 'jump or zoom' functionalight to drag highlight feature. Redmine #709.
• src/hg/js/utils.js
  • lines changed 49, context: html, text, full: html, text
    Checking in new feature 'drag-select highlight', which was originally coded by Larry. Redmine #709 (been on the shelf for awhile).
• src/hg/lib/haplotypes.c
  • lines changed 1, context: html, text, full: html, text
    corrections after code review refs #12524. These changes probably don'tneed to reviewed anymore, as Angie has already seen them, I copied them into
    the ticket #12524.
    
• src/hg/lib/hdb.c
  • lines changed 18, context: html, text, full: html, text
    corrections after code review refs #12524. These changes probably don'tneed to reviewed anymore, as Angie has already seen them, I copied them into
    the ticket #12524.
    
• src/hg/lib/hgFind.c
  • lines changed 8, context: html, text, full: html, text
    corrections after code review refs #12524. These changes probably don'tneed to reviewed anymore, as Angie has already seen them, I copied them into
    the ticket #12524.
    
• src/hg/lib/jksql.c
  • lines changed 35, context: html, text, full: html, text
    corrections after code review refs #12524. These changes probably don'tneed to reviewed anymore, as Angie has already seen them, I copied them into
    the ticket #12524.
    
  • lines changed 2, context: html, text, full: html, text
    Exporting sqlExcapeTabFileString and improving it's opening comment.
• src/hg/lib/jsHelper.c
  • lines changed 35, context: html, text, full: html, text
    Make cell abbrev table into a collapsible section to reduce clutter on details page
• src/hg/lib/lav.c
  • lines changed 156, context: html, text, full: html, text
    move common lav reading business into the library and fixup more lavToPsl bugs and add to lav testing refs #12502
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    move common lav reading business into the library and fixup more lavToPsl bugs and add to lav testing refs #12502
• src/hg/lib/pubsArticle.as
  • lines changed 8, context: html, text, full: html, text
    fixing .as files, refs #12212
• src/hg/lib/pubsArticle.sql
  • lines changed 13, context: html, text, full: html, text
    fixing .as files, refs #12212
• src/hg/lib/pubsBingArticle.as
  • lines changed 10, context: html, text, full: html, text
    fixing .as files, refs #12212
  • lines changed 23, context: html, text, full: html, text
    removing files after code review, refs #12524
• src/hg/lib/pubsBingArticle.sql
  • lines changed 14, context: html, text, full: html, text
    fixing .as files, refs #12212
  • lines changed 28, context: html, text, full: html, text
    removing files after code review, refs #12524
• src/hg/lib/pubsBingBlat.as
  • lines changed 30, context: html, text, full: html, text
    removing files after code review, refs #12524
• src/hg/lib/pubsBingBlat.sql
  • lines changed 34, context: html, text, full: html, text
    removing files after code review, refs #12524
• src/hg/lib/pubsBingBlatPsl.as
  • lines changed 26, context: html, text, full: html, text
    removing files after code review, refs #12524
• src/hg/lib/pubsBingBlatPsl.sql
  • lines changed 28, context: html, text, full: html, text
    removing files after code review, refs #12524
• src/hg/lib/pubsBingSequenceAnnot.as
  • lines changed 2, context: html, text, full: html, text
    fixing .as files, refs #12212
  • lines changed 1, context: html, text, full: html, text
    fixing typo in last commit
  • lines changed 13, context: html, text, full: html, text
    removing files after code review, refs #12524
• src/hg/lib/pubsBingSequenceAnnot.sql
  • lines changed 2, context: html, text, full: html, text
    fixing .as files, refs #12212
  • lines changed 1, context: html, text, full: html, text
    fixing typo in last commit
  • lines changed 16, context: html, text, full: html, text
    removing files after code review, refs #12524
• src/hg/lib/pubsBlatPsl.as
  • lines changed 1, context: html, text, full: html, text
    adding missing field to .as, refs #12212
• src/hg/lib/pubsMarker.as
  • lines changed 12, context: html, text, full: html, text
    removing files after code review, refs #12524
• src/hg/lib/pubsMarker.sql
  • lines changed 14, context: html, text, full: html, text
    removing files after code review, refs #12524
• src/hg/lib/pubsMarkerAnnot.as
  • lines changed 12, context: html, text, full: html, text
    removing files after code review, refs #12524
• src/hg/lib/pubsMarkerAnnot.sql
  • lines changed 14, context: html, text, full: html, text
    removing files after code review, refs #12524
• src/hg/lib/pubsMarkerBand.as
  • lines changed 9, context: html, text, full: html, text
    removing files after code review, refs #12524
• src/hg/lib/pubsMarkerBand.sql
  • lines changed 11, context: html, text, full: html, text
    removing files after code review, refs #12524
• src/hg/lib/pubsMarkerGene.as
  • lines changed 9, context: html, text, full: html, text
    removing files after code review, refs #12524
• src/hg/lib/pubsMarkerGene.sql
  • lines changed 11, context: html, text, full: html, text
    removing files after code review, refs #12524
• src/hg/lib/search.c
  • lines changed 8, context: html, text, full: html, text
    corrections after code review refs #12524. These changes probably don'tneed to reviewed anymore, as Angie has already seen them, I copied them into
    the ticket #12524.
    
