All File Changes
v321_preview2 to v321_base (2015-08-17 to 2015-08-24) v321
- src/hg/cirm/cdw/flowCharts/sqlToTxt/sqlToTxt.c
- lines changed 273, context: html, text, full: html, text
A program for Jim that queries SQL tables and makes flowcharts, still a very early prototype
- lines changed 208, context: html, text, full: html, text
The basic program is working now, it still needs a lot more work though...
- lines changed 297, context: html, text, full: html, text
A program for the CIRM project. Seems to be at a decent working point, the output printing still needs some fine tuning
- lines changed 42, context: html, text, full: html, text
Ironing out the pixel placement, the program now runs and prints a .json file that can be used to generate a flowchart with the go.js javascript module
- lines changed 30, context: html, text, full: html, text
The program now has two output options, go.js and D3 forcelayout
- lines changed 22, context: html, text, full: html, text
The program has a .html file embeded in it, now with the forceLayout option the program will print a .json file and a .html file.
- src/hg/hgCustom/hgCustom.c
- lines changed 20, context: html, text, full: html, text
reorderd list of data types: remotes first, then alpha. Added bigGenePred to list of remote data types
- src/hg/hgTracks/config.c
- lines changed 3, context: html, text, full: html, text
revert changes made for #6551
- src/hg/hgTracks/extTools.c
- lines changed 11, context: html, text, full: html, text
adding chopchop and nebcutter and fixing an obvious bug. Also adding a
little tool that parse a Chrome HTTP trace and creates the extTools.ra
entry mostly automatically. refs #15113
- lines changed 18, context: html, text, full: html, text
simpliying code and fixing a bug where there was one slash too many, no
need for npu here. refs #15113
- src/hg/hgTracks/extTools.ra
- lines changed 240, context: html, text, full: html, text
adapt spelling and activate mouse overs in extTools menu, refs #15113
- lines changed 71, context: html, text, full: html, text
adding chopchop and nebcutter and fixing an obvious bug. Also adding a
little tool that parse a Chrome HTTP trace and creates the extTools.ra
entry mostly automatically. refs #15113
- lines changed 1, context: html, text, full: html, text
forgot one line in last commit
- lines changed 47, context: html, text, full: html, text
adding external tool regrna2, refs #15113
- lines changed 268, context: html, text, full: html, text
sorting tools by topic, refs #15113, note 80
- src/hg/hgTracks/hgTracks.c
- lines changed 8, context: html, text, full: html, text
fix a few problems that Brian found in #6551
- lines changed 10, context: html, text, full: html, text
another round of trying to get visibilities in the cart to work right
- lines changed 46, context: html, text, full: html, text
revert changes made for #6551
- src/hg/hgTracks/menu.c
- lines changed 3, context: html, text, full: html, text
adapt spelling and activate mouse overs in extTools menu, refs #15113
- lines changed 8, context: html, text, full: html, text
fixing mouse overs in extTools, refs #15113
- lines changed 2, context: html, text, full: html, text
Recapitalized a couple of menu items, refs #15113
- src/hg/hgc/hgc.c
- lines changed 15, context: html, text, full: html, text
a little tweak for hgc bigPsl support so only item clicked on is shown
- src/hg/htdocs/FAQ/FAQformat.html
- lines changed 1, context: html, text, full: html, text
suggested at an engineering meeting
- src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
- lines changed 15, context: html, text, full: html, text
adding HAL as a supported type for Track Hubs
- src/hg/htdocs/goldenPath/newsarch.html
- lines changed 22, context: html, text, full: html, text
adding [sold out] to ashg announcement. adding mention of blog post that was pushed last week, but apparently never checked in
- src/hg/htdocs/images/Brugia_malayi.jpg
- lines changed 0, context: html, text, full: html, text
photo from CDC refs #15209
- src/hg/htdocs/images/Bursaphelenchus_xylophilus.jpg
- lines changed 0, context: html, text, full: html, text
adding photo for burXyl1 from USDA photo refs #15209
- src/hg/htdocs/images/Haemonchus_contortus.jpg
- lines changed 0, context: html, text, full: html, text
adding image for haeCon from CSIRO refs #15209
- src/hg/htdocs/images/Meloidogyne_incognita.jpg
- lines changed 0, context: html, text, full: html, text
adding photo for melInc from USDA images refs #15209
