All File Changes

v408_base to v409_preview (2020-12-07 to 2021-01-04) v409

• confs/asia.hg.conf
  • lines changed 4, context: html, text, full: html, text
    5bf29012eeede40db3a949d431a8c05230f1ecc3 Sun Dec 20 01:12:02 2020 -0800
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
  • lines changed 4, context: html, text, full: html, text
    5bf29012eeede40db3a949d431a8c05230f1ecc3 Sun Dec 20 01:12:02 2020 -0800
    Installing updated hg.conf files from UCSC servers
• confs/hgwbeta.hg.conf
  • lines changed 4, context: html, text, full: html, text
    e82f1fbee1f7f61fe4abb712cabf66140ca7a43d Sun Dec 13 01:11:39 2020 -0800
    Installing updated hg.conf files from UCSC servers
• confs/hgwdev.hg.conf
  • lines changed 0, context: html, text, full: html, text
    5bf29012eeede40db3a949d431a8c05230f1ecc3 Sun Dec 20 01:12:02 2020 -0800
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 4, context: html, text, full: html, text
    5bf29012eeede40db3a949d431a8c05230f1ecc3 Sun Dec 20 01:12:02 2020 -0800
    Installing updated hg.conf files from UCSC servers
• src/hca/fromGeo/geoToHcaStorm/geoToHcaStorm.c
  • lines changed 1, context: html, text, full: html, text
    b626835f2a7ce78bb6b5b40100d656d225f9f3ca Sat Dec 19 11:33:35 2020 -0800
    Removing debugging message.
• src/hca/hcaUnpack5/hcaUnpack5.c
  • lines changed 699, context: html, text, full: html, text
    0354af7336d81b28d019287703d37be09d32d5c4 Sat Jan 2 19:39:26 2021 -0800
    This made a useful output for the heart cell atlas muscle subset in hdf5 format, converting this file to stuff the cell browser and genome browser understand.
• src/hca/hcaUnpack5/makefile
  • lines changed 4, context: html, text, full: html, text
    0354af7336d81b28d019287703d37be09d32d5c4 Sat Jan 2 19:39:26 2021 -0800
    This made a useful output for the heart cell atlas muscle subset in hdf5 format, converting this file to stuff the cell browser and genome browser understand.
• src/hca/hcat/hcatParseParth/hcatParseParth.c
  • lines changed 45, context: html, text, full: html, text
    5f2b7d5a6a6942d6676b0a98427ad1b91dbee4c9 Wed Oct 9 15:46:07 2019 -0700
    Adjusting for them turning everything into lists.
  • lines changed 14, context: html, text, full: html, text
    114397ec2020824f4cdd0eae3ddce83c86f5c4e7 Sat Dec 19 11:33:09 2020 -0800
    Finally committing this small fix. This should be viewed as one-shot code as it is just a way to pull down data from a server no longer maintained.
• src/hca/hcat/mysite/hcat/admin.py
  • lines changed 44, context: html, text, full: html, text
    d32a1c4535597376154d2e4726edceb34a7b1612 Tue Oct 8 15:28:26 2019 -0700
    Addressing feedback in issues 1-5 including rearrangements of Projects page, renaming AssayTech to CdnaLibraryPrep, adding doc strings to the models in models.py, making project title and a few other fields get more space.
  • lines changed 1, context: html, text, full: html, text
    97ca263e551d4fada76b8c33ad34e5056fa0e88f Thu Oct 17 19:44:40 2019 -0700
    Adding in handling for landing page (aka index.html).
• src/hca/hcat/mysite/hcat/api.py
  • lines changed 9, context: html, text, full: html, text
    d32a1c4535597376154d2e4726edceb34a7b1612 Tue Oct 8 15:28:26 2019 -0700
    Addressing feedback in issues 1-5 including rearrangements of Projects page, renaming AssayTech to CdnaLibraryPrep, adding doc strings to the models in models.py, making project title and a few other fields get more space.
  • lines changed 7, context: html, text, full: html, text
    07c2d16f9b66b21fd315c56c7b68a8f8b6e80f28 Fri Oct 18 00:15:55 2019 -0700
    Removing lab affiliation from API. Seems like less is more these days in terms of tracking information on people. There's no clear case for people needing to know.
• src/hca/hcat/mysite/hcat/api_urls.py
  • lines changed 1, context: html, text, full: html, text
    d32a1c4535597376154d2e4726edceb34a7b1612 Tue Oct 8 15:28:26 2019 -0700
    Addressing feedback in issues 1-5 including rearrangements of Projects page, renaming AssayTech to CdnaLibraryPrep, adding doc strings to the models in models.py, making project title and a few other fields get more space.
• src/hca/hcat/mysite/hcat/index_urls.py
  • lines changed 9, context: html, text, full: html, text
    97ca263e551d4fada76b8c33ad34e5056fa0e88f Thu Oct 17 19:44:40 2019 -0700
    Adding in handling for landing page (aka index.html).
• src/hca/hcat/mysite/hcat/models.py
  • lines changed 42, context: html, text, full: html, text
    d32a1c4535597376154d2e4726edceb34a7b1612 Tue Oct 8 15:28:26 2019 -0700
    Addressing feedback in issues 1-5 including rearrangements of Projects page, renaming AssayTech to CdnaLibraryPrep, adding doc strings to the models in models.py, making project title and a few other fields get more space.
  • lines changed 1, context: html, text, full: html, text
    97ca263e551d4fada76b8c33ad34e5056fa0e88f Thu Oct 17 19:44:40 2019 -0700
    Adding in handling for landing page (aka index.html).
• src/hca/hcat/mysite/hcat/views.py
  • lines changed 5, context: html, text, full: html, text
    97ca263e551d4fada76b8c33ad34e5056fa0e88f Thu Oct 17 19:44:40 2019 -0700
    Adding in handling for landing page (aka index.html).
• src/hca/hcat/mysite/mysite/urls.py
  • lines changed 1, context: html, text, full: html, text
    97ca263e551d4fada76b8c33ad34e5056fa0e88f Thu Oct 17 19:44:40 2019 -0700
    Adding in handling for landing page (aka index.html).
• src/hca/hcat/mysite/templates/hcat/index.html
  • lines changed 57, context: html, text, full: html, text
    97ca263e551d4fada76b8c33ad34e5056fa0e88f Thu Oct 17 19:44:40 2019 -0700
    Adding in handling for landing page (aka index.html).
  • lines changed 11, context: html, text, full: html, text
    cb844abff2d989553c620ff26c1f0511ed38254d Thu Oct 17 20:06:18 2019 -0700
    Edited down most sections, but beefing up API section.
  • lines changed 8, context: html, text, full: html, text
    9618a297ae6763524ac07d192cc60b1cc5667ece Thu Oct 17 23:08:04 2019 -0700
    Finishing documenting API. Replacing HCA logo with a picture of a tuatara and changing formatting a bit.
  • lines changed 13, context: html, text, full: html, text
    03c16bfda2fc34d3db89d5c0ec0e03b82323cf86 Thu Oct 17 23:36:07 2019 -0700
    Tweaking formatting a little.
• src/hca/hcat/mysite/versions.txt
  • lines changed 4, context: html, text, full: html, text
    c83c7ebf5494774741e0916eeb4a918b6cb552d4 Tue Oct 8 15:31:21 2019 -0700
    Documenting changes.