• src/hg/lib/web.c
  • lines changed 18, context: html, text, full: html, text
    Make cell abbrev table into a collapsible section to reduce clutter on details page
• src/hg/lib/wigDataStream.c
  • lines changed 1, context: html, text, full: html, text
    corrections after code review refs #12524. These changes probably don'tneed to reviewed anymore, as Angie has already seen them, I copied them into
    the ticket #12524.
    
• src/hg/makeDb/doc/canFam3.txt
  • lines changed 99, context: html, text, full: html, text
    Built snp139 for canFam3 and snp138 for galGal4. Moved some perlthat has been copy-pasted around hg19.txt (etc) into proper scripts.
    
• src/hg/makeDb/doc/galGal4.txt
  • lines changed 165, context: html, text, full: html, text
    Built snp139 for canFam3 and snp138 for galGal4. Moved some perlthat has been copy-pasted around hg19.txt (etc) into proper scripts.
    
• src/hg/makeDb/doc/hg19.txt
  • lines changed 28, context: html, text, full: html, text
    update cosmic to v67 refs #10158
  • lines changed 28, context: html, text, full: html, text
    update cosmic to v67 refs #10158
• src/hg/makeDb/doc/hg38.txt
  • lines changed 87, context: html, text, full: html, text
    working up lineage specific repeats refs #11681
  • lines changed 28, context: html, text, full: html, text
    add ctgPos2 GRC Contigs track construction refs #11681
  • lines changed 17, context: html, text, full: html, text
    starting make downloads to be completed refs #11681
  • lines changed 9, context: html, text, full: html, text
    Continuing downloads set up. refs #11681
  • lines changed 5, context: html, text, full: html, text
    Added final details for hgdownloads task. refs #11681
• src/hg/makeDb/doc/proteins/140122.txt
  • lines changed 206, context: html, text, full: html, text
    start the UCSC genes build for mm10
• src/hg/makeDb/doc/ucscGenes/mm10.ucscGenes14.csh
  • lines changed 1561, context: html, text, full: html, text
    start the UCSC genes build for mm10
• src/hg/makeDb/doc/uniProt/sp140122.txt
  • lines changed 62, context: html, text, full: html, text
    start the UCSC genes build for mm10
• src/hg/makeDb/trackDb/chimp/trackDb.chainNet.ra
  • lines changed 3, context: html, text, full: html, text
    Added rn5 override section (redmine #12547)
• src/hg/makeDb/trackDb/dog/canFam3/snp139.html
  • lines changed 25, context: html, text, full: html, text
    Built snp139 for canFam3 and snp138 for galGal4. Moved some perlthat has been copy-pasted around hg19.txt (etc) into proper scripts.
    