- src/hg/htdocs/images/Panagrellus_redivivus.jpg
- lines changed 0, context: html, text, full: html, text
photo for panRed1 from wikimedia commons refs #15209
- src/hg/htdocs/images/Pristionchus_exspectatus.jpg
- lines changed 0, context: html, text, full: html, text
adding Pristionchus photo from Max Planck Institute refs #15209
- src/hg/htdocs/indexNews.html
- lines changed 57, context: html, text, full: html, text
adding [sold out] to ashg announcement. adding mention of blog post that was pushed last week, but apparently never checked in
- src/hg/htdocs/style/nice_menu.css
- lines changed 3, context: html, text, full: html, text
comitting stylesheet without capitalize attribute, refs #15113
- src/hg/htdocs/training/index.html
- lines changed 1, context: html, text, full: html, text
adding [sold out] to ashg announcement. adding mention of blog post that was pushed last week, but apparently never checked in
- src/hg/inc/cart.h
- lines changed 1, context: html, text, full: html, text
revert changes made for #6551
- src/hg/inc/versionInfo.h
- src/hg/js/model/hgChooseDb/hgChooseDbModel.js
- lines changed 1, context: html, text, full: html, text
Concurrent POSTs by multiple ui event handlers were causing
cart-saving race conditions like this: on the JS/client side, ui
handler A sets a new cart var while sending a cartJson command, and
concurrently ui handler B sends some other command. On the server
side, if command B starts before command A finishes, and then B
finishes after A finishes, then A's new cart var won't be in the cart
that B closes out, and the new cart var will be lost.
We still want concurrent POSTs so that we can fetch big old trackDb
concurrently with smaller things that may arrive first. We can avoid
losing cart vars by accumulating cart var settings from all cartJson
commands, while queueing up the command objects. When all ui handlers
have fired, the queue is flushed; it POSTs each command along with the
accumulated set of cart vars, so that no matter which command finishes
last, all of the cart var settings will be stored in the cart.
The catch is that now we have to remember to cart.flush! ImModel
takes care of it for ui handlers, but models that send out requests
when initializing have to call it too.
An ugly hack to manually merge cart vars has been removed from
CladeOrgDbMixin and hgIntegrator -- cart.js merges them now.
There could still be race conditions from conflicting or dependent
commands running concurrently -- developers still need to prevent
those.
- src/hg/js/model/hgIntegrator/hgIntegratorModel.js
- lines changed 5, context: html, text, full: html, text
Concurrent POSTs by multiple ui event handlers were causing
cart-saving race conditions like this: on the JS/client side, ui
handler A sets a new cart var while sending a cartJson command, and
concurrently ui handler B sends some other command. On the server
side, if command B starts before command A finishes, and then B
finishes after A finishes, then A's new cart var won't be in the cart
that B closes out, and the new cart var will be lost.
We still want concurrent POSTs so that we can fetch big old trackDb
concurrently with smaller things that may arrive first. We can avoid
losing cart vars by accumulating cart var settings from all cartJson
commands, while queueing up the command objects. When all ui handlers
have fired, the queue is flushed; it POSTs each command along with the
accumulated set of cart vars, so that no matter which command finishes
last, all of the cart var settings will be stored in the cart.
The catch is that now we have to remember to cart.flush! ImModel
takes care of it for ui handlers, but models that send out requests
when initializing have to call it too.
An ugly hack to manually merge cart vars has been removed from
CladeOrgDbMixin and hgIntegrator -- cart.js merges them now.
There could still be race conditions from conflicting or dependent
commands running concurrently -- developers still need to prevent
those.
- src/hg/js/model/lib/CladeOrgDbMixin.js
- lines changed 15, context: html, text, full: html, text
Concurrent POSTs by multiple ui event handlers were causing
cart-saving race conditions like this: on the JS/client side, ui
handler A sets a new cart var while sending a cartJson command, and
concurrently ui handler B sends some other command. On the server
side, if command B starts before command A finishes, and then B
finishes after A finishes, then A's new cart var won't be in the cart
that B closes out, and the new cart var will be lost.
