All File Changes

v314_preview2 to v314_base (2015-03-23 to 2015-03-30) v314

• confs/preview.hg.conf
  • lines changed 5, context: html, text, full: html, text
    Removing unused comment
    
• src/hg/encode/getTrackReferences/getTrackReferences
  • lines changed 1, context: html, text, full: html, text
    Update to find paper URLs on pubmed again
    
• src/hg/hgChooseDb/hgChooseDb.c
  • lines changed 16, context: html, text, full: html, text
    Code review feedback from Kate: libify inclusion of libs for new React framework.
    refs #14965
    
• src/hg/hgCustom/hgCustom.c
  • lines changed 4, context: html, text, full: html, text
    This is a go at libifing the CGI startup code. For all CGIs, we need to
    call a few basic setup funtions, like UDC config and CGI apoptosis.
    (For most CGIs also bottleneck). Instead of adding it to all of our
    30+ CGIs, I changed the cart*Shell functions. I think most CGIs call
    at least one of these functions. This commit removes the existing
    copy/pasted code from a few CGIs and replaces it with one call.
    Adding this to the cart-setup means that (like before), UDC is
    setup even for small JSON calls and a process is spawned to watch
    the CGI and kill it ("Apoptosis"). Any comments on whether this should
    be implemented differently are appreciated. I have not added bottleneck
    to this function right now as apparently we're calling bottleneck only
    from some of our CGIs.
    
  • lines changed 4, context: html, text, full: html, text
    Revert "This is a go at libifing the CGI startup code. For all CGIs, we need to"
    
    This reverts commit 6696987406845625c252a13b690e0c4d7d9e59fa.
    
• src/hg/hgIntegrator/hgIntegrator.c
  • lines changed 18, context: html, text, full: html, text
    Code review feedback from Kate: libify inclusion of libs for new React framework.
    refs #14965
    
• src/hg/hgLogin/hgLogin.c
  • lines changed 11, context: html, text, full: html, text
    changing hgLogin to add special message on mirrors, refs #14718
    
• src/hg/hgNotYet/hgNotYet.c
  • lines changed 7, context: html, text, full: html, text
    Removing GSAID code. BrianR said that's OK.
    
  • lines changed 7, context: html, text, full: html, text
    Revert "Removing GSAID code. BrianR said that's OK."
    
    This reverts commit 324e56bb2fe619534c60a35706fb7bfc188c737f.
    
• src/hg/hgSession/hgSession.c
  • lines changed 12, context: html, text, full: html, text
    Warn user if they're about to clobber a session due to MySQL/latin1's case insensitivity.
    Thanks b0b for finding that!
    fixes #15051
    
• src/hg/hgTables/gffOut.c
  • lines changed 2, context: html, text, full: html, text
    In a genome-wide query, bed2GffLines is called once per assembly sequence;
    for scaffold-based assemblies, it can be called hundreds of thousands of times.
    When called on a very small table with rows for relatively few sequences, it
    may be called tens of thousands of times without producing any output.
    Combined with the inefficiency of allocating a sizeable hash regardless
    of whether it had any items to work on, the long delays were causing
    web timeouts. Now, if there are no incoming items, it returns immediately.
    There are still some delays from the hundreds of thousands of queries that
    return no data, but they are manageable (~45s for ~200k scaffolds).
    refs #15043
    
• src/hg/hgTables/great.c
  • lines changed 6, context: html, text, full: html, text
    allow hg18 to go to the archive server refs #14881
    
• src/hg/hgTables/greatData/supportedAssemblies.txt
  • lines changed 1, context: html, text, full: html, text
    allow hg18 to go to the archive server refs #14881
    
• src/hg/hgTables/hgTables.c
  • lines changed 7, context: html, text, full: html, text
    This is a go at libifing the CGI startup code. For all CGIs, we need to
    call a few basic setup funtions, like UDC config and CGI apoptosis.
    (For most CGIs also bottleneck). Instead of adding it to all of our
    30+ CGIs, I changed the cart*Shell functions. I think most CGIs call
    at least one of these functions. This commit removes the existing
    copy/pasted code from a few CGIs and replaces it with one call.
    Adding this to the cart-setup means that (like before), UDC is
    setup even for small JSON calls and a process is spawned to watch
    the CGI and kill it ("Apoptosis"). Any comments on whether this should
    be implemented differently are appreciated. I have not added bottleneck
    to this function right now as apparently we're calling bottleneck only
    from some of our CGIs.
    
