All File Changes

v325_preview to v325_preview2 (2015-11-02 to 2015-11-09) v325

• src/hg/cirm/cdw/wrangle/addMetaDataToJson/addMetaDataToJson
  • lines changed 14, context: html, text, full: html, text
    Fixing this program up a bit so it works in the rnaSeq pipeline, refs #16244
    
• src/hg/cirm/cdw/wrangle/matrixFilter/makefile
  • lines changed 6, context: html, text, full: html, text
    Makefile for matrixFilter
    
• src/hg/cirm/cdw/wrangle/matrixFilter/matrixFilter
  • lines changed 101, context: html, text, full: html, text
    A small project for CIRM that filters a matrix, not used directly but a nice bit of code
    
• src/hg/hgIntegrator/hgIntegrator.c
  • lines changed 10, context: html, text, full: html, text
    Adding a very simple output header comment and user-defined region comments.
    
• src/hg/hgMirror/hgMirror
  • lines changed 12, context: html, text, full: html, text
    restart mysql after cancelled download in hgMirror, refs #16294
    
• src/hg/hgTracks/bamTrack.c
  • lines changed 16, context: html, text, full: html, text
    sometimes Complete Genomics bams have records with no alignment in them.
    Ignore them #16339
    
• src/hg/hgTracks/chainTrack.c
  • lines changed 12, context: html, text, full: html, text
    implement score and chromosome filter in bigChain load function #16314
    
  • lines changed 1, context: html, text, full: html, text
    oops, fix a problem with bigChain filtering that Angie found
    
• src/hg/hgTracks/extTools.c
  • lines changed 5, context: html, text, full: html, text
    fixing off-by-one errors in external tools menu, refs #16308
    
• src/hg/hgTracks/extTools.ra
  • lines changed 5, context: html, text, full: html, text
    fixing off-by-one errors in external tools menu, refs #16308
    
  • lines changed 12, context: html, text, full: html, text
    adding PFAM to external tools menu refs #16308
    
• src/hg/hgTracks/hgTracks.c
  • lines changed 8, context: html, text, full: html, text
    a very basic instrumentation of UDC (no redmine)
    
• src/hg/hgTracks/menu.c
  • lines changed 1, context: html, text, full: html, text
    fixing uppercase/lowercase issue in menu, refs #16307
    
• src/hg/hgTracks/wigMafTrack.c
  • lines changed 9, context: html, text, full: html, text
    a very basic instrumentation of UDC (no redmine)
    
• src/hg/hgc/hgc.c
  • lines changed 4, context: html, text, full: html, text
    Re-adding code removed by mistake to deal with gcc warnings for -Wunused-but-set-variable, fixes Ecores track display in fugu, refs #16121
    
• src/hg/hgc/mafClick.c
  • lines changed 524, context: html, text, full: html, text
    remove GSID code from mafClick.c (no redmine)
    
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 18, context: html, text, full: html, text
    Updating index page with top menu bar dropdown links announcement refs #16022
    
• src/hg/htdocs/inc/globalNavBar.inc
  • lines changed 2, context: html, text, full: html, text
    Correctly the related link information for the dropdown menu refs #16022
    
  • lines changed 1, context: html, text, full: html, text
    Correcting menu #16022
    
• src/hg/htdocs/indexNews.html
  • lines changed 47, context: html, text, full: html, text
    Updating index page with top menu bar dropdown links announcement refs #16022
    
• src/hg/js/hgTracks.js
  • lines changed 1, context: html, text, full: html, text
    fixing off-by-one errors in external tools menu, refs #16308
    
• src/hg/js/model/hgIntegrator/hgIntegratorModel.js
  • lines changed 3, context: html, text, full: html, text
    When no user regions have been defined, don't clobber hgi_range to position
    unless it was already set to userRegions.
    
• src/hg/lib/hgMaf.c
  • lines changed 1, context: html, text, full: html, text
    use ';' to separate MAF lines in bigMaf instead of '\001' #15935
    
• src/hg/lib/trackDbCustom.c
  • lines changed 1, context: html, text, full: html, text
    implement score and chromosome filter in bigChain load function #16314
    
• src/hg/lib/web.c
  • lines changed 1, context: html, text, full: html, text
    Undoing base tag addition to fix unintended bug, refs #16326
    
• src/hg/makeDb/doc/oreganno/oreganno.txt
  • lines changed 136, context: html, text, full: html, text
    Adding ORegAnno track documentation, refs #15957
    
• src/hg/makeDb/schema/all.joiner
  • lines changed 5, context: html, text, full: html, text
    Added rules for Yale Pseudogenes 60 track; refs #16284
    
• src/hg/makeDb/trackDb/human/hg19/pseudoYale60.html
  • lines changed 12, context: html, text, full: html, text
    Updating Yale Pseudo 60 Description Page
    
• src/inc/udc.h
  • lines changed 2, context: html, text, full: html, text
    a very basic instrumentation of UDC (no redmine)
    
• src/lib/net.c
  • lines changed 4, context: html, text, full: html, text
    user got EINTR Error (Interrupted system call) so we should retry.
    
• src/lib/udc.c
  • lines changed 28, context: html, text, full: html, text
    a very basic instrumentation of UDC (no redmine)
    
• src/utils/qa/weeklybld/boxRelease.csh
  • lines changed 6, context: html, text, full: html, text
    adding one more paranoid check that the root account dsa keys have been removed
    
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v325 preview2 refs #16299
    
• src/utils/qa/weeklybld/cherryPickCommits.csh
  • lines changed 1, context: html, text, full: html, text
    fixing email addresses
    
• src/utils/qa/weeklybld/doHgNearTestRobot.csh
  • lines changed 2, context: html, text, full: html, text
    fixing email addresses
    
• src/utils/qa/weeklybld/doNewBranch.csh
  • lines changed 5, context: html, text, full: html, text
    fixing email addresses
    
• src/utils/qa/weeklybld/doNewReview.csh
  • lines changed 1, context: html, text, full: html, text
    fixing email addresses
    
• src/utils/qa/weeklybld/doNewReview2.csh
  • lines changed 1, context: html, text, full: html, text
    fixing email addresses
    
• src/utils/qa/weeklybld/doSearchRobot.csh
  • lines changed 2, context: html, text, full: html, text
    fixing email addresses
    
• src/utils/qa/weeklybld/patchBranch.csh
  • lines changed 1, context: html, text, full: html, text
    fixing email addresses
    
• src/utils/qa/weeklybld/revertCommits.csh
  • lines changed 1, context: html, text, full: html, text
    fixing email addresses
    
• src/utils/qa/weeklybld/updateBrowserboxbeta.csh
  • lines changed 3, context: html, text, full: html, text
    fixing email addresses
    
  • lines changed 2, context: html, text, full: html, text
    little tweak
    

• lines changed: 1029
• files changed: 43