We still want concurrent POSTs so that we can fetch big old trackDb
concurrently with smaller things that may arrive first. We can avoid
losing cart vars by accumulating cart var settings from all cartJson
commands, while queueing up the command objects. When all ui handlers
have fired, the queue is flushed; it POSTs each command along with the
accumulated set of cart vars, so that no matter which command finishes
last, all of the cart var settings will be stored in the cart.
The catch is that now we have to remember to cart.flush! ImModel
takes care of it for ui handlers, but models that send out requests
when initializing have to call it too.
An ugly hack to manually merge cart vars has been removed from
CladeOrgDbMixin and hgIntegrator -- cart.js merges them now.
There could still be race conditions from conflicting or dependent
commands running concurrently -- developers still need to prevent
those.
- src/hg/js/model/lib/ImModel.js
- lines changed 1, context: html, text, full: html, text
Concurrent POSTs by multiple ui event handlers were causing
cart-saving race conditions like this: on the JS/client side, ui
handler A sets a new cart var while sending a cartJson command, and
concurrently ui handler B sends some other command. On the server
side, if command B starts before command A finishes, and then B
finishes after A finishes, then A's new cart var won't be in the cart
that B closes out, and the new cart var will be lost.
We still want concurrent POSTs so that we can fetch big old trackDb
concurrently with smaller things that may arrive first. We can avoid
losing cart vars by accumulating cart var settings from all cartJson
commands, while queueing up the command objects. When all ui handlers
have fired, the queue is flushed; it POSTs each command along with the
accumulated set of cart vars, so that no matter which command finishes
last, all of the cart var settings will be stored in the cart.
The catch is that now we have to remember to cart.flush! ImModel
takes care of it for ui handlers, but models that send out requests
when initializing have to call it too.
An ugly hack to manually merge cart vars has been removed from
CladeOrgDbMixin and hgIntegrator -- cart.js merges them now.
There could still be race conditions from conflicting or dependent
commands running concurrently -- developers still need to prevent
those.
- src/hg/js/model/lib/cart.js
- lines changed 224, context: html, text, full: html, text
Concurrent POSTs by multiple ui event handlers were causing
cart-saving race conditions like this: on the JS/client side, ui
handler A sets a new cart var while sending a cartJson command, and
concurrently ui handler B sends some other command. On the server
side, if command B starts before command A finishes, and then B
finishes after A finishes, then A's new cart var won't be in the cart
that B closes out, and the new cart var will be lost.
We still want concurrent POSTs so that we can fetch big old trackDb
concurrently with smaller things that may arrive first. We can avoid
losing cart vars by accumulating cart var settings from all cartJson
commands, while queueing up the command objects. When all ui handlers
have fired, the queue is flushed; it POSTs each command along with the
accumulated set of cart vars, so that no matter which command finishes
last, all of the cart var settings will be stored in the cart.
The catch is that now we have to remember to cart.flush! ImModel
takes care of it for ui handlers, but models that send out requests
when initializing have to call it too.
An ugly hack to manually merge cart vars has been removed from
CladeOrgDbMixin and hgIntegrator -- cart.js merges them now.
There could still be race conditions from conflicting or dependent
commands running concurrently -- developers still need to prevent
those.
- src/hg/lib/annoStreamDb.c
- lines changed 9, context: html, text, full: html, text
Watch out for another class of unsorted tables -- pubs*.
- src/hg/lib/cart.c
- lines changed 5, context: html, text, full: html, text
revert changes made for #6551
- src/hg/lib/cartJson.c
- lines changed 19, context: html, text, full: html, text
Wrapping an errCatch around cartTrackDbInit so that if we switch to
some database on hgwdev that is in dbDb but doesn't have a trackDb,
we can return an empty groupedTrackDb instead of causing a JSON parse
error.