  • lines changed 7, context: html, text, full: html, text
    Revert "This is a go at libifing the CGI startup code. For all CGIs, we need to"
    
    This reverts commit 6696987406845625c252a13b690e0c4d7d9e59fa.
    
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 2, context: html, text, full: html, text
    Add pipeline image and improve track description for hg38 DNase tracks. Tweak trackUi to leave out downloads and contact links for non-ENCODE2 assemblies. Also, update ENCODE link label to reflect its UCSC-only ENCODE.
    
• src/hg/hgTracks/hgTracks.c
  • lines changed 5, context: html, text, full: html, text
    Removing GSAID code. BrianR said that's OK.
    
  • lines changed 5, context: html, text, full: html, text
    the measureTiming for the cart must be the first call in the function.
    I got that wrong when I added the bottleneck measureTiming call.
    
  • lines changed 4, context: html, text, full: html, text
    This is a go at libifing the CGI startup code. For all CGIs, we need to
    call a few basic setup funtions, like UDC config and CGI apoptosis.
    (For most CGIs also bottleneck). Instead of adding it to all of our
    30+ CGIs, I changed the cart*Shell functions. I think most CGIs call
    at least one of these functions. This commit removes the existing
    copy/pasted code from a few CGIs and replaces it with one call.
    Adding this to the cart-setup means that (like before), UDC is
    setup even for small JSON calls and a process is spawned to watch
    the CGI and kill it ("Apoptosis"). Any comments on whether this should
    be implemented differently are appreciated. I have not added bottleneck
    to this function right now as apparently we're calling bottleneck only
    from some of our CGIs.
    
  • lines changed 4, context: html, text, full: html, text
    Revert "This is a go at libifing the CGI startup code. For all CGIs, we need to"
    
    This reverts commit 6696987406845625c252a13b690e0c4d7d9e59fa.
    
  • lines changed 5, context: html, text, full: html, text
    Revert "the measureTiming for the cart must be the first call in the function."
    
    This reverts commit ae082c232f3bf6ef30c9993e7c4ee1b7256c2f57.
    
  • lines changed 5, context: html, text, full: html, text
    Revert "Removing GSAID code. BrianR said that's OK."
    
    This reverts commit 324e56bb2fe619534c60a35706fb7bfc188c737f.
    
• src/hg/hgTracks/mainMain.c
  • lines changed 5, context: html, text, full: html, text
    Removing GSAID code. BrianR said that's OK.
    
  • lines changed 4, context: html, text, full: html, text
    This is a go at libifing the CGI startup code. For all CGIs, we need to
    call a few basic setup funtions, like UDC config and CGI apoptosis.
    (For most CGIs also bottleneck). Instead of adding it to all of our
    30+ CGIs, I changed the cart*Shell functions. I think most CGIs call
    at least one of these functions. This commit removes the existing
    copy/pasted code from a few CGIs and replaces it with one call.
    Adding this to the cart-setup means that (like before), UDC is
    setup even for small JSON calls and a process is spawned to watch
    the CGI and kill it ("Apoptosis"). Any comments on whether this should
    be implemented differently are appreciated. I have not added bottleneck
    to this function right now as apparently we're calling bottleneck only
    from some of our CGIs.
    
  • lines changed 4, context: html, text, full: html, text
    Revert "This is a go at libifing the CGI startup code. For all CGIs, we need to"
    
    This reverts commit 6696987406845625c252a13b690e0c4d7d9e59fa.
    
  • lines changed 5, context: html, text, full: html, text
    Revert "Removing GSAID code. BrianR said that's OK."
    
    This reverts commit 324e56bb2fe619534c60a35706fb7bfc188c737f.
    
• src/hg/hgTracks/pslTrack.c
  • lines changed 115, context: html, text, full: html, text
    Removing GSAID code. BrianR said that's OK.
    
  • lines changed 10, context: html, text, full: html, text
    This is a go at libifing the CGI startup code. For all CGIs, we need to
    call a few basic setup funtions, like UDC config and CGI apoptosis.
    (For most CGIs also bottleneck). Instead of adding it to all of our
    30+ CGIs, I changed the cart*Shell functions. I think most CGIs call
    at least one of these functions. This commit removes the existing
    copy/pasted code from a few CGIs and replaces it with one call.
    Adding this to the cart-setup means that (like before), UDC is
    setup even for small JSON calls and a process is spawned to watch
    the CGI and kill it ("Apoptosis"). Any comments on whether this should
    be implemented differently are appreciated. I have not added bottleneck
    to this function right now as apparently we're calling bottleneck only
    from some of our CGIs.
    