  • lines changed 8, context: html, text, full: html, text
    d5bcf70e2252b482781fce5e87afaef852983354 Fri Oct 18 00:22:31 2019 -0700
    Documenting recent changes
• src/hg/geneBounds/clusterGenes/clusterGenes.c
  • lines changed 29, context: html, text, full: html, text
    83657216000f3e3ae3673d8a2a7d04feaf8cd147 Tue Dec 15 13:21:22 2020 -0800
    fixed bug were clusterGenes -ignoreBases would drop small transcripts
• src/hg/geneBounds/clusterGenes/tests/expected/ignoreBasesTinyTest.gl
  • lines changed 5, context: html, text, full: html, text
    83657216000f3e3ae3673d8a2a7d04feaf8cd147 Tue Dec 15 13:21:22 2020 -0800
    fixed bug were clusterGenes -ignoreBases would drop small transcripts
• src/hg/geneBounds/clusterGenes/tests/input/Mt-tRNA.gp
  • lines changed 4, context: html, text, full: html, text
    83657216000f3e3ae3673d8a2a7d04feaf8cd147 Tue Dec 15 13:21:22 2020 -0800
    fixed bug were clusterGenes -ignoreBases would drop small transcripts
• src/hg/geneBounds/clusterGenes/tests/makefile
  • lines changed 7, context: html, text, full: html, text
    83657216000f3e3ae3673d8a2a7d04feaf8cd147 Tue Dec 15 13:21:22 2020 -0800
    fixed bug were clusterGenes -ignoreBases would drop small transcripts
• src/hg/hgGateway/hgGateway.c
  • lines changed 13, context: html, text, full: html, text
    d8357a44b9fb15ee8262a36d4fbcc43c90fae358 Mon Dec 14 16:42:26 2020 -0800
    Make hgGateway use previously browsed position when changing databases, also fix hgHubConnect assembly redirect to use last used position, refs #14481
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 1, context: html, text, full: html, text
    d8357a44b9fb15ee8262a36d4fbcc43c90fae358 Mon Dec 14 16:42:26 2020 -0800
    Make hgGateway use previously browsed position when changing databases, also fix hgHubConnect assembly redirect to use last used position, refs #14481
• src/hg/hgPhyloPlace/hgPhyloPlace.c
  • lines changed 18, context: html, text, full: html, text
    b7c2dcc865207dd23298429f93057c9068acef68 Wed Dec 9 15:48:34 2020 -0800
    hgPhyloPlace: Add config option treeChoices: tab-sep file of {protobuf, metadata, source, description} so we can offer the user a choice between GISAID and public sequence trees (possibly different releases for reproducibility).
• src/hg/hgPhyloPlace/phyloPlace.c
  • lines changed 11, context: html, text, full: html, text
    cd9c54f4262db97f1c9201411a0d84460de87690 Thu Dec 3 15:30:13 2020 -0800
    Try harder to look up sample metadata in the absence of EPI or GenBank acc: if name from protobuf is name|id|... then look up name and id.
  • lines changed 90, context: html, text, full: html, text
    b7c2dcc865207dd23298429f93057c9068acef68 Wed Dec 9 15:48:34 2020 -0800
    hgPhyloPlace: Add config option treeChoices: tab-sep file of {protobuf, metadata, source, description} so we can offer the user a choice between GISAID and public sequence trees (possibly different releases for reproducibility).
• src/hg/hgPhyloPlace/phyloPlace.h
  • lines changed 19, context: html, text, full: html, text
    b7c2dcc865207dd23298429f93057c9068acef68 Wed Dec 9 15:48:34 2020 -0800
    hgPhyloPlace: Add config option treeChoices: tab-sep file of {protobuf, metadata, source, description} so we can offer the user a choice between GISAID and public sequence trees (possibly different releases for reproducibility).
• src/hg/hgPhyloPlace/phyloPlaceMain.c
  • lines changed 1, context: html, text, full: html, text
    b7c2dcc865207dd23298429f93057c9068acef68 Wed Dec 9 15:48:34 2020 -0800
    hgPhyloPlace: Add config option treeChoices: tab-sep file of {protobuf, metadata, source, description} so we can offer the user a choice between GISAID and public sequence trees (possibly different releases for reproducibility).
• src/hg/hgPhyloPlace/treeToAuspiceJson.c
  • lines changed 3, context: html, text, full: html, text
    bba5c10004bdcf6538a2d3ea07e7542eada31e0e Thu Dec 3 15:32:07 2020 -0800
    Don't overwrite name from protobuf with strain name; not necessary and loses info about condensed nodes.
  • lines changed 14, context: html, text, full: html, text
    b7c2dcc865207dd23298429f93057c9068acef68 Wed Dec 9 15:48:34 2020 -0800
    hgPhyloPlace: Add config option treeChoices: tab-sep file of {protobuf, metadata, source, description} so we can offer the user a choice between GISAID and public sequence trees (possibly different releases for reproducibility).
• src/hg/hgTracks/cds.c
  • lines changed 4, context: html, text, full: html, text
    ff51fb89b5ea359ce375fe2219d76b2f4c45a996 Mon Dec 7 10:16:57 2020 -0800
    be smarter about when to go into codon numbering mode on genePreds #26628
• src/hg/hgTracks/config.c
  • lines changed 22, context: html, text, full: html, text
    093995328667118cf901ec6bb93e36c4464c93c4 Mon Dec 7 10:37:41 2020 -0800
    move a routine into a different file so it has access to the global definitions of fonts
• src/hg/hgTracks/hgTracks.c
  • lines changed 1, context: html, text, full: html, text
    ff51fb89b5ea359ce375fe2219d76b2f4c45a996 Mon Dec 7 10:16:57 2020 -0800
    be smarter about when to go into codon numbering mode on genePreds #26628
  • lines changed 23, context: html, text, full: html, text
    093995328667118cf901ec6bb93e36c4464c93c4 Mon Dec 7 10:37:41 2020 -0800
    move a routine into a different file so it has access to the global definitions of fonts
  • lines changed 2, context: html, text, full: html, text
    9c9af0a5de97e512c5ab9b9b8dd5928499c3f78c Sat Dec 12 22:06:07 2020 -0800
    fixed debug print of CGI URL and arguments
• src/hg/hgTracks/hgTracks.h
  • lines changed 1, context: html, text, full: html, text
    ff51fb89b5ea359ce375fe2219d76b2f4c45a996 Mon Dec 7 10:16:57 2020 -0800
    be smarter about when to go into codon numbering mode on genePreds #26628
  • lines changed 2, context: html, text, full: html, text
    093995328667118cf901ec6bb93e36c4464c93c4 Mon Dec 7 10:37:41 2020 -0800
    move a routine into a different file so it has access to the global definitions of fonts
• src/hg/hgTracks/imageV2.c
  • lines changed 7, context: html, text, full: html, text
    71ca786dd00a42ee4f187619b3d6746cb54a82eb Mon Dec 14 15:33:56 2020 -0800
    fiddling with the mouseovers #26330
• src/hg/hgTracks/lollyTrack.c
  • lines changed 93, context: html, text, full: html, text
    4efa2a1c3d370f0c36bfae6a4e96cb6c36fb83ff Mon Dec 7 11:46:58 2020 -0800
    scale fonts used on the y axis labels in lollipop graphs
• src/hg/hgTracks/simpleTracks.c
  • lines changed 1, context: html, text, full: html, text
    ff51fb89b5ea359ce375fe2219d76b2f4c45a996 Mon Dec 7 10:16:57 2020 -0800
    be smarter about when to go into codon numbering mode on genePreds #26628
  • lines changed 9, context: html, text, full: html, text
    02836b99a074f08b3be77de8933bf7fb5f0fe00c Wed Dec 16 06:26:34 2020 -0800
    show exon numbers configuration option was ignored for genePred and bigGenePred tracks, the exonNumbers cart variable now is taken into account refs #25325
• src/hg/hgTracks/snakeTrack.c
  • lines changed 1, context: html, text, full: html, text
    a102654e776e2ba96af731cac5b8cda1803fa3cb Sat Dec 12 22:05:26 2020 -0800
    make it more obvious that HAL screwed up and didn't set error message
  • lines changed 1, context: html, text, full: html, text
    13a74772a9f4e38f7d13746542de8733a998c07f Sun Dec 13 11:07:22 2020 -0800
    don't add next/prev item to snakes, they are not implemented and crash in a confusing way in code for database tracks
  • lines changed 1, context: html, text, full: html, text
    61308020150706a0ce4437616eea098620f92f6d Sun Dec 13 11:31:03 2020 -0800
    fixed snake track requesting a negative length of DNA in self-alignments #25987
• src/hg/hgc/barChartClick.c
  • lines changed 56, context: html, text, full: html, text
    646ff06654a53214f1b47fa6b92742ec6a44934a Mon Dec 21 12:16:42 2020 -0800
    Adding simple barchart display without box plots when no expMatrix available.