- src/hg/makeDb/doc/hg18.txt
- lines changed 2, context: html, text, full: html, text
Updating DGV with new files after they fixed a couple bad names found by Matt.
refs #15767
- src/hg/makeDb/doc/hg19.txt
- lines changed 6, context: html, text, full: html, text
Updating DGV with new files after they fixed a couple bad names found by Matt.
refs #15767
- src/hg/makeDb/doc/hg38/hg19MassiveLift.txt
- lines changed 7, context: html, text, full: html, text
Documentation for the non-coding RNA track, refs #11694
- src/hg/makeDb/doc/hg38/hg38.txt
- lines changed 25, context: html, text, full: html, text
update cloneEndbadEnds table load for BAC ends refs #13713
- src/hg/makeDb/doc/hg38/lastzRuns.txt
- lines changed 194, context: html, text, full: html, text
completed lastz runs for vicPac2 orcOrc1 speTri2 loxAfr3 hetGla2 felCat8 musFur1 dasNov3 panHod1 capHir1 triMan1 conCri1 echTel2 micMur2 refs #14560
- src/hg/makeDb/doc/hg38/stsMap.txt
- lines changed 294, context: html, text, full: html, text
done with stsMap track build refs #15524
- lines changed 6, context: html, text, full: html, text
fix leaked in hg19 results into stsMap refs #15524
- src/hg/makeDb/doc/hg38/variation.txt
- lines changed 6, context: html, text, full: html, text
Updating DGV with new files after they fixed a couple bad names found by Matt.
refs #15767
- src/hg/makeDb/doc/mm10.txt
- lines changed 45, context: html, text, full: html, text
pslClone needs to clone the statistics as well (no redmine)
- src/hg/makeDb/doc/worms/ascSuu1.txt
- lines changed 57, context: html, text, full: html, text
done with genbank run refs #15209
- src/hg/makeDb/doc/worms/bruMal2.txt
- lines changed 92, context: html, text, full: html, text
rerun assembly with wolbachia sequence and add correct photo refs #15209
- src/hg/makeDb/doc/worms/haeCon2.txt
- lines changed 17, context: html, text, full: html, text
adding correct photo from CSIRO refs #15209
- src/hg/makeDb/doc/worms/lastz.ancCey1.txt
- lines changed 812, context: html, text, full: html, text
collected make doc from lastz runs refs #15209
- src/hg/makeDb/doc/worms/lastz.ascSuu1.txt
- lines changed 638, context: html, text, full: html, text
collected make doc from lastz runs refs #15209
- src/hg/makeDb/doc/worms/lastz.bruMal2.txt
- lines changed 116, context: html, text, full: html, text
collected make doc from lastz runs refs #15209
- src/hg/makeDb/doc/worms/lastz.burXyl1.txt
- lines changed 348, context: html, text, full: html, text
collected make doc from lastz runs refs #15209
- src/hg/makeDb/doc/worms/lastz.caeAng2.txt
- lines changed 1083, context: html, text, full: html, text
collected make doc from lastz runs refs #15209
- src/hg/makeDb/doc/worms/lastz.caeJap4.txt
- lines changed 1197, context: html, text, full: html, text
collected make doc from lastz runs refs #15209
- src/hg/makeDb/doc/worms/lastz.caePb3.txt
- lines changed 1368, context: html, text, full: html, text
collected make doc from lastz runs refs #15209
- src/hg/makeDb/doc/worms/lastz.caeRem4.txt
- lines changed 1311, context: html, text, full: html, text
collected make doc from lastz runs refs #15209
- src/hg/makeDb/doc/worms/lastz.caeSp111.txt
- lines changed 1140, context: html, text, full: html, text
collected make doc from lastz runs refs #15209
- src/hg/makeDb/doc/worms/lastz.caeSp51.txt
- lines changed 1032, context: html, text, full: html, text
collected make doc from lastz runs refs #15209
- src/hg/makeDb/doc/worms/lastz.cb4.txt
- lines changed 1254, context: html, text, full: html, text
collected make doc from lastz runs refs #15209
- src/hg/makeDb/doc/worms/lastz.dirImm1.txt
- lines changed 290, context: html, text, full: html, text
collected make doc from lastz runs refs #15209
- src/hg/makeDb/doc/worms/lastz.haeCon2.txt