  • lines changed 10, context: html, text, full: html, text
    Revert "This is a go at libifing the CGI startup code. For all CGIs, we need to"
    
    This reverts commit 6696987406845625c252a13b690e0c4d7d9e59fa.
    
  • lines changed 115, context: html, text, full: html, text
    Revert "Removing GSAID code. BrianR said that's OK."
    
    This reverts commit 324e56bb2fe619534c60a35706fb7bfc188c737f.
    
• src/hg/hgVai/hgVai.c
  • lines changed 5, context: html, text, full: html, text
    This is a go at libifing the CGI startup code. For all CGIs, we need to
    call a few basic setup funtions, like UDC config and CGI apoptosis.
    (For most CGIs also bottleneck). Instead of adding it to all of our
    30+ CGIs, I changed the cart*Shell functions. I think most CGIs call
    at least one of these functions. This commit removes the existing
    copy/pasted code from a few CGIs and replaces it with one call.
    Adding this to the cart-setup means that (like before), UDC is
    setup even for small JSON calls and a process is spawned to watch
    the CGI and kill it ("Apoptosis"). Any comments on whether this should
    be implemented differently are appreciated. I have not added bottleneck
    to this function right now as apparently we're calling bottleneck only
    from some of our CGIs.
    
  • lines changed 5, context: html, text, full: html, text
    Revert "This is a go at libifing the CGI startup code. For all CGIs, we need to"
    
    This reverts commit 6696987406845625c252a13b690e0c4d7d9e59fa.
    
• src/hg/hgVarAnnogrator/hgVarAnnogrator.c
  • lines changed 6, context: html, text, full: html, text
    This is a go at libifing the CGI startup code. For all CGIs, we need to
    call a few basic setup funtions, like UDC config and CGI apoptosis.
    (For most CGIs also bottleneck). Instead of adding it to all of our
    30+ CGIs, I changed the cart*Shell functions. I think most CGIs call
    at least one of these functions. This commit removes the existing
    copy/pasted code from a few CGIs and replaces it with one call.
    Adding this to the cart-setup means that (like before), UDC is
    setup even for small JSON calls and a process is spawned to watch
    the CGI and kill it ("Apoptosis"). Any comments on whether this should
    be implemented differently are appreciated. I have not added bottleneck
    to this function right now as apparently we're calling bottleneck only
    from some of our CGIs.
    
  • lines changed 6, context: html, text, full: html, text
    Revert "This is a go at libifing the CGI startup code. For all CGIs, we need to"
    
    This reverts commit 6696987406845625c252a13b690e0c4d7d9e59fa.
    
• src/hg/hgc/bamClick.c
  • lines changed 4, context: html, text, full: html, text
    This is a go at libifing the CGI startup code. For all CGIs, we need to
    call a few basic setup funtions, like UDC config and CGI apoptosis.
    (For most CGIs also bottleneck). Instead of adding it to all of our
    30+ CGIs, I changed the cart*Shell functions. I think most CGIs call
    at least one of these functions. This commit removes the existing
    copy/pasted code from a few CGIs and replaces it with one call.
    Adding this to the cart-setup means that (like before), UDC is
    setup even for small JSON calls and a process is spawned to watch
    the CGI and kill it ("Apoptosis"). Any comments on whether this should
    be implemented differently are appreciated. I have not added bottleneck
    to this function right now as apparently we're calling bottleneck only
    from some of our CGIs.
    
  • lines changed 4, context: html, text, full: html, text
    Revert "This is a go at libifing the CGI startup code. For all CGIs, we need to"
    
    This reverts commit 6696987406845625c252a13b690e0c4d7d9e59fa.
    
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    Bug fix for broken click-through on restriction enzymes. refs #15052
    
  • lines changed 2, context: html, text, full: html, text
    don't require l or r in hgc links #15065
    
  • lines changed 5, context: html, text, full: html, text
    Removing GSAID code. BrianR said that's OK.
    
  • lines changed 5, context: html, text, full: html, text
    Revert "Removing GSAID code. BrianR said that's OK."
    
    This reverts commit 324e56bb2fe619534c60a35706fb7bfc188c737f.
    