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra
  • lines changed 26, context: html, text, full: html, text
    Rename motif tables for consistency
  • lines changed 3, context: html, text, full: html, text
    Add trackDb setting, 'motifDrawDefault', and UI checkbox to alter whether motifs are highlighted. refs #9092
  • lines changed 2, context: html, text, full: html, text
    Add motif info to ENCODE regulation TF ChIP track description.
  • lines changed 2, context: html, text, full: html, text
    Format track references.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRegTfbsClusteredV3.html
  • lines changed 85, context: html, text, full: html, text
    Add motif info to ENCODE regulation TF ChIP track description.
  • lines changed 28, context: html, text, full: html, text
    Format track references.
• src/hg/makeDb/trackDb/human/hg38/altSequences.ra
  • lines changed 20, context: html, text, full: html, text
    adding NCBI mappings next to UCSC mappings refs #11681
• src/hg/makeDb/trackDb/human/hg38/description.html
  • lines changed 94, context: html, text, full: html, text
    Adding latest changes (redmine #11706)
  • lines changed 57, context: html, text, full: html, text
    Checking in latest updates (redmine #11706)
• src/hg/makeDb/trackDb/miRNA.html
  • lines changed 2, context: html, text, full: html, text
    Changing url according to code review, refs #12526
  • lines changed 1, context: html, text, full: html, text
    Changing link per Code Review, refs #12526
• src/hg/makeDb/trackDb/rat/trackDb.chainNet.ra
  • lines changed 5, context: html, text, full: html, text
    Added panTro4 override section with values based on getChainLine.csh and getMatrixLines.csh (redmine #12547)
• src/hg/makeDb/trackDb/snp139.shared.html
  • lines changed 458, context: html, text, full: html, text
    Built snp139 for canFam3 and snp138 for galGal4. Moved some perlthat has been copy-pasted around hg19.txt (etc) into proper scripts.
    
• src/hg/makeDb/trackDb/snp139CommonMention.html
  • lines changed 2, context: html, text, full: html, text
    Built snp139 for canFam3 and snp138 for galGal4. Moved some perlthat has been copy-pasted around hg19.txt (etc) into proper scripts.
    
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 2, context: html, text, full: html, text
    Add trackDb setting, 'motifDrawDefault', and UI checkbox to alter whether motifs are highlighted. refs #9092
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 44, context: html, text, full: html, text
    Built snp139 for canFam3 and snp138 for galGal4. Moved some perlthat has been copy-pasted around hg19.txt (etc) into proper scripts.
    