- lines changed 696, context: html, text, full: html, text
collected make doc from lastz runs refs #15209
- src/hg/makeDb/doc/worms/lastz.hetBac1.txt
- lines changed 986, context: html, text, full: html, text
collected make doc from lastz runs refs #15209
- src/hg/makeDb/doc/worms/lastz.loaLoa1.txt
- lines changed 232, context: html, text, full: html, text
collected make doc from lastz runs refs #15209
- src/hg/makeDb/doc/worms/lastz.melHap1.txt
- lines changed 464, context: html, text, full: html, text
collected make doc from lastz runs refs #15209
- src/hg/makeDb/doc/worms/lastz.melInc2.txt
- lines changed 406, context: html, text, full: html, text
collected make doc from lastz runs refs #15209
- src/hg/makeDb/doc/worms/lastz.necAme1.txt
- lines changed 754, context: html, text, full: html, text
collected make doc from lastz runs refs #15209
- src/hg/makeDb/doc/worms/lastz.oncVol1.txt
- lines changed 116, context: html, text, full: html, text
collected make doc from lastz runs refs #15209
- src/hg/makeDb/doc/worms/lastz.panRed1.txt
- lines changed 870, context: html, text, full: html, text
collected make doc from lastz runs refs #15209
- src/hg/makeDb/doc/worms/lastz.priExs1.txt
- lines changed 580, context: html, text, full: html, text
collected make doc from lastz runs refs #15209
- src/hg/makeDb/doc/worms/lastz.priPac3.txt
- lines changed 522, context: html, text, full: html, text
collected make doc from lastz runs refs #15209
- src/hg/makeDb/doc/worms/lastz.strRat2.txt
- lines changed 928, context: html, text, full: html, text
collected make doc from lastz runs refs #15209
- src/hg/makeDb/doc/worms/lastz.triSpi1.txt
- lines changed 58, context: html, text, full: html, text
collected make doc from lastz runs refs #15209
- src/hg/makeDb/doc/worms/panRed1.txt
- lines changed 19, context: html, text, full: html, text
adding correct photo from WikiMedia Commons refs #15209
- src/hg/makeDb/doc/worms/priExs1.txt
- lines changed 11, context: html, text, full: html, text
adding a Pristionchus photo from Max Planck Institute refs #15209
- src/hg/makeDb/genbank/etc/align.dbs
- lines changed 1, context: html, text, full: html, text
Added ascSuu1 - Ascaris suum/Pig roundworm refs #15209
- src/hg/makeDb/genbank/etc/genbank.conf
- lines changed 20, context: html, text, full: html, text
Added ascSuu1 - Pig roundworm/Ascaris suum refs #15209
- lines changed 11, context: html, text, full: html, text
fixup ascSuu1 definitions for better results refs #15209
- lines changed 17, context: html, text, full: html, text
Added priExs1 - P. exspectatus refs #15209
- src/hg/makeDb/genbank/etc/hgwdev.dbs
- lines changed 1, context: html, text, full: html, text
Added ascSuu1 - Ascaris suum/Pig roundworm refs #15209
- src/hg/makeDb/genbank/src/lib/gbGenome.c
- lines changed 2, context: html, text, full: html, text
Added ascSuu1 - Pig roundworm/Ascaris suum refs #15209
- lines changed 2, context: html, text, full: html, text
Added priExsNames - P. exspectatus refs #15209
- src/hg/makeDb/outside/gencode/gencodeLoad.mk
- lines changed 4, context: html, text, full: html, text
pslClone needs to clone the statistics as well (no redmine)
- src/hg/makeDb/schema/all.joiner
- lines changed 1, context: html, text, full: html, text
Adding all.joiner entry for cloneEnds tracks. Missed in previous commit. refs #13713
- src/hg/makeDb/trackDb/alpaca/vicPac1/gap.html
- lines changed 1, context: html, text, full: html, text
Updating links on alpaca (vicPac1) track description pages, no redmine
- src/hg/makeDb/trackDb/alpaca/vicPac1/gold.html
- lines changed 1, context: html, text, full: html, text
Updating links on alpaca (vicPac1) track description pages, no redmine
- src/hg/makeDb/trackDb/drosophila/bdtnpChipperOld.html
- lines changed 13, context: html, text, full: html, text