  • lines changed 21, context: html, text, full: html, text
    7538532d26dbee720c6ee3426fab17680d242dd1 Tue Dec 22 11:02:24 2020 -0800
    Estimating width of label based on helvetica font in memory.
  • lines changed 2, context: html, text, full: html, text
    7a66ec026712b92017d2bf9d2e313ad079eea28f Tue Dec 22 11:04:39 2020 -0800
    Fine tuning some layout constants.
  • lines changed 35, context: html, text, full: html, text
    9a3b1674fd367695d5ba29e8eab4a60280877bd8 Tue Dec 22 12:32:35 2020 -0800
    Adding label row to expression barchart table.
  • lines changed 33, context: html, text, full: html, text
    dab44418c480b8c931d0b86af916bbb3bf64ffe3 Fri Jan 1 08:06:26 2021 -0800
    Adding barChartStatsUrl tag. Right now it is ignored by the browser if barChartMatrixUrl is present. It points to a tab separated file with a label row and a few required fields.
• src/hg/hgc/bigBedClick.c
  • lines changed 1, context: html, text, full: html, text
    f83f8061a76cad5ed033b6320f73321cf7b8ffcb Wed Dec 9 11:20:08 2020 -0800
    Fix bug I introduced into bigBed extra field printing when adding bigBed extra field URL substitution, refs #26662
• src/hg/hgc/hgc.c
  • lines changed 132, context: html, text, full: html, text
    004d56eff1d9b74e312104b30ea872201e92cf97 Thu Dec 10 15:50:57 2020 -0800
    add the ability for bigPsl tracks to show query sequences like genePred if they have the sequence and CDS. #24672
  • lines changed 15, context: html, text, full: html, text
    a879c24ca720e1de4c34d4a1e3407f4baa0259d6 Mon Dec 14 15:35:45 2020 -0800
    some tweaks to sequence output from bigPsl if they have sequence and maybe cds
• src/hg/htdocs/FAQ/FAQlink.html
  • lines changed 12, context: html, text, full: html, text
    791ff217c3dcd05a79344eb2c9e335fe40d7ab7c Tue Dec 8 13:41:41 2020 -0800
    Adding a note about default URL parameter in wiki refs #26650
• src/hg/htdocs/FAQ/FAQreleases.html
  • lines changed 1, context: html, text, full: html, text
    9fe471a051c4ef427d5ff9175ea0fa8504aa1f50 Wed Dec 9 16:09:36 2020 -0800
    New entries for neoSch1, refs #19883
• src/hg/htdocs/admin/git.html
  • lines changed 3, context: html, text, full: html, text
    00ae373acdcab1995d8554c348be8be4d67a2be5 Mon Dec 21 08:45:45 2020 -0800
    Fixed Static Page Cronjob 404 links, date 2020-12-15
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 26, context: html, text, full: html, text
    9fe471a051c4ef427d5ff9175ea0fa8504aa1f50 Wed Dec 9 16:09:36 2020 -0800
    New entries for neoSch1, refs #19883
• src/hg/htdocs/goldenPath/help/bigBed.html
  • lines changed 19, context: html, text, full: html, text
    4fcea62ede5b34df814333e242a865fb20dfb821 Thu Dec 10 02:57:37 2020 -0800
    adding linux commands to bigBed example 2, no redmine yet, but probably coming.
  • lines changed 72, context: html, text, full: html, text
    16a0bb49dfcbf27c039d99e4ab40a41c59814400 Fri Dec 11 05:56:03 2020 -0800
    a quickstart section for the bigBed.html page, may be not optimal yet, but to illustrate the idea more
  • lines changed 19, context: html, text, full: html, text
    679e26dcf187dd96851052d91081abf9c6864d4b Mon Dec 14 05:44:14 2020 -0800
    small fixed to bigBed docs page, refs #26677
  • lines changed 24, context: html, text, full: html, text
    b036e61e75f5a6626d9fd3b4febe41c69cf97b5d Mon Dec 14 17:03:46 2020 -0800
    Adding some changes to Max's changes to bigBed.html refs #26677
• src/hg/htdocs/goldenPath/help/bigLolly.html
  • lines changed 75, context: html, text, full: html, text
    21cf7d650326c986fe0e779075e082a3fe73ede5 Tue Dec 22 15:06:29 2020 -0800
    Adding chages to bigLolly.html, refs #26481
  • lines changed 1, context: html, text, full: html, text
    8e55ded7b333f5f621a85a5190f68a714ab19b9b Tue Dec 22 17:48:41 2020 -0800
    Renamed the autoSql definition file name for bigLolly.html, refs #26481
• src/hg/htdocs/goldenPath/help/gbic.html
  • lines changed 76, context: html, text, full: html, text
    e06433e5a691534449ed3cb9ec070b2be6cf07b7 Mon Dec 28 15:09:39 2020 -0800
    Catching up the github README for GBiC to match the gbic.html documentation. refs #23297
  • lines changed 57, context: html, text, full: html, text
    ec7a214792ae943389d82a2d32d1774acf211b0b Mon Dec 28 15:28:30 2020 -0800
    Escaping a single quote, refs #23297
  • lines changed 1, context: html, text, full: html, text
    1a5e0c8a18a754369662bac65abca9b1f64fee64 Tue Dec 29 11:37:29 2020 -0800
    Escaping a period that gets encoded differently on the HTML page, refs #23297
• src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html
  • lines changed 1, context: html, text, full: html, text
    f0cf6c47c691584bbc41d6b83dea263183727b8a Tue Dec 8 13:23:55 2020 -0800
    Changing example isPcr in GBiB to be localhost fitting the rest of the example refs #21446
• src/hg/htdocs/goldenPath/help/mirrorManual.html
  • lines changed 6, context: html, text, full: html, text
    00ae373acdcab1995d8554c348be8be4d67a2be5 Mon Dec 21 08:45:45 2020 -0800
    Fixed Static Page Cronjob 404 links, date 2020-12-15
• src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
  • lines changed 1, context: html, text, full: html, text
    eb6a35ecac2424ecf5b2b874dff935353e4f0a53 Wed Dec 9 01:29:24 2020 -0800
    another super old trackDb docs mistake, no redmine
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 117, context: html, text, full: html, text
    093e1ebb7379b648b34f76949a6dc13c014b7ec0 Tue Dec 8 16:21:07 2020 -0800
    Making link changes per code review input refs #26650
  • lines changed 46, context: html, text, full: html, text
    60ac6fcbb6586c38b9b2de9b3464e3425997c519 Wed Dec 9 15:55:43 2020 -0800
    Updating news for neoSch1, refs #19883
  • lines changed 24, context: html, text, full: html, text
    73d60270fcd4c7a026ba90a953681d8c4e5236b6 Mon Dec 14 12:51:22 2020 -0800
    News announcement for GENCODE V35 refs #26524
  • lines changed 17, context: html, text, full: html, text
    7163b3185a62d72d7e055a6f161c7c71744e63f4 Wed Dec 16 10:19:40 2020 -0800
    Updating news for assembly hubs isPcr feature, refs #21446
  • lines changed 41, context: html, text, full: html, text
    750e46fd9085b25b3e40445330c196cc85232b52 Wed Dec 23 10:09:17 2020 -0800
    News announcement for clinvar interpretations track refs #26330
  • lines changed 2, context: html, text, full: html, text
    b57f86a73dd4a9a9541f95fc78cdb7249203b1c2 Wed Dec 23 12:06:55 2020 -0800
    Removing old newsArch image, and fixing image description refs #26330
• src/hg/htdocs/images/CovidGwasLollies.png
  • lines changed 0, context: html, text, full: html, text