• src/hg/mouseStuff/axtFilter/axtFilter.c
  • lines changed 4, context: html, text, full: html, text
    gather in the diaspora of haplotype check routines and add hg38 haplotype recognition refs #11681
• src/hg/mouseStuff/chainFilter/chainFilter.c
  • lines changed 3, context: html, text, full: html, text
    gather in the diaspora of haplotype check routines and add hg38 haplotype recognition refs #11681
• src/hg/mouseStuff/chainNet/chainNet.c
  • lines changed 3, context: html, text, full: html, text
    gather in the diaspora of haplotype check routines and add hg38 haplotype recognition refs #11681
• src/hg/mouseStuff/chainPreNet/chainPreNet.c
  • lines changed 3, context: html, text, full: html, text
    gather in the diaspora of haplotype check routines and add hg38 haplotype recognition refs #11681
• src/hg/mouseStuff/lavToAxt/lavToAxt.c
  • lines changed 164, context: html, text, full: html, text
    move common lav reading business into the library and fixup more lavToPsl bugs and add to lav testing refs #12502
• src/hg/mouseStuff/lavToPsl/lavToPsl.c
  • lines changed 144, context: html, text, full: html, text
    move common lav reading business into the library and fixup more lavToPsl bugs and add to lav testing refs #12502
• src/hg/mouseStuff/lavToPsl/tests/input/hg19.chrom.sizes.gz
  • lines changed 0, context: html, text, full: html, text
    move common lav reading business into the library and fixup more lavToPsl bugs and add to lav testing refs #12502
• src/hg/mouseStuff/lavToPsl/tests/input/mm10.chrom.sizes.gz
  • lines changed 0, context: html, text, full: html, text
    move common lav reading business into the library and fixup more lavToPsl bugs and add to lav testing refs #12502
• src/hg/mouseStuff/lavToPsl/tests/input/trimEndsBug.lav
  • lines changed 35, context: html, text, full: html, text
    move common lav reading business into the library and fixup more lavToPsl bugs and add to lav testing refs #12502
• src/hg/mouseStuff/lavToPsl/tests/makefile
  • lines changed 66, context: html, text, full: html, text
    move common lav reading business into the library and fixup more lavToPsl bugs and add to lav testing refs #12502
• src/hg/mouseStuff/netFilter/netFilter.c
  • lines changed 3, context: html, text, full: html, text
    gather in the diaspora of haplotype check routines and add hg38 haplotype recognition refs #11681
• src/hg/oneShot/freen/freen.c
  • lines changed 9, context: html, text, full: html, text
    Freen tests ways to parse comma separated lists
• src/hg/utils/automation/collectNcbiFuncAnnotations.pl
  • lines changed 49, context: html, text, full: html, text
    Built snp139 for canFam3 and snp138 for galGal4. Moved some perlthat has been copy-pasted around hg19.txt (etc) into proper scripts.
    
• src/hg/utils/automation/doDbSnp.pl
  • lines changed 76, context: html, text, full: html, text
    Automated the fetching of the NCBI Assembly Report file, usingEUtils queries suggested by NCBI's helpdesk. refs #12490
    
• src/hg/utils/automation/fixNcbiFuncCoords.pl
  • lines changed 58, context: html, text, full: html, text
    Built snp139 for canFam3 and snp138 for galGal4. Moved some perlthat has been copy-pasted around hg19.txt (etc) into proper scripts.
    
• src/hg/utils/automation/makeDownloads.pl
  • lines changed 1, context: html, text, full: html, text
    gather in the diaspora of haplotype check routines and add hg38 haplotype recognition refs #11681
• src/hg/utils/gff3ToPsl/gff3ToPsl.c
  • lines changed 4, context: html, text, full: html, text
    fix gff3ToPsl to work on the negative strand
  • lines changed 4, context: html, text, full: html, text
    fix gff3ToPsl to work with NCBI's gff alignments of haplotype chroms toreference chroms.
    
• src/hg/utils/gff3ToPsl/tests/README
  • lines changed 11, context: html, text, full: html, text
    fix gff3ToPsl to work on the negative strand
• src/hg/utils/gff3ToPsl/tests/expected/patch1test.2.axt
  • lines changed 6470966, context: html, text, full: html, text
    fix gff3ToPsl to work on the negative strand
  • lines changed 21329, context: html, text, full: html, text
    fix gff3ToPsl to work with NCBI's gff alignments of haplotype chroms toreference chroms.
    
• src/hg/utils/gff3ToPsl/tests/expected/patch1test.2.stats
  • lines changed 267, context: html, text, full: html, text
    fix gff3ToPsl to work with NCBI's gff alignments of haplotype chroms toreference chroms.
    
• src/hg/utils/gff3ToPsl/tests/expected/patch1test.psl
  • lines changed 266, context: html, text, full: html, text
    fix gff3ToPsl to work on the negative strand
  • lines changed 266, context: html, text, full: html, text
    fix gff3ToPsl to work with NCBI's gff alignments of haplotype chroms toreference chroms.
    