• src/hg/hgc/vcfClick.c
  • lines changed 3, context: html, text, full: html, text
    This is a go at libifing the CGI startup code. For all CGIs, we need to
    call a few basic setup funtions, like UDC config and CGI apoptosis.
    (For most CGIs also bottleneck). Instead of adding it to all of our
    30+ CGIs, I changed the cart*Shell functions. I think most CGIs call
    at least one of these functions. This commit removes the existing
    copy/pasted code from a few CGIs and replaces it with one call.
    Adding this to the cart-setup means that (like before), UDC is
    setup even for small JSON calls and a process is spawned to watch
    the CGI and kill it ("Apoptosis"). Any comments on whether this should
    be implemented differently are appreciated. I have not added bottleneck
    to this function right now as apparently we're calling bottleneck only
    from some of our CGIs.
    
  • lines changed 3, context: html, text, full: html, text
    Revert "This is a go at libifing the CGI startup code. For all CGIs, we need to"
    
    This reverts commit 6696987406845625c252a13b690e0c4d7d9e59fa.
    
• src/hg/hgc/virusClick.c
  • lines changed 1, context: html, text, full: html, text
    previous commit was way overzealous, re-adding stubs for old gisaid code.
    Should have not touched this, sorry.
    
  • lines changed 1, context: html, text, full: html, text
    Revert "previous commit was way overzealous, re-adding stubs for old gisaid code."
    
    This reverts commit a9d79df3cbd3f62b8607f053db951ccc0b7647da.
    
• src/hg/htdocs/goldenPath/help/gbib.html
  • lines changed 19, context: html, text, full: html, text
    Adding a GEO wget example to GBiB page, MLQ refs #15061
    
  • lines changed 16, context: html, text, full: html, text
    Adding a proxy note in GBiB help page refs #15022
    
  • lines changed 1, context: html, text, full: html, text
    Small edit to html on GBiB page, refs #15022
    
• src/hg/htdocs/goldenPath/help/sessions.html
  • lines changed 88, context: html, text, full: html, text
    initial skeleton for this page
    
  • lines changed 22, context: html, text, full: html, text
    some more ideas for the page
    
• src/hg/htdocs/images/Chlorocebus_sabaeus.jpg
  • lines changed 0, context: html, text, full: html, text
    adding photo for chlSab2 refs #11172 from wikimedia commons user Atamari
    
• src/hg/htdocs/images/encodeDnasePipeline.png
  • lines changed 0, context: html, text, full: html, text
    Add pipeline image and improve track description for hg38 DNase tracks. Tweak trackUi to leave out downloads and contact links for non-ENCODE2 assemblies. Also, update ENCODE link label to reflect its UCSC-only ENCODE.
    
• src/hg/htdocs/robots.rr.txt
  • lines changed 3, context: html, text, full: html, text
    Updating robots.txt
    
• src/hg/htdocs/robots.txt
  • lines changed 4, context: html, text, full: html, text
    Updating robots.txt
    
• src/hg/htdocs/staff.html
  • lines changed 3, context: html, text, full: html, text
    removing CBSE from Administrative Staff section
    
• src/hg/inc/hCommon.h
  • lines changed 18, context: html, text, full: html, text
    previous commit was way overzealous, re-adding stubs for old gisaid code.
    Should have not touched this, sorry.
    
  • lines changed 18, context: html, text, full: html, text
    Revert "previous commit was way overzealous, re-adding stubs for old gisaid code."
    
    This reverts commit a9d79df3cbd3f62b8607f053db951ccc0b7647da.
    
• src/hg/inc/hui.h
  • lines changed 3, context: html, text, full: html, text
    Add pipeline image and improve track description for hg38 DNase tracks. Tweak trackUi to leave out downloads and contact links for non-ENCODE2 assemblies. Also, update ENCODE link label to reflect its UCSC-only ENCODE.
    
• src/hg/inc/jsHelper.h
  • lines changed 4, context: html, text, full: html, text
    Code review feedback from Kate: libify inclusion of libs for new React framework.
    refs #14965
    
• src/hg/inc/versionInfo.h
  • lines changed 1, context: html, text, full: html, text
    New version number v314
    
• src/hg/js/model/hgIntegrator/hgIntegratorModel.js
  • lines changed 5, context: html, text, full: html, text
    Code review feedback from Kate: DRY
    refs #14965
    
• src/hg/js/react/lib/LabeledSelect.jsx
  • lines changed 3, context: html, text, full: html, text
    Code review feedback from Kate: clarify comment.
    refs #14965
    
• src/hg/lib/cart.c
  • lines changed 11, context: html, text, full: html, text
    This is a go at libifing the CGI startup code. For all CGIs, we need to
    call a few basic setup funtions, like UDC config and CGI apoptosis.
    (For most CGIs also bottleneck). Instead of adding it to all of our
    30+ CGIs, I changed the cart*Shell functions. I think most CGIs call
    at least one of these functions. This commit removes the existing
    copy/pasted code from a few CGIs and replaces it with one call.
    Adding this to the cart-setup means that (like before), UDC is
    setup even for small JSON calls and a process is spawned to watch
    the CGI and kill it ("Apoptosis"). Any comments on whether this should
    be implemented differently are appreciated. I have not added bottleneck
    to this function right now as apparently we're calling bottleneck only
    from some of our CGIs.
    