    16e287ed90c91ff8a5f47efcf1f63194c1c94f62 Tue Dec 22 14:53:56 2020 -0800
    Adding images for bigLolly.html, refs #26481
• src/hg/htdocs/images/bigLollyExample3.png
  • lines changed 0, context: html, text, full: html, text
    16e287ed90c91ff8a5f47efcf1f63194c1c94f62 Tue Dec 22 14:53:56 2020 -0800
    Adding images for bigLolly.html, refs #26481
• src/hg/htdocs/images/clinVarInt.png
  • lines changed 0, context: html, text, full: html, text
    fa973a2e6d16b346ae9d8b37e5de61fb7dd20393 Tue Dec 22 15:31:42 2020 -0800
    Adding image for clinvar interpretations news archive announcement refs #26330
  • lines changed 0, context: html, text, full: html, text
    b57f86a73dd4a9a9541f95fc78cdb7249203b1c2 Wed Dec 23 12:06:55 2020 -0800
    Removing old newsArch image, and fixing image description refs #26330
• src/hg/htdocs/images/clinVarInterp.png
  • lines changed 0, context: html, text, full: html, text
    8416dd9bffbbe9bf6108da7641387db8cbd0e71f Wed Dec 23 12:04:07 2020 -0800
    Fixing up the clinvar interp image refs #26330
• src/hg/htdocs/images/phylo/mm39_35way.png
  • lines changed 0, context: html, text, full: html, text
    59afd780130dec857011bcad89e2c496d034ace6 Mon Dec 21 15:04:58 2020 -0800
    image for mm39 35-way alignment refs #26584
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    60ac6fcbb6586c38b9b2de9b3464e3425997c519 Wed Dec 9 15:55:43 2020 -0800
    Updating news for neoSch1, refs #19883
  • lines changed 12, context: html, text, full: html, text
    73d60270fcd4c7a026ba90a953681d8c4e5236b6 Mon Dec 14 12:51:22 2020 -0800
    News announcement for GENCODE V35 refs #26524
  • lines changed 12, context: html, text, full: html, text
    7163b3185a62d72d7e055a6f161c7c71744e63f4 Wed Dec 16 10:19:40 2020 -0800
    Updating news for assembly hubs isPcr feature, refs #21446
  • lines changed 12, context: html, text, full: html, text
    750e46fd9085b25b3e40445330c196cc85232b52 Wed Dec 23 10:09:17 2020 -0800
    News announcement for clinvar interpretations track refs #26330
• src/hg/htdocs/training/index.html
  • lines changed 33, context: html, text, full: html, text
    9b5a2af0d673fad3f960fb3f33a816b7d0d8abce Wed Dec 23 12:04:42 2020 -0800
    dropping genetic counselors meeting. adding city of hope
• src/hg/hubApi/apiUtils.c
  • lines changed 1, context: html, text, full: html, text
    cff0a237099d06f16896ec781a85cccb1a663849 Mon Dec 21 14:21:59 2020 -0800
    make sure that trackDb cache on hubs keeps track of files that are included in the trackDb.txt file
• src/hg/inc/trackDb.h
  • lines changed 8, context: html, text, full: html, text
    cff0a237099d06f16896ec781a85cccb1a663849 Mon Dec 21 14:21:59 2020 -0800
    make sure that trackDb cache on hubs keeps track of files that are included in the trackDb.txt file
• src/hg/inc/trackHub.h
  • lines changed 3, context: html, text, full: html, text
    cff0a237099d06f16896ec781a85cccb1a663849 Mon Dec 21 14:21:59 2020 -0800
    make sure that trackDb cache on hubs keeps track of files that are included in the trackDb.txt file
• src/hg/js/hgGateway.js
  • lines changed 1, context: html, text, full: html, text
    d8357a44b9fb15ee8262a36d4fbcc43c90fae358 Mon Dec 14 16:42:26 2020 -0800
    Make hgGateway use previously browsed position when changing databases, also fix hgHubConnect assembly redirect to use last used position, refs #14481
• src/hg/js/hgTracks.js
  • lines changed 1, context: html, text, full: html, text
    a115ebc88f157c14032c4bb63ca8f7b453998ce5 Tue Dec 15 03:40:00 2020 -0800
    UniProt track should not show title but label on mouseover rightclick, refs #26687
• src/hg/lib/cart.c
  • lines changed 3, context: html, text, full: html, text
    d8357a44b9fb15ee8262a36d4fbcc43c90fae358 Mon Dec 14 16:42:26 2020 -0800
    Make hgGateway use previously browsed position when changing databases, also fix hgHubConnect assembly redirect to use last used position, refs #14481
• src/hg/lib/customFactory.c
  • lines changed 2, context: html, text, full: html, text
    54edad8bebf1ef9763b9f16ec2c34143c447aafa Thu Dec 10 06:17:14 2020 -0800
    auto-detecting track type bigInteract if custom track file ends with .inter.bb or .inter.bigBed, no redmine
• src/hg/lib/customTrack.c
  • lines changed 2, context: html, text, full: html, text
    54edad8bebf1ef9763b9f16ec2c34143c447aafa Thu Dec 10 06:17:14 2020 -0800
    auto-detecting track type bigInteract if custom track file ends with .inter.bb or .inter.bigBed, no redmine
• src/hg/lib/hdb.c
  • lines changed 1, context: html, text, full: html, text
    cff0a237099d06f16896ec781a85cccb1a663849 Mon Dec 21 14:21:59 2020 -0800
    make sure that trackDb cache on hubs keeps track of files that are included in the trackDb.txt file
• src/hg/lib/hubConnect.c
  • lines changed 4, context: html, text, full: html, text
    cff0a237099d06f16896ec781a85cccb1a663849 Mon Dec 21 14:21:59 2020 -0800
    make sure that trackDb cache on hubs keeps track of files that are included in the trackDb.txt file
• src/hg/lib/mafGene.c
  • lines changed 14, context: html, text, full: html, text
    e1ba1d9a147724de16cb65a1d5006ecd6c4cfdc8 Wed Dec 23 14:57:42 2020 -0800
    a silly hack to get mafGene to work on alignments that have assembly names with a dot in them
• src/hg/lib/trackDbCache.c
  • lines changed 54, context: html, text, full: html, text
    cff0a237099d06f16896ec781a85cccb1a663849 Mon Dec 21 14:21:59 2020 -0800
    make sure that trackDb cache on hubs keeps track of files that are included in the trackDb.txt file
• src/hg/lib/trackDbCustom.c
  • lines changed 10, context: html, text, full: html, text
    cff0a237099d06f16896ec781a85cccb1a663849 Mon Dec 21 14:21:59 2020 -0800
    make sure that trackDb cache on hubs keeps track of files that are included in the trackDb.txt file
• src/hg/lib/trackHub.c
  • lines changed 5, context: html, text, full: html, text
    cff0a237099d06f16896ec781a85cccb1a663849 Mon Dec 21 14:21:59 2020 -0800
    make sure that trackDb cache on hubs keeps track of files that are included in the trackDb.txt file
  • lines changed 1, context: html, text, full: html, text
    dab44418c480b8c931d0b86af916bbb3bf64ffe3 Fri Jan 1 08:06:26 2021 -0800
    Adding barChartStatsUrl tag. Right now it is ignored by the browser if barChartMatrixUrl is present. It points to a tab separated file with a label row and a few required fields.
• src/hg/logCrawl/dbTrackAndSearchUsage/generateUsageStats.py
  • lines changed 3, context: html, text, full: html, text
    d13f1c8f1fada76cc569fc0c6f073f76fdeace92 Thu Oct 1 17:03:37 2020 -0700
    We have a shell script that does this so slowly on big files it is painful, so I wrote this in C.