changing links on dm2 and droYak1 track description pages, no redmine
- src/hg/makeDb/trackDb/drosophila/dm2/flyreg2.html
- lines changed 1, context: html, text, full: html, text
changing links on dm2 and droYak1 track description pages, no redmine
- src/hg/makeDb/trackDb/drosophila/dm2/picTar.html
- lines changed 1, context: html, text, full: html, text
changing links on dm2 and droYak1 track description pages, no redmine
- src/hg/makeDb/trackDb/drosophila/geneMapper.html
- lines changed 1, context: html, text, full: html, text
changing links on dm2 and droYak1 track description pages, no redmine
- src/hg/makeDb/trackDb/ebola/eboVir3/iedbBcell.html
- lines changed 1, context: html, text, full: html, text
Changing links on ebola (eboVir3) track description pages, no redmine
- src/hg/makeDb/trackDb/ebola/eboVir3/iedbBcellNeg.html
- lines changed 1, context: html, text, full: html, text
Changing links on ebola (eboVir3) track description pages, no redmine
- src/hg/makeDb/trackDb/ebola/eboVir3/iedbPred.html
- lines changed 2, context: html, text, full: html, text
Changing links on ebola (eboVir3) track description pages, no redmine
- src/hg/makeDb/trackDb/ebola/eboVir3/iedbPred1.html
- lines changed 1, context: html, text, full: html, text
Changing links on ebola (eboVir3) track description pages, no redmine
- src/hg/makeDb/trackDb/ebola/eboVir3/iedbPredClassIMac.html
- lines changed 1, context: html, text, full: html, text
Changing links on ebola (eboVir3) track description pages, no redmine
- src/hg/makeDb/trackDb/ebola/eboVir3/iedbSupp3.html
- lines changed 1, context: html, text, full: html, text
Changing links on ebola (eboVir3) track description pages, no redmine
- src/hg/makeDb/trackDb/ebola/eboVir3/iedbTcellI.html
- lines changed 1, context: html, text, full: html, text
Changing links on ebola (eboVir3) track description pages, no redmine
- src/hg/makeDb/trackDb/ebola/eboVir3/iedbTcellII.html
- lines changed 1, context: html, text, full: html, text
Changing links on ebola (eboVir3) track description pages, no redmine
- src/hg/makeDb/trackDb/ebola/eboVir3/pdb.html
- lines changed 1, context: html, text, full: html, text
Changing links on ebola (eboVir3) track description pages, no redmine
- src/hg/makeDb/trackDb/ebola/eboVir3/spAnnot.html
- lines changed 1, context: html, text, full: html, text
Changing links on ebola (eboVir3) track description pages, no redmine
- src/hg/makeDb/trackDb/ebola/eboVir3/spMut.html
- lines changed 1, context: html, text, full: html, text
Changing links on ebola (eboVir3) track description pages, no redmine
- src/hg/makeDb/trackDb/ebola/eboVir3/spStruct.html
- lines changed 1, context: html, text, full: html, text
Changing links on ebola (eboVir3) track description pages, no redmine
- src/hg/makeDb/trackDb/ferret/musFur1/description.html
- lines changed 1, context: html, text, full: html, text
changing links on various assembly gateway pages, no redmine
- src/hg/makeDb/trackDb/hedgehog/eriEur1/description.html
- lines changed 1, context: html, text, full: html, text
changing links on various assembly gateway pages, no redmine
- src/hg/makeDb/trackDb/human/cloneEnd.trackDb.ra
- lines changed 2, context: html, text, full: html, text
Shortening shortLabels to fit within our conventions, refs #13713
- lines changed 2, context: html, text, full: html, text
Adding all.joiner entry for cloneEnds tracks. Increasing default track height for clone ends coverage tracks, refs #13713
- src/hg/makeDb/trackDb/human/cnvDevDelay.html
- lines changed 48, context: html, text, full: html, text
Finalized changes to CNV Developmental Delay description page; refs #9391
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra
- lines changed 1, context: html, text, full: html, text
Fixing another entry where 'bed N .' should be 'bed N +'.