• src/hg/utils/gff3ToPsl/tests/input/GL339449.2bit
  • lines changed 0, context: html, text, full: html, text
    fix gff3ToPsl to work on the negative strand
  • lines changed 0, context: html, text, full: html, text
    fix gff3ToPsl to work with NCBI's gff alignments of haplotype chroms toreference chroms.
    
• src/hg/utils/gff3ToPsl/tests/input/GL339450_CM000671.gff
  • lines changed 7, context: html, text, full: html, text
    fix gff3ToPsl to work on the negative strand
  • lines changed 7, context: html, text, full: html, text
    fix gff3ToPsl to work with NCBI's gff alignments of haplotype chroms toreference chroms.
    
• src/hg/utils/gff3ToPsl/tests/input/chrom.sizes
  • lines changed 26, context: html, text, full: html, text
    fix gff3ToPsl to work on the negative strand
  • lines changed 26, context: html, text, full: html, text
    fix gff3ToPsl to work with NCBI's gff alignments of haplotype chroms toreference chroms.
    
• src/hg/utils/gff3ToPsl/tests/input/haploMaps.gff
  • lines changed 269, context: html, text, full: html, text
    fix gff3ToPsl to work with NCBI's gff alignments of haplotype chroms toreference chroms.
    
• src/hg/utils/gff3ToPsl/tests/input/locusToChrom.sed
  • lines changed 24, context: html, text, full: html, text
    fix gff3ToPsl to work on the negative strand
  • lines changed 24, context: html, text, full: html, text
    fix gff3ToPsl to work with NCBI's gff alignments of haplotype chroms toreference chroms.
    
• src/hg/utils/gff3ToPsl/tests/makefile
  • lines changed 3, context: html, text, full: html, text
    fix gff3ToPsl to work on the negative strand
  • lines changed 7, context: html, text, full: html, text
    fix gff3ToPsl to work with NCBI's gff alignments of haplotype chroms toreference chroms.
    
• src/hg/utils/gffToBed/test.gff
  • lines changed 61300, context: html, text, full: html, text
    Getting rid of a test input that is too big.
• src/hg/utils/pslMap/tests/expected/mrnaChainMapBug.mapinfo
  • lines changed 2, context: html, text, full: html, text
    removed test case where the input chain was huge. Bug was mechanical, a second loop missing to traverse colliding entires, so it should not regress
• src/hg/utils/pslMap/tests/expected/mrnaChainMapBug.psl
  • lines changed 1, context: html, text, full: html, text
    removed test case where the input chain was huge. Bug was mechanical, a second loop missing to traverse colliding entires, so it should not regress
• src/hg/utils/pslMap/tests/input/mrnaChainMapRefSeq.chain
  • lines changed 610956, context: html, text, full: html, text
    removed test case where the input chain was huge. Bug was mechanical, a second loop missing to traverse colliding entires, so it should not regress
• src/hg/utils/pslMap/tests/input/mrnaChainMapRefSeq.psl
  • lines changed 1, context: html, text, full: html, text
    removed test case where the input chain was huge. Bug was mechanical, a second loop missing to traverse colliding entires, so it should not regress
• src/hg/utils/pslMap/tests/makefile
  • lines changed 8, context: html, text, full: html, text
    removed test case where the input chain was huge. Bug was mechanical, a second loop missing to traverse colliding entires, so it should not regress
• src/inc/common.h
  • lines changed 4, context: html, text, full: html, text
    gather in the diaspora of haplotype check routines and add hg38 haplotype recognition refs #11681
  • lines changed 10, context: html, text, full: html, text
    Adding slUnsigned to our basic listy types like slInt...
• src/inc/hash.h
  • lines changed 4, context: html, text, full: html, text
    corrections after code review refs #12524. These changes probably don'tneed to reviewed anymore, as Angie has already seen them, I copied them into
    the ticket #12524.
    
• src/inc/udc.h
  • lines changed 5, context: html, text, full: html, text
    corrections after code review refs #12524. These changes probably don'tneed to reviewed anymore, as Angie has already seen them, I copied them into
    the ticket #12524.
    