• src/hg/makeDb/doc/asmHubs/README.txt
  • lines changed 128, context: html, text, full: html, text
    90720ea4153ead9a125115daa0272dba39d3927b Mon Dec 7 14:06:40 2020 -0800
    documentation how to operate this process refs #23891
• src/hg/makeDb/doc/asmHubs/hgdownload.index.html
  • lines changed 75, context: html, text, full: html, text
    e1bad6bcd71bef15344d18cd16d2e416b9840078 Mon Dec 14 19:00:35 2020 -0800
    a copy of index.html from hgdownload (generated there by script) update to today refs #23891
• src/hg/makeDb/doc/asmHubs/master.run.list
  • lines changed 77, context: html, text, full: html, text
    6289d9f62a0feda12bb77d511003fa7c06d4a610 Tue Dec 8 13:44:32 2020 -0800
    catching up to current set including plants refs #23891
  • lines changed 11, context: html, text, full: html, text
    2aef12dde4b14b26e8bb10a5b6670ad772a4c6dc Mon Dec 14 16:41:42 2020 -0800
    catching up hubs done refs #23891
  • lines changed 28, context: html, text, full: html, text
    8dc7ac330f07414e7225020625b651c2f135e662 Mon Dec 14 17:15:28 2020 -0800
    catching up hubs done and now matching hgdownload dir list refs #23891
• src/hg/makeDb/doc/canFam4/initialBuild.txt
  • lines changed 43, context: html, text, full: html, text
    549cc338cbe2531334b345274c87fac55edee6c2 Mon Dec 7 13:01:44 2020 -0800
    adding annotations from Lindblad-Toh lab refs #26657
  • lines changed 2, context: html, text, full: html, text
    4249ea7c261b62acbdff737b76468640e7ffa9eb Mon Dec 7 13:18:05 2020 -0800
    adding annotations from Lindblad-Toh lab refs #26657
• src/hg/makeDb/doc/covid/covidHgiGwas.txt
  • lines changed 197, context: html, text, full: html, text
    b85941107d295df78e38d8020dffa07896fe7cbb Tue Dec 22 13:07:58 2020 -0800
    Adding make doc for R4 track. refs #26616
• src/hg/makeDb/doc/fishAsmHub/fish.orderList.tsv
  • lines changed 9, context: html, text, full: html, text
    f0c04b37955a2915d9b44724823f6042706fa877 Mon Dec 14 18:18:35 2020 -0800
    catching up recently built hubs refs #23891
• src/hg/makeDb/doc/hg19.gencode.txt
  • lines changed 48, context: html, text, full: html, text
    f2825cfe9d599d3970bf2379395e912451080d15 Mon Dec 21 23:16:17 2020 -0800
    import of gencdoe V36lift37
• src/hg/makeDb/doc/hg19.txt
  • lines changed 4, context: html, text, full: html, text
    71ca786dd00a42ee4f187619b3d6746cb54a82eb Mon Dec 14 15:33:56 2020 -0800
    fiddling with the mouseovers #26330
  • lines changed 77, context: html, text, full: html, text
    3dd09a4b5f9dd8ad5122483b7b040dcec14ac1f4 Mon Dec 14 16:40:51 2020 -0800
    lastz chainNet per user request hg19 bosTau9 refs #26638
  • lines changed 31, context: html, text, full: html, text
    54197358a1407de6898c360a38df822257338112 Tue Dec 15 05:33:49 2020 -0800
    updating hgmd and ncbiRefseqHgmd to HGMD 2020, refs #24625
• src/hg/makeDb/doc/hg38/clinvarSubLolly.txt
  • lines changed 4, context: html, text, full: html, text
    71ca786dd00a42ee4f187619b3d6746cb54a82eb Mon Dec 14 15:33:56 2020 -0800
    fiddling with the mouseovers #26330
• src/hg/makeDb/doc/hg38/gencode.txt
  • lines changed 35, context: html, text, full: html, text
    8f6ed988e6b529bea3c89bd51a04055956a91327 Sun Dec 20 13:38:03 2020 -0800
    import of all gencode V35
  • lines changed 34, context: html, text, full: html, text
    f695b16331ac22d8925e99a05aecd7ce563e0a08 Mon Dec 21 21:29:40 2020 -0800
    import gencodeV36
• src/hg/makeDb/doc/hg38/hgmd.txt
  • lines changed 2, context: html, text, full: html, text
    54197358a1407de6898c360a38df822257338112 Tue Dec 15 05:33:49 2020 -0800
    updating hgmd and ncbiRefseqHgmd to HGMD 2020, refs #24625
• src/hg/makeDb/doc/hg38/ncbiRefSeq.txt
  • lines changed 2, context: html, text, full: html, text
    54197358a1407de6898c360a38df822257338112 Tue Dec 15 05:33:49 2020 -0800
    updating hgmd and ncbiRefseqHgmd to HGMD 2020, refs #24625
• src/hg/makeDb/doc/legacyAsmHub/legacy.orderList.tsv
  • lines changed 5, context: html, text, full: html, text
    f0c04b37955a2915d9b44724823f6042706fa877 Mon Dec 14 18:18:35 2020 -0800
    catching up recently built hubs refs #23891
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 5, context: html, text, full: html, text
    f0c04b37955a2915d9b44724823f6042706fa877 Mon Dec 14 18:18:35 2020 -0800
    catching up recently built hubs refs #23891
• src/hg/makeDb/doc/mm39/multiz35way.txt
  • lines changed 2250, context: html, text, full: html, text
    3c614c8b6f65a275dec519d292b870afeec12335 Sat Dec 19 09:07:59 2020 -0800
    multiz done running up iRows refs #26584
  • lines changed 171, context: html, text, full: html, text
    346748ca6fae57c82810e5ae94166c7f5547b940 Mon Dec 21 15:39:19 2020 -0800
    read to continue with gene annotation refs #26584
  • lines changed 491, context: html, text, full: html, text
    95599ae77e60f8b8a9bbfc9894e9051afbfe9384 Tue Dec 22 09:45:44 2020 -0800
    frames done refs #26584
  • lines changed 351, context: html, text, full: html, text
    c4700dd1959b6c45050fbb1b0733397d58916f57 Tue Dec 22 21:34:32 2020 -0800
    ready for downloads and running up hgPal files refs #25864
  • lines changed 34, context: html, text, full: html, text
    9f629656dd1bb546fb3e222ae28e9c68486936cb Wed Dec 23 17:03:31 2020 -0800
    ready for wiki summary pages and download README files refs #25864
• src/hg/makeDb/doc/mm39/sizeStats.pl
  • lines changed 111, context: html, text, full: html, text
    2591cf6978567ffca7f402d6311000810993d196 Mon Dec 21 15:38:40 2020 -0800
    output chain stats table for 35-way refs #26584
• src/hg/makeDb/doc/plantsAsmHub/hub.txt
  • lines changed 6, context: html, text, full: html, text
    6d3ef228a206f70d8cde9e5e89d280e7d7c6000b Thu Dec 10 14:53:57 2020 -0800
    first pass on plants hub listings refs #23891
• src/hg/makeDb/doc/plantsAsmHub/makefile
  • lines changed 26, context: html, text, full: html, text
    6d3ef228a206f70d8cde9e5e89d280e7d7c6000b Thu Dec 10 14:53:57 2020 -0800
    first pass on plants hub listings refs #23891
• src/hg/makeDb/doc/plantsAsmHub/plants.orderList.tsv
  • lines changed 109, context: html, text, full: html, text
    6d3ef228a206f70d8cde9e5e89d280e7d7c6000b Thu Dec 10 14:53:57 2020 -0800
    first pass on plants hub listings refs #23891
  • lines changed 1, context: html, text, full: html, text
    f0c04b37955a2915d9b44724823f6042706fa877 Mon Dec 14 18:18:35 2020 -0800
    catching up recently built hubs refs #23891
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 3, context: html, text, full: html, text
    f0c04b37955a2915d9b44724823f6042706fa877 Mon Dec 14 18:18:35 2020 -0800
    catching up recently built hubs refs #23891
• src/hg/makeDb/doc/vgpAsmHub/vgp.legacy.orderList.tsv
  • lines changed 6, context: html, text, full: html, text
    f0c04b37955a2915d9b44724823f6042706fa877 Mon Dec 14 18:18:35 2020 -0800