- src/hg/makeDb/trackDb/human/hg38/nonCodingRNAs.html
- lines changed 76, context: html, text, full: html, text
The .ra file and .html file for the new super track Non-coding RNAs, refs #11694
- src/hg/makeDb/trackDb/human/hg38/nonCodingRNAs.ra
- lines changed 264, context: html, text, full: html, text
The .ra file and .html file for the new super track Non-coding RNAs, refs #11694
- src/hg/makeDb/trackDb/human/hg38/trackDb.ra
- lines changed 2, context: html, text, full: html, text
making some Big tracks be hidden by default (as they should have been in
the first place)
- lines changed 6, context: html, text, full: html, text
The .ra file and .html file for the new super track Non-coding RNAs, refs #11694
- src/hg/makeDb/trackDb/human/trackDb.pgSnp.ra
- lines changed 13, context: html, text, full: html, text
changed names in Personal Genomes SNPs track from ABT to ABTutu so it's more obvious we have the archbishops sequence in there. this can go out whenever the next track on hg19 gets pushed
- src/hg/makeDb/trackDb/human/trackDb.ra
- lines changed 1, context: html, text, full: html, text
removed mention of NIH in OMIM track, though this is an old one. OMIM may have been published at NIH but it was never theirs. It belongs to John Hopkins
- lines changed 20, context: html, text, full: html, text
Consolidating release versions of dgvPlus track, refs #15767
- src/hg/makeDb/trackDb/platypus/ornAna1/description.html
- lines changed 1, context: html, text, full: html, text
changing links on various assembly gateway pages, no redmine
- src/hg/makeDb/trackDb/pubs.html
- lines changed 9, context: html, text, full: html, text
chanigng links on yeast (sacCer2 and sacCer3) track description pages, no redmine
- src/hg/makeDb/trackDb/sacCer/sacCer2/description.html
- lines changed 2, context: html, text, full: html, text
chanigng links on yeast (sacCer2 and sacCer3) track description pages, no redmine
- src/hg/makeDb/trackDb/sacCer/sacCer2/gold.html
- lines changed 1, context: html, text, full: html, text
chanigng links on yeast (sacCer2 and sacCer3) track description pages, no redmine
- src/hg/makeDb/trackDb/sacCer/sacCer3/description.html
- lines changed 1, context: html, text, full: html, text
chanigng links on yeast (sacCer2 and sacCer3) track description pages, no redmine
- src/hg/makeDb/trackDb/sacCer/uwFootprints.html
- lines changed 1, context: html, text, full: html, text
chanigng links on yeast (sacCer2 and sacCer3) track description pages, no redmine
- src/hg/makeDb/trackDb/spUniprot.html
- lines changed 1, context: html, text, full: html, text
Changing links on ebola (eboVir3) track description pages, no redmine
- src/hg/makeDb/trackDb/turkey/melGal1/description.html
- lines changed 10, context: html, text, full: html, text
changing links on various assembly gateway pages, no redmine
- src/hg/makeDb/trackDb/worm/bruMal2/description.html
- lines changed 1, context: html, text, full: html, text
updated photo refs #15209
- src/hg/makeDb/trackDb/worm/burXyl1/description.html
- lines changed 4, context: html, text, full: html, text
adding correct photo refs #15209
- lines changed 2, context: html, text, full: html, text
correct image size in the href refs #15209
- src/hg/makeDb/trackDb/worm/haeCon1/description.html
- lines changed 9, context: html, text, full: html, text
correct photo from CSIRO refs #15209
- src/hg/makeDb/trackDb/worm/haeCon2/description.html
- lines changed 4, context: html, text, full: html, text
correct photo from CSIRO refs #15209
- src/hg/makeDb/trackDb/worm/melInc1/description.html
- lines changed 6, context: html, text, full: html, text
correct photo from USDA refs #15209
- src/hg/makeDb/trackDb/worm/melInc2/description.html
- lines changed 4, context: html, text, full: html, text
correct photo from USDA refs #15209
- src/hg/makeDb/trackDb/worm/ncbiGenes.html
- lines changed 31, context: html, text, full: html, text
adding NCBI gene track definition refs #15209
- src/hg/makeDb/trackDb/worm/panRed1/description.html
- lines changed 4, context: html, text, full: html, text
correct photo from WikiMedia Commons refs #15209