• src/lib/bbiWrite.c
  • lines changed 10, context: html, text, full: html, text
    Improving handling of empty data sets by bedToBigBed and bigBedInfo.
• src/lib/cirTree.c
  • lines changed 7, context: html, text, full: html, text
    Improving handling of empty data sets by bedToBigBed and bigBedInfo.
• src/lib/common.c
  • lines changed 9, context: html, text, full: html, text
    gather in the diaspora of haplotype check routines and add hg38 haplotype recognition refs #11681
  • lines changed 9, context: html, text, full: html, text
    Adding slUnsigned to our basic listy types like slInt...
• src/lib/hash.c
  • lines changed 15, context: html, text, full: html, text
    corrections after code review refs #12524. These changes probably don'tneed to reviewed anymore, as Angie has already seen them, I copied them into
    the ticket #12524.
    
• src/lib/linefile.c
  • lines changed 9, context: html, text, full: html, text
    corrections after code review refs #12524. These changes probably don'tneed to reviewed anymore, as Angie has already seen them, I copied them into
    the ticket #12524.
    
• src/lib/psl.c
  • lines changed 45, context: html, text, full: html, text
    fix gff3ToPsl to work on the negative strand
  • lines changed 45, context: html, text, full: html, text
    fix gff3ToPsl to work with NCBI's gff alignments of haplotype chroms toreference chroms.
    
• src/lib/tests/udcTest.c
  • lines changed 12, context: html, text, full: html, text
    corrections after code review refs #12524. These changes probably don'tneed to reviewed anymore, as Angie has already seen them, I copied them into
    the ticket #12524.
    
• src/lib/udc.c
  • lines changed 24, context: html, text, full: html, text
    corrections after code review refs #12524. These changes probably don'tneed to reviewed anymore, as Angie has already seen them, I copied them into
    the ticket #12524.
    
  • lines changed 2, context: html, text, full: html, text
    Removing a warning from udc.c, Angie agreed in refs #12524
• src/makefile
  • lines changed 1, context: html, text, full: html, text
    Expanded libraries that get tagged.
• src/oneShot/sqlToAs/sqlToAs
  • lines changed 5, context: html, text, full: html, text
    fixing .as files, refs #12212
  • lines changed 2, context: html, text, full: html, text
    tiny update for sqlToAs
• src/parasol/inc/paraVersion.h
  • lines changed 1, context: html, text, full: html, text
    Documenting code change and bumping version.
• src/parasol/parasol/parasol.c
  • lines changed 2, context: html, text, full: html, text
    Jim accidentally dropped the option -out from usage message. I have restored it with a little clarification.
  • lines changed 2, context: html, text, full: html, text
    Fixing command line usage statement problem Galt fingered in review.
• src/parasol/version.doc
  • lines changed 2, context: html, text, full: html, text
    Documenting code change and bumping version.
• src/product/ex.hg.conf
  • lines changed 1, context: html, text, full: html, text
    document special hg.conf value to skip hgLogin emails, refs #11957
• src/product/scripts/trashCleanMonitor.sh
  • lines changed 1, context: html, text, full: html, text
    pass along SCRIPTS in scriptsDir refs #12540
• src/test/buildTableDescriptions.pl
  • lines changed 1, context: html, text, full: html, text
    Fixed regex for enum fields in .as files - should now match properly, refs #11394
• src/utils/bedToBigBed/bedToBigBed.c
  • lines changed 13, context: html, text, full: html, text
    Improving handling of empty data sets by bedToBigBed and bigBedInfo.
  • lines changed 4, context: html, text, full: html, text
    Bumped version number and started version log.
• src/utils/bigBedInfo/bigBedInfo.c
  • lines changed 8, context: html, text, full: html, text
    Improving handling of empty data sets by bedToBigBed and bigBedInfo.
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v295 preview2 refs #12352

• lines changed: 8705650
• files changed: 270