    catching up recently built hubs refs #23891
• src/hg/makeDb/doc/vgpAsmHub/vgp.primary.orderList.tsv
  • lines changed 10, context: html, text, full: html, text
    f0c04b37955a2915d9b44724823f6042706fa877 Mon Dec 14 18:18:35 2020 -0800
    catching up recently built hubs refs #23891
• src/hg/makeDb/doc/vgpAsmHub/vgp.trio.orderList.tsv
  • lines changed 1, context: html, text, full: html, text
    f0c04b37955a2915d9b44724823f6042706fa877 Mon Dec 14 18:18:35 2020 -0800
    catching up recently built hubs refs #23891
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • lines changed 2, context: html, text, full: html, text
    e540bd66281fd544026b2ce5bf81ce0651a795d3 Mon Dec 14 16:37:33 2020 -0800
    Turning on GenBank updates for new assembly #25917
• src/hg/makeDb/gnomad/gnomadVcfBedToBigBed
  • lines changed 329, context: html, text, full: html, text
    9b031666dc8ef873fefdb6201c39366d257f4632 Tue Dec 8 16:58:42 2020 -0800
    Adding gnomAD vcf to bed conversion script, refs #25010, #26652
• src/hg/makeDb/hgFindSpec/hgFindSpec.c
  • lines changed 1, context: html, text, full: html, text
    0e7d9cb854ff492af1565a061fe0070a3f0f693e Thu Dec 17 17:33:44 2020 -0800
    add a flush tables after loading trackDb and hgFindSpec tables to prevent an error with myisamchk saying that they are still open
• src/hg/makeDb/hgTrackDb/hgTrackDb.c
  • lines changed 1, context: html, text, full: html, text
    0e7d9cb854ff492af1565a061fe0070a3f0f693e Thu Dec 17 17:33:44 2020 -0800
    add a flush tables after loading trackDb and hgFindSpec tables to prevent an error with myisamchk saying that they are still open
  • lines changed 1, context: html, text, full: html, text
    780985dafe4ff8687576e91b84596d94a0a4ad2d Mon Dec 21 14:47:21 2020 -0800
    oops, missed a place
• src/hg/makeDb/outside/covid/covidHgiGwas.as
  • lines changed 1, context: html, text, full: html, text
    40725e1032aa093a8bd38073dfd5bddcb1c7207b Mon Dec 14 08:38:53 2020 -0800
    Update track build to support Release 4 and pvalue lolly height. refs #26616
• src/hg/makeDb/outside/covid/makeCovidHgiGwas.pl
  • lines changed 19, context: html, text, full: html, text
    9c54f7b9a4adb03a98fe14179ae1426a804854bf Mon Dec 7 15:18:35 2020 -0800
    Add track for recently released data (Release 4, October 2020). refs #26129
  • lines changed 30, context: html, text, full: html, text
    75919aa5b7ff1e9c80ae10a2f2aa5947f2ed00f0 Mon Dec 14 08:33:06 2020 -0800
    Update track build to support Release 4 and pvalue lolly height. refs #26616
  • lines changed 9, context: html, text, full: html, text
    3a05d18b3a907bdd6868dac95dfe983dcc52d73f Fri Dec 18 19:30:27 2020 -0800
    Polishing up COVID GWAS Oct 2020 track(s). refs #26616
• src/hg/makeDb/outside/gencode/bin/gencodeGenerateTrackDbsOldSchema
  • lines changed 2, context: html, text, full: html, text
    f695b16331ac22d8925e99a05aecd7ce563e0a08 Mon Dec 21 21:29:40 2020 -0800
    import gencodeV36
• src/hg/makeDb/outside/gencode/gencodeLoad.mk
  • lines changed 2, context: html, text, full: html, text
    8f6ed988e6b529bea3c89bd51a04055956a91327 Sun Dec 20 13:38:03 2020 -0800
    import of all gencode V35
  • lines changed 8, context: html, text, full: html, text
    f695b16331ac22d8925e99a05aecd7ce563e0a08 Mon Dec 21 21:29:40 2020 -0800
    import gencodeV36
  • lines changed 4, context: html, text, full: html, text
    f2825cfe9d599d3970bf2379395e912451080d15 Mon Dec 21 23:16:17 2020 -0800
    import of gencdoe V36lift37
• src/hg/makeDb/schema/all.joiner
  • lines changed 94, context: html, text, full: html, text
    f695b16331ac22d8925e99a05aecd7ce563e0a08 Mon Dec 21 21:29:40 2020 -0800
    import gencodeV36
  • lines changed 91, context: html, text, full: html, text
    f2825cfe9d599d3970bf2379395e912451080d15 Mon Dec 21 23:16:17 2020 -0800
    import of gencdoe V36lift37
• src/hg/makeDb/trackDb/dog/canFam4/altAllele.html
  • lines changed 33, context: html, text, full: html, text
    997dccc5fff868b5238753b1975e21c9377b34d0 Mon Dec 7 12:46:11 2020 -0800
    adding track descriptions from Lindblat-Toh group refs #25279
• src/hg/makeDb/trackDb/dog/canFam4/altAllele.ra
  • lines changed 2, context: html, text, full: html, text
    997dccc5fff868b5238753b1975e21c9377b34d0 Mon Dec 7 12:46:11 2020 -0800
    adding track descriptions from Lindblat-Toh group refs #25279
  • lines changed 2, context: html, text, full: html, text
    843dc17757684b16196d7c03cafb01ed5e869e1b Wed Dec 23 14:04:16 2020 -0800
    Adding pennantIcons to new tracks refs #26657
• src/hg/makeDb/trackDb/dog/canFam4/miRNA.html
  • lines changed 35, context: html, text, full: html, text
    997dccc5fff868b5238753b1975e21c9377b34d0 Mon Dec 7 12:46:11 2020 -0800
    adding track descriptions from Lindblat-Toh group refs #25279
• src/hg/makeDb/trackDb/dog/canFam4/miRNA.ra
  • lines changed 2, context: html, text, full: html, text
    843dc17757684b16196d7c03cafb01ed5e869e1b Wed Dec 23 14:04:16 2020 -0800
    Adding pennantIcons to new tracks refs #26657
• src/hg/makeDb/trackDb/dog/canFam4/structVar.html
  • lines changed 33, context: html, text, full: html, text
    997dccc5fff868b5238753b1975e21c9377b34d0 Mon Dec 7 12:46:11 2020 -0800
    adding track descriptions from Lindblat-Toh group refs #25279
• src/hg/makeDb/trackDb/dog/canFam4/structVar.ra
  • lines changed 2, context: html, text, full: html, text
    843dc17757684b16196d7c03cafb01ed5e869e1b Wed Dec 23 14:04:16 2020 -0800
    Adding pennantIcons to new tracks refs #26657
• src/hg/makeDb/trackDb/dog/canFam4/uuGene.html
  • lines changed 34, context: html, text, full: html, text
    997dccc5fff868b5238753b1975e21c9377b34d0 Mon Dec 7 12:46:11 2020 -0800
    adding track descriptions from Lindblat-Toh group refs #25279
• src/hg/makeDb/trackDb/dog/canFam4/uuGene.ra
  • lines changed 2, context: html, text, full: html, text
    997dccc5fff868b5238753b1975e21c9377b34d0 Mon Dec 7 12:46:11 2020 -0800
    adding track descriptions from Lindblat-Toh group refs #25279
  • lines changed 2, context: html, text, full: html, text
    843dc17757684b16196d7c03cafb01ed5e869e1b Wed Dec 23 14:04:16 2020 -0800
    Adding pennantIcons to new tracks refs #26657
• src/hg/makeDb/trackDb/human/covidHgiGwas.ra
  • lines changed 47, context: html, text, full: html, text
    9c54f7b9a4adb03a98fe14179ae1426a804854bf Mon Dec 7 15:18:35 2020 -0800
    Add track for recently released data (Release 4, October 2020). refs #26129
  • lines changed 8, context: html, text, full: html, text
    72b81b56d5a8e434d283e2307220e0ae2826ef1e Mon Dec 7 16:14:51 2020 -0800
    Fixing some swapped labels and filters. refs #26616
  • lines changed 1, context: html, text, full: html, text
    74f7bc1b74e3688bb2ffe92826fea2dfc7d92ce0 Mon Dec 7 16:26:22 2020 -0800
    Another label fix. refs #26616
  • lines changed 44, context: html, text, full: html, text