- src/hg/makeDb/trackDb/worm/priExs1/description.html
- lines changed 3, context: html, text, full: html, text
adding photo from Max Planck Institute refsw #15209
- src/hg/makeDb/trackDb/worm/trackDb.chainNet.ra
- lines changed 306, context: html, text, full: html, text
adding track chainNets for hetBac1 ancCey1 necAme1 ascSuu1 priExs1 and loaLoa1 refs #15209
- src/hg/makeDb/trackDb/worm/trackDb.ra
- lines changed 18, context: html, text, full: html, text
adding NCBI gene track definition refs #15209
- src/hg/makeDb/trackDb/zebrafish/UMassChIP-Seq.html
- lines changed 20, context: html, text, full: html, text
changing links on zebrafish (danRer5) track description pages, no redmine
- src/hg/makeDb/trackDb/zebrafish/mgcFullMrna.html
- lines changed 4, context: html, text, full: html, text
changing links on zebrafish (danRer5) track description pages, no redmine
- src/hg/mouseStuff/axtChain/axtChain.c
- lines changed 18, context: html, text, full: html, text
better error messages instead of SegFault and can find no use for seqList refs #15899
- src/hg/pslFilterPrimers/pslFilterPrimers.c
- lines changed 12, context: html, text, full: html, text
bring up to spec for hg38 stsMap build refs #15524
- src/hg/stsMarkers/combineSeqPrimerPos
- lines changed 1, context: html, text, full: html, text
update to correct /usr/bin/env perl invocation line refs #15524
- src/hg/stsMarkers/findAccession.pl
- lines changed 15, context: html, text, full: html, text
fixup to naming scheme of hg38 refs #15524
- src/hg/utils/hubCheck/hubCheck.c
- lines changed 2, context: html, text, full: html, text
Fix mis-placed line in usage statement. Thanks BrianL.(no redmine)
- lines changed 0, context: html, text, full: html, text
Whitespace fixes in usage message. (no redmine)
- src/lib/annoFormatTab.c
- lines changed 11, context: html, text, full: html, text
Make sure the #header line begins with a '#' and not a '\t' in the unlikely event that all fields of the primary streamer (or even of all streamers) are deselected.
- src/lib/asParse.c
- lines changed 2, context: html, text, full: html, text
autoSql uses longblob not blob, but some .sql files have been tweaked
to use blob; treat blob same as longblob.
- src/lib/psl.c
- lines changed 8, context: html, text, full: html, text
pslClone needs to clone the statistics as well (no redmine)
- src/product/README.mysql.setup
- src/tagStorm/tagStormRenameTags/makefile
- lines changed 3, context: html, text, full: html, text
Added new tagStormRenameTags program that renames tags in a tagStorm file based on input from a 2-column file
- src/tagStorm/tagStormRenameTags/tagStormRenameTags.c
- lines changed 75, context: html, text, full: html, text
Added new tagStormRenameTags program that renames tags in a tagStorm file based on input from a 2-column file
- src/tagStorm/tagStormRenameTags/test.2col
- lines changed 7, context: html, text, full: html, text
Added new tagStormRenameTags program that renames tags in a tagStorm file based on input from a 2-column file
- src/tagStorm/tagStormRenameTags/test.in
- lines changed 5011, context: html, text, full: html, text
Added new tagStormRenameTags program that renames tags in a tagStorm file based on input from a 2-column file
- src/tagStorm/tagStormRenameTags/test.out
- lines changed 5011, context: html, text, full: html, text
Added new tagStormRenameTags program that renames tags in a tagStorm file based on input from a 2-column file
- src/utils/extToolsChromeParse
- lines changed 77, context: html, text, full: html, text
adding chopchop and nebcutter and fixing an obvious bug. Also adding a
little tool that parse a Chrome HTTP trace and creates the extTools.ra
entry mostly automatically. refs #15113
- src/utils/makefile
- lines changed 2, context: html, text, full: html, text
adding chopchop and nebcutter and fixing an obvious bug. Also adding a
little tool that parse a Chrome HTTP trace and creates the extTools.ra
entry mostly automatically. refs #15113
- src/utils/qa/weeklybld/buildEnv.csh
- lines changed 3, context: html, text, full: html, text
v321 final build refs #15836
- lines changed: 31234
- files changed: 163