  • lines changed 11, context: html, text, full: html, text
    Revert "This is a go at libifing the CGI startup code. For all CGIs, we need to"
    
    This reverts commit 6696987406845625c252a13b690e0c4d7d9e59fa.
    
• src/hg/lib/hCommon.c
  • lines changed 29, context: html, text, full: html, text
    Removing GSAID code. BrianR said that's OK.
    
  • lines changed 17, context: html, text, full: html, text
    previous commit was way overzealous, re-adding stubs for old gisaid code.
    Should have not touched this, sorry.
    
  • lines changed 29, context: html, text, full: html, text
    This is a go at libifing the CGI startup code. For all CGIs, we need to
    call a few basic setup funtions, like UDC config and CGI apoptosis.
    (For most CGIs also bottleneck). Instead of adding it to all of our
    30+ CGIs, I changed the cart*Shell functions. I think most CGIs call
    at least one of these functions. This commit removes the existing
    copy/pasted code from a few CGIs and replaces it with one call.
    Adding this to the cart-setup means that (like before), UDC is
    setup even for small JSON calls and a process is spawned to watch
    the CGI and kill it ("Apoptosis"). Any comments on whether this should
    be implemented differently are appreciated. I have not added bottleneck
    to this function right now as apparently we're calling bottleneck only
    from some of our CGIs.
    
  • lines changed 29, context: html, text, full: html, text
    Revert "This is a go at libifing the CGI startup code. For all CGIs, we need to"
    
    This reverts commit 6696987406845625c252a13b690e0c4d7d9e59fa.
    
  • lines changed 17, context: html, text, full: html, text
    Revert "previous commit was way overzealous, re-adding stubs for old gisaid code."
    
    This reverts commit a9d79df3cbd3f62b8607f053db951ccc0b7647da.
    
  • lines changed 29, context: html, text, full: html, text
    Revert "Removing GSAID code. BrianR said that's OK."
    
    This reverts commit 324e56bb2fe619534c60a35706fb7bfc188c737f.
    
• src/hg/lib/hdb.c
  • lines changed 3, context: html, text, full: html, text
    Removing GSAID code. BrianR said that's OK.
    
  • lines changed 3, context: html, text, full: html, text
    Revert "Removing GSAID code. BrianR said that's OK."
    
    This reverts commit 324e56bb2fe619534c60a35706fb7bfc188c737f.
    
• src/hg/lib/hui.c
  • lines changed 7, context: html, text, full: html, text
    Add pipeline image and improve track description for hg38 DNase tracks. Tweak trackUi to leave out downloads and contact links for non-ENCODE2 assemblies. Also, update ENCODE link label to reflect its UCSC-only ENCODE.
    
• src/hg/lib/jsHelper.c
  • lines changed 23, context: html, text, full: html, text
    Code review feedback from Kate: libify inclusion of libs for new React framework.
    refs #14965
    
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Removing GSAID code. BrianR said that's OK.
    
  • lines changed 1, context: html, text, full: html, text
    taking back another gisaid change.
    
  • lines changed 1, context: html, text, full: html, text
    Revert "taking back another gisaid change."
    
    This reverts commit 89fc2fe7eba3cff4710396b22d8bf641b63d0765.
    
  • lines changed 1, context: html, text, full: html, text
    Revert "Removing GSAID code. BrianR said that's OK."
    
    This reverts commit 324e56bb2fe619534c60a35706fb7bfc188c737f.
    
• src/hg/lib/ucscRetroInfo.as
  • lines changed 5, context: html, text, full: html, text
    Updated column descriptions.
    
• src/hg/lib/ucscRetroInfo.c
  • lines changed 4, context: html, text, full: html, text
    Removed old code that was commented out.
    
• src/hg/lib/ucscRetroInfo.sql
  • lines changed 8, context: html, text, full: html, text
    Updated column descriptions.
    
• src/hg/lib/validateGisaid.c
  • lines changed 21, context: html, text, full: html, text
    Removing GSAID code. BrianR said that's OK.
    