    a16a2e7942c15da92cb03dbe35770bf76f3f5fee Fri Dec 11 09:32:54 2020 -0800
    First cut COVID GWAS Oct. 2020 data release. refs #26616
  • lines changed 4, context: html, text, full: html, text
    7c611b6c6e9a8b3a47651b8499525a4af7e9d421 Fri Dec 11 12:10:09 2020 -0800
    Adding release tags to subtracks refs #26616
  • lines changed 37, context: html, text, full: html, text
    3a05d18b3a907bdd6868dac95dfe983dcc52d73f Fri Dec 18 19:30:27 2020 -0800
    Polishing up COVID GWAS Oct 2020 track(s). refs #26616
  • lines changed 2, context: html, text, full: html, text
    b8663b9ecba8668b58966601e972f8de2cad89d6 Mon Dec 21 08:24:15 2020 -0800
    improved desc page and track labels refs #26616
  • lines changed 75, context: html, text, full: html, text
    67486cac9734e8590a43442a31ee396eedd714e1 Mon Dec 21 12:44:41 2020 -0800
    Polish track labels and subtrack ordering after Ana consult. refs #26616
  • lines changed 4, context: html, text, full: html, text
    a5e0acda0a4da7d3e89cc36f1f64e1e2a3d5f267 Mon Dec 21 17:06:35 2020 -0800
    Reload track with per-analysis median coloring, as per Ana suggestion. refs #26616
  • lines changed 10, context: html, text, full: html, text
    c15e02af297b6d6f82492bb6a370225cebe15f67 Wed Dec 23 17:00:55 2020 -0800
    Releasing the highly anticipated COVID GWAS v4 refs #26616
• src/hg/makeDb/trackDb/human/covidHgiGwasR4.html
  • lines changed 131, context: html, text, full: html, text
    3a05d18b3a907bdd6868dac95dfe983dcc52d73f Fri Dec 18 19:30:27 2020 -0800
    Polishing up COVID GWAS Oct 2020 track(s). refs #26616
• src/hg/makeDb/trackDb/human/covidHgiGwasR4Pval.html
  • lines changed 128, context: html, text, full: html, text
    b8663b9ecba8668b58966601e972f8de2cad89d6 Mon Dec 21 08:24:15 2020 -0800
    improved desc page and track labels refs #26616
  • lines changed 1, context: html, text, full: html, text
    f67498a54f360b24b1e25b2787be0cd8c9067fc6 Mon Dec 21 08:42:42 2020 -0800
    corrected url link refs #26616
  • lines changed 114, context: html, text, full: html, text
    c4e4aacbfde6ff4f11779828a95a513d80b53a39 Mon Dec 21 15:00:55 2020 -0800
    improved track description refs #26616
  • lines changed 18, context: html, text, full: html, text
    ee754a9166c5d010129381cf231715d2588dcfef Tue Dec 22 12:40:01 2020 -0800
    Add links gene regions on description page (by Ana). refs #26616
  • lines changed 1, context: html, text, full: html, text
    361ca0a4783780b16d7201cc132861ba7f35408f Tue Dec 22 12:43:41 2020 -0800
    Cosmetics on description page. refs #26616
  • lines changed 11, context: html, text, full: html, text
    c15e02af297b6d6f82492bb6a370225cebe15f67 Wed Dec 23 17:00:55 2020 -0800
    Releasing the highly anticipated COVID GWAS v4 refs #26616
• src/hg/makeDb/trackDb/human/hg19/gnomad.html
  • lines changed 8, context: html, text, full: html, text
    c2242ea3e6e61c9cf0b9ab1a1784cd4a852330a1 Wed Dec 23 12:54:00 2020 -0800
    Pushing html for the new gnomAD track and hiding the old one res #25010
  • lines changed 1, context: html, text, full: html, text
    9ed5b916e8178c02307052ea99789f70b473bdc4 Wed Dec 23 13:48:04 2020 -0800
    Typo fix refs #25010
• src/hg/makeDb/trackDb/human/hg19/gnomadExomesGenomes.html
  • lines changed 170, context: html, text, full: html, text
    a8745ce945b6f69b13846cf345fd1f400b252cd1 Tue Dec 8 16:54:37 2020 -0800
    Adding a description page for the new bigBed formatted gnomAD v2.1.1 tracks, refs #25010
  • lines changed 16, context: html, text, full: html, text
    8bb72ffae9ce2d1fad653846fd1b479c4e420eff Wed Dec 9 13:27:22 2020 -0800
    Fixing typos and style thigns #25010
• src/hg/makeDb/trackDb/human/hg19/trackDb.gencode.ra
  • lines changed 1, context: html, text, full: html, text
    f2825cfe9d599d3970bf2379395e912451080d15 Mon Dec 21 23:16:17 2020 -0800
    import of gencdoe V36lift37
• src/hg/makeDb/trackDb/human/hg19/trackDb.gnomad.ra
  • lines changed 1, context: html, text, full: html, text
    61c6951478b837ef6dffeb190a780e7579130686 Mon Dec 7 13:06:45 2020 -0800
    Fixing missing south asian population data from gnomad v2.1.1 exomes track, refs #25010
  • lines changed 2, context: html, text, full: html, text
    a8745ce945b6f69b13846cf345fd1f400b252cd1 Tue Dec 8 16:54:37 2020 -0800
    Adding a description page for the new bigBed formatted gnomAD v2.1.1 tracks, refs #25010
  • lines changed 2, context: html, text, full: html, text
    9bed28f8891d5e70aec638b53b82ccc18b41143b Fri Dec 11 12:18:53 2020 -0800
    Staging gnomad on beta refs #25525
  • lines changed 8, context: html, text, full: html, text
    c2242ea3e6e61c9cf0b9ab1a1784cd4a852330a1 Wed Dec 23 12:54:00 2020 -0800
    Pushing html for the new gnomAD track and hiding the old one res #25010
  • lines changed 43, context: html, text, full: html, text
    98727c090ca482d62cec5ddbe2f64403ebdc4f36 Wed Dec 23 13:24:47 2020 -0800
    Removing old track refs #25010
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 60, context: html, text, full: html, text
    cc5790bf736b10d5284eccccb3a332d8e5722732 Thu Dec 17 16:28:32 2020 -0800
    Commenting out peptideAtlas superTrack on dev, harmonizing the track with beta/RR. See RM for more info refs #26703
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeSuper.html
  • lines changed 5, context: html, text, full: html, text
    f2825cfe9d599d3970bf2379395e912451080d15 Mon Dec 21 23:16:17 2020 -0800
    import of gencdoe V36lift37
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV34lift37.ra
  • lines changed 1, context: html, text, full: html, text
    315c5b78e092290f9049fd803965d1c4f303a16a Mon Dec 14 10:42:16 2020 -0800
    Fixing visibilities for new GENCODE lift track refs #26524
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV36lift37.html
  • lines changed 32, context: html, text, full: html, text
    f2825cfe9d599d3970bf2379395e912451080d15 Mon Dec 21 23:16:17 2020 -0800
    import of gencdoe V36lift37
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV36lift37.ra
  • lines changed 224, context: html, text, full: html, text
    f2825cfe9d599d3970bf2379395e912451080d15 Mon Dec 21 23:16:17 2020 -0800
    import of gencdoe V36lift37
• src/hg/makeDb/trackDb/human/hg38/gnomad.ra
  • lines changed 1, context: html, text, full: html, text
    5595f79ea5536f735706cf56966cc3c7be7ca8c1 Mon Dec 28 09:27:58 2020 -0800
    Fixing gnomad v3.1 track name as periods in table names are not allowed or the table browser and data integrator complain, refs #26449
• src/hg/makeDb/trackDb/human/hg38/trackDb.241way.ra
  • lines changed 106, context: html, text, full: html, text
    2080e04c842d2016e324d9e31fe0a7b4e867f976 Fri Dec 18 12:39:01 2020 -0800
    viewing maf file from Cactus 241-way alignment refs #11636
  • lines changed 8, context: html, text, full: html, text