  • lines changed 12, context: html, text, full: html, text
    previous commit was way overzealous, re-adding stubs for old gisaid code.
    Should have not touched this, sorry.
    
  • lines changed 12, context: html, text, full: html, text
    Revert "previous commit was way overzealous, re-adding stubs for old gisaid code."
    
    This reverts commit a9d79df3cbd3f62b8607f053db951ccc0b7647da.
    
  • lines changed 21, context: html, text, full: html, text
    Revert "Removing GSAID code. BrianR said that's OK."
    
    This reverts commit 324e56bb2fe619534c60a35706fb7bfc188c737f.
    
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeHaibGenotype.txt
  • lines changed 13, context: html, text, full: html, text
    Add data correction from Flo Pauli at HudsonAlpha. refs #14946
    
• src/hg/makeDb/doc/nanPar1/initialBuild.txt
  • lines changed 70, context: html, text, full: html, text
    running up genbank refs #15056
    
• src/hg/makeDb/doc/rhiRox1/fetchChrMt.sh
  • lines changed 14, context: html, text, full: html, text
    done with rhiRox1 build refs #14438
    
• src/hg/makeDb/doc/rhiRox1/initialBuild.txt
  • lines changed 554, context: html, text, full: html, text
    done with rhiRox1 build refs #14438
    
• src/hg/makeDb/doc/rhiRox1/lastzRuns.txt
  • lines changed 77, context: html, text, full: html, text
    done with rhiRox1 build refs #14438
    
• src/hg/makeDb/doc/rhiRox1/unplaced.pl
  • lines changed 48, context: html, text, full: html, text
    done with rhiRox1 build refs #14438
    
• src/hg/makeDb/doc/xenTro2.txt
  • lines changed 15, context: html, text, full: html, text
    adding liftovers from frog to frog versions refs #15023
    
• src/hg/makeDb/doc/xenTro3.txt
  • lines changed 14, context: html, text, full: html, text
    adding liftovers from frog to frog versions refs #15023
    
• src/hg/makeDb/doc/xenTro7.txt
  • lines changed 29, context: html, text, full: html, text
    adding liftovers from frog to frog versions refs #15023
    
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 1, context: html, text, full: html, text
    turning on chlSab2 refs #11172
    
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 22, context: html, text, full: html, text
    Added nanPar Nanorana parkeri refs #15056
    
  • lines changed 23, context: html, text, full: html, text
    Added chlSab Chlorocebus sabaeus refs #11172
    
  • lines changed 103, context: html, text, full: html, text
    DO NOT NEED genbank.mrna.xeno except for human, mouse refs #11172
    
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • lines changed 2, context: html, text, full: html, text
    Added danRer10 to hgwbeta.dbs; re-added danRer7 to hgwdev.dbs; refs #14017
    
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 1, context: html, text, full: html, text
    Added danRer10 to hgwbeta.dbs; re-added danRer7 to hgwdev.dbs; refs #14017
    
  • lines changed 1, context: html, text, full: html, text
    turning on chlSab2 refs #11172
    
• src/hg/makeDb/genbank/src/lib/gbGenome.c
  • lines changed 2, context: html, text, full: html, text
    Added nanPar Nanorana parkeri refs #15056
    
  • lines changed 2, context: html, text, full: html, text
    Added chlSab Chlorocebus sabaeus refs #11172
    
• src/hg/makeDb/schema/all.joiner
  • lines changed 10, context: html, text, full: html, text
    add rhiRox1 rules refs #14438
    
  • lines changed 11, context: html, text, full: html, text
    adding chlSab2 refs #11172
    
• src/hg/makeDb/trackDb/affyAllExonProbes.html
  • lines changed 2, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/birds/geoFor1/cons7way.html
  • lines changed 5, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/cat/felCat3/multiz4way.html
  • lines changed 2, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/cat/felCat4/cons6way.html
  • lines changed 7, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/chicken/galGal3/multiz7way.html
  • lines changed 2, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/chimp/panTro3/cons12way.html
  • lines changed 5, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/chlorocebus/chlSab2/description.html
  • lines changed 63, context: html, text, full: html, text
    initial files for chlSab2 refs #11172
    
• src/hg/makeDb/trackDb/chlorocebus/chlSab2/gap.html
  • lines changed 31, context: html, text, full: html, text
    initial files for chlSab2 refs #11172
    
• src/hg/makeDb/trackDb/chlorocebus/chlSab2/gold.html
  • lines changed 34, context: html, text, full: html, text
    initial files for chlSab2 refs #11172
    
• src/hg/makeDb/trackDb/chlorocebus/chlSab2/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    initial files for chlSab2 refs #11172
    
  • lines changed 5, context: html, text, full: html, text
    add gold table search rule refs #11172
    
• src/hg/makeDb/trackDb/cow/bosTau4/multiz5way.html
  • lines changed 4, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/drosophila/dm2/multiz15way.html
  • lines changed 1, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/drosophila/dm3/multiz15way.html
  • lines changed 1, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/drosophila/dm6/cons27way.html
  • lines changed 5, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/ebola/bunEbo1/cons160way.html
  • lines changed 2, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/ebola/eboVir2/cons49way.html
  • lines changed 2, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/ebola/eboVir3/cons160way.html
  • lines changed 5, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/ebola/resEbo1/cons160way.html
  • lines changed 2, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/ebola/sudEbo1/cons160way.html
  • lines changed 2, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/ebola/taiEbo1/cons160way.html
  • lines changed 2, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/ebola/zaiEbo1/cons160way.html
  • lines changed 2, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/fugu/fr2/multiz5way.html
  • lines changed 2, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/gorilla/gorGor3/cons11way.html
  • lines changed 5, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/horse/equCab2/multiz6way.html
  • lines changed 4, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/human/affyHuEx1.html
  • lines changed 2, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/human/chainNetVertebrate.ra
  • lines changed 17, context: html, text, full: html, text
    Added danRer10 section for zebrafish chain/net track on hg38; corrected entry in danRer7 section; refs #14017
    
• src/hg/makeDb/trackDb/human/hg16/exoniphy.html
  • lines changed 2, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/human/hg17/encodeDless.html
  • lines changed 1, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/human/hg17/encodeMavidCons.html
  • lines changed 3, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/human/hg17/encodeMavidElements.html
  • lines changed 4, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/human/hg17/encodeMlaganCons.html
  • lines changed 3, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/human/hg17/encodeMlaganElements.html
  • lines changed 4, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/human/hg17/encodeMsaElements.html
  • lines changed 3, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/human/hg17/encodeTbaCons.html
  • lines changed 4, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/human/hg17/encodeTbaElements.html
  • lines changed 5, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/human/hg17/exoniphy.html
  • lines changed 1, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/human/hg17/exoniphyHMR.html
  • lines changed 1, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/human/hg17/multiz10way.html
  • lines changed 2, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/human/hg17/multiz17way.html
  • lines changed 2, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/human/hg17/multiz7way.html
  • lines changed 2, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/human/hg17/seg.html
  • lines changed 2, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/human/hg18/cons44way.html
  • lines changed 5, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/human/hg18/exoniphy.html
  • lines changed 1, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/human/hg18/mammalPsg.html
  • lines changed 5, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/human/hg18/multiz28way.html
  • lines changed 4, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/human/hg18/multizPrimate.html
  • lines changed 4, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/human/hg18/phyloPCons28way.html
  • lines changed 4, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/human/hg18/phyloPConsLs44way.html
  • lines changed 13, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/human/hg19/cons100way.html
  • lines changed 5, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/human/hg19/cons46way.html
  • lines changed 5, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/human/hg19/exoniphy.html
  • lines changed 1, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/human/hg38/cons7way.html
  • lines changed 4, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeRegDnase.html
  • lines changed 24, context: html, text, full: html, text
    Add pipeline image and improve track description for hg38 DNase tracks. Tweak trackUi to leave out downloads and contact links for non-ENCODE2 assemblies. Also, update ENCODE link label to reflect its UCSC-only ENCODE.
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeRegDnase.ra
  • lines changed 3, context: html, text, full: html, text
    Add pipeline image and improve track description for hg38 DNase tracks. Tweak trackUi to leave out downloads and contact links for non-ENCODE2 assemblies. Also, update ENCODE link label to reflect its UCSC-only ENCODE.
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeRegDnaseClustered.html
  • lines changed 23, context: html, text, full: html, text
    Add pipeline image and improve track description for hg38 DNase tracks. Tweak trackUi to leave out downloads and contact links for non-ENCODE2 assemblies. Also, update ENCODE link label to reflect its UCSC-only ENCODE.
    
• src/hg/makeDb/trackDb/human/hg38/wgEncodeRegDnaseSignal.html
  • lines changed 18, context: html, text, full: html, text
    Add pipeline image and improve track description for hg38 DNase tracks. Tweak trackUi to leave out downloads and contact links for non-ENCODE2 assemblies. Also, update ENCODE link label to reflect its UCSC-only ENCODE.
    
• src/hg/makeDb/trackDb/human/iscaComposite.html
  • lines changed 19, context: html, text, full: html, text
    some changes to change ISCA to ClinGen
    
• src/hg/makeDb/trackDb/human/phastBias.html
  • lines changed 2, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 21, context: html, text, full: html, text
    some changes to change ISCA to ClinGen
    
• src/hg/makeDb/trackDb/lamprey/petMar1/multiz6way.html
  • lines changed 4, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/lamprey/petMar2/cons7way.html
  • lines changed 5, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/lancelet/braFlo1/multiz5way.html
  • lines changed 4, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/lizard/anoCar2/cons7way.html
  • lines changed 5, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    initial files for chlSab2 refs #11172
    
• src/hg/makeDb/trackDb/marmoset/calJac1/multiz9way.html
  • lines changed 4, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/marmoset/calJac3/cons13way.html
  • lines changed 5, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/medaka/oryLat1/multiz5way.html
  • lines changed 2, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/medaka/oryLat2/multiz5way.html
  • lines changed 2, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/mouse/mm10/cons60way.html
  • lines changed 5, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/mouse/mm8/multiz17way.html
  • lines changed 2, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/mouse/mm9/cons30way.html
  • lines changed 7, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/mouse/mm9/exoniphy.html
  • lines changed 1, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/mouse/mm9/multiz30way.html
  • lines changed 4, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/opossum/monDom4/multiz7way.html
  • lines changed 2, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/opossum/monDom5/multiz9way.html
  • lines changed 2, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/orangutan/ponAbe2/multiz8way.html
  • lines changed 4, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/phastConsElements.html
  • lines changed 1, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/platypus/ornAna1/multiz6way.html
  • lines changed 2, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/rat/rn4/multiz9way.html
  • lines changed 2, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/rat/rn5/cons13way.html
  • lines changed 5, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/refGene.html
  • lines changed 2, context: html, text, full: html, text
    Made changes to track visibility settings; made minor changes to description pages; refs #14017
    
• src/hg/makeDb/trackDb/refGene.new.html
  • lines changed 2, context: html, text, full: html, text
    Made changes to track visibility settings; made minor changes to description pages; refs #14017
    
• src/hg/makeDb/trackDb/rhinopithecus/rhiRox1/trackDb.ra
  • lines changed 5, context: html, text, full: html, text
    add gold table search rule #14438
    
• src/hg/makeDb/trackDb/stickleback/gasAcu1/multiz8way.html
  • lines changed 2, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/worm/ce10/cons7way.html
  • lines changed 5, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/worm/ce10/cons9way.html
  • lines changed 5, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/worm/ce6/multiz6way.html
  • lines changed 4, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/worm/ce9/cons10way.html
  • lines changed 5, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/xenTro/xenTro3/cons9way.html
  • lines changed 5, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/zebrafish/danRer10/trackDb.ra
  • lines changed 6, context: html, text, full: html, text
    Made changes to track visibility settings; made minor changes to description pages; refs #14017
    
• src/hg/makeDb/trackDb/zebrafish/danRer4/multiz7way.html
  • lines changed 2, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/zebrafish/danRer6/multiz6way.html
  • lines changed 3, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/zebrafish/danRer7/cons8way.html
  • lines changed 5, context: html, text, full: html, text
    Updating links to Adam Siepels site at CSHL, refs #15050
    
• src/hg/makeDb/trackDb/zebrafish/mgcFullMrna.html
  • lines changed 5, context: html, text, full: html, text
    Made changes to track visibility settings; made minor changes to description pages; refs #14017
    
• src/hg/makeDb/trackDb/zebrafish/trackDb.chainNet.ra
  • lines changed 6, context: html, text, full: html, text
    Added hg38 entry so proper values would be displayed on chain/net track description page; refs #14017
    
• src/hg/utils/automation/makePushQSql.pl
  • lines changed 5, context: html, text, full: html, text
    correctly setup file lists for reciprocalBest downloads refs #14560
    
• src/hg/utils/automation/ncbiToUcsc.sh
  • lines changed 178, context: html, text, full: html, text
    convert NCBI download files into 2bit and AGP file with UCSC naming scheme refs #14560
    
• src/hg/utils/makefile
  • lines changed 1, context: html, text, full: html, text
    adding genePredToBigGenePred to the build refs #15067
    
• src/utils/qa/qaAutoTrack.sh
  • lines changed 50, context: html, text, full: html, text
    Moving showHelp function to section with other functions
    
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v314 final build refs #14991
    

• lines changed: 2762
• files changed: 205