    d709b2a9f0d7ecffd5a80066f99882a05ec334e7 Mon Dec 21 14:35:42 2020 -0800
    begin to organize into clades refs #11636
• src/hg/makeDb/trackDb/human/hg38/trackDb.gencode.ra
  • lines changed 2, context: html, text, full: html, text
    f695b16331ac22d8925e99a05aecd7ce563e0a08 Mon Dec 21 21:29:40 2020 -0800
    import gencodeV36
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    2080e04c842d2016e324d9e31fe0a7b4e867f976 Fri Dec 18 12:39:01 2020 -0800
    viewing maf file from Cactus 241-way alignment refs #11636
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeSuper.html
  • lines changed 4, context: html, text, full: html, text
    f695b16331ac22d8925e99a05aecd7ce563e0a08 Mon Dec 21 21:29:40 2020 -0800
    import gencodeV36
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV35.html
  • lines changed 1, context: html, text, full: html, text
    8f6ed988e6b529bea3c89bd51a04055956a91327 Sun Dec 20 13:38:03 2020 -0800
    import of all gencode V35
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV36.html
  • lines changed 47, context: html, text, full: html, text
    f695b16331ac22d8925e99a05aecd7ce563e0a08 Mon Dec 21 21:29:40 2020 -0800
    import gencodeV36
• src/hg/makeDb/trackDb/human/hg38/wgEncodeGencodeV36.ra
  • lines changed 286, context: html, text, full: html, text
    f695b16331ac22d8925e99a05aecd7ce563e0a08 Mon Dec 21 21:29:40 2020 -0800
    import gencodeV36
• src/hg/makeDb/trackDb/human/trackDb.clinvar.ra
  • lines changed 1, context: html, text, full: html, text
    bd1a1532cd786aa1b6d42d8c50528747b9e8f3ed Wed Dec 23 12:09:37 2020 -0800
    Adding new pennantIcon for track refs #26330
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 5, context: html, text, full: html, text
    f6d8c8393632dfff192a1287ecce346cb83469d9 Tue Dec 8 11:09:16 2020 -0800
    try using bigPsl display parameters as used by blat custom track refs #24672
  • lines changed 1, context: html, text, full: html, text
    b9a38e782ce3445f2e73876c9664ccd125794ded Tue Dec 8 11:18:09 2020 -0800
    better genomicCodons for baseColorDefault on LRG bigPsl refs #24672
  • lines changed 1, context: html, text, full: html, text
    d79c89ce226eed40e2d000d423f9d23b28e26391 Thu Dec 10 15:53:00 2020 -0800
    add bigDataUrl for LRG track
  • lines changed 1, context: html, text, full: html, text
    44799e00a493d9626429d085e3d76a4b7d2964d7 Thu Dec 17 14:10:39 2020 -0800
    Adding updated pennantIcon to HGMD refs #24625
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.placentalsChainNet.ra
  • lines changed 16, context: html, text, full: html, text
    6b0af49f2d8868ba7ca4deda0207e180ad99addb Mon Dec 14 15:49:31 2020 -0800
    Adding canFam5 to placental chain/net refs #25917
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.35way.ra
  • lines changed 116, context: html, text, full: html, text
    69e951f0f4d62bc8577211a850d73a4199e4b72a Sat Dec 19 15:57:28 2020 -0800
    mm39 35-way now with maf summary table refs #26584
  • lines changed 11, context: html, text, full: html, text
    fa579fd8c0dd3c21af3673f3f606a1093d141f68 Sun Dec 20 23:21:20 2020 -0800
    more correct grouping of species refs #26584
  • lines changed 1, context: html, text, full: html, text
    051feecd9e300cf077787a56af4cd1b9dd4fb497 Tue Dec 22 10:36:30 2020 -0800
    turing on frames refs #26584
  • lines changed 4, context: html, text, full: html, text
    2b7291b093bad5d90337189e1de7a7168f049439 Tue Dec 22 21:22:38 2020 -0800
    now with phastCons and phyloP and mostConserved refs #26584
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    69e951f0f4d62bc8577211a850d73a4199e4b72a Sat Dec 19 15:57:28 2020 -0800
    mm39 35-way now with maf summary table refs #26584
• src/hg/makeDb/trackDb/seal/neoSch1/description.html
  • lines changed 3, context: html, text, full: html, text
    82e2dbe39acb29741c2b9ef8c2c30202c8a65ba4 Tue Dec 8 14:55:17 2020 -0800
    Fixing links to work for credits page, refs #19883
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 4, context: html, text, full: html, text
    b58decb00bc76c1cf7335f186f71875c0baca4bf Mon Dec 21 14:36:49 2020 -0800
    clades for hg38 241-way refs #11636
  • lines changed 1, context: html, text, full: html, text
    dab44418c480b8c931d0b86af916bbb3bf64ffe3 Fri Jan 1 08:06:26 2021 -0800
    Adding barChartStatsUrl tag. Right now it is ignored by the browser if barChartMatrixUrl is present. It points to a tab separated file with a label row and a few required fields.
• src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra
  • lines changed 57, context: html, text, full: html, text
    6a32124d5346a77980465373a1f78692956ff721 Wed Dec 9 14:49:45 2020 -0800
    adding definition for Chinese hamster now with dots in sequence names as well as assembly/organism name refs #26584
• src/hg/makeDb/trackDb/zebrafish/affyZonWildType.html
  • lines changed 1, context: html, text, full: html, text
    e79ddd0a12e743fa6b444713f45c71e79b627168 Thu Dec 10 09:28:18 2020 -0800
    Updating http to https for danRer5, uiLinks cronjob.
• src/hg/oneShot/freen/freen.c
  • lines changed 78, context: html, text, full: html, text
    6ff0c3e3a83b03257780785c6366ac492a468e9e Fri Jan 1 16:36:46 2021 -0800
    Freen helps me understand how to read strings from heartcellatlas hdf5 files.
  • lines changed 10, context: html, text, full: html, text
    4e97a66a0e7013279c1726f581fdd5dab079a023 Sat Jan 2 19:41:33 2021 -0800
    Some experiments with hdf5 files from heartcellatlas.org
• src/hg/oneShot/freen/makefile
  • lines changed 1, context: html, text, full: html, text
    4e97a66a0e7013279c1726f581fdd5dab079a023 Sat Jan 2 19:41:33 2021 -0800
    Some experiments with hdf5 files from heartcellatlas.org
• src/hg/sqlUpdateRelated/sqlUpdateRelated.doc
  • lines changed 1, context: html, text, full: html, text
    80545e15696d2b9c4a6ee26d8a381674af33f0f9 Sat Dec 19 11:30:09 2020 -0800
    Minor doc polish.
• src/hg/txGraph/makefile
  • lines changed 1, context: html, text, full: html, text
    f6ef041a6fa43e86f7b0c17f79371cb0fdeeaf8f Fri Dec 18 16:28:29 2020 -0800
    Adding utility to help pull out genes positions from a bunch of transcripts and a gene/transcript table.
• src/hg/txGraph/txBedToGraph/makeGraph.c
  • lines changed 18, context: html, text, full: html, text
    7460f8b77f30387b332655cd1579ced133d9cd03 Fri Dec 18 16:31:46 2020 -0800
    Fixing bug where a trimmed out graph could linger and cause problems.
• src/hg/txGraph/txBedToGraph/txBedToGraph.c
  • lines changed 1, context: html, text, full: html, text
    7460f8b77f30387b332655cd1579ced133d9cd03 Fri Dec 18 16:31:46 2020 -0800
    Fixing bug where a trimmed out graph could linger and cause problems.
• src/hg/txGraph/txgToGeneBed/makefile
  • lines changed 3, context: html, text, full: html, text
    f6ef041a6fa43e86f7b0c17f79371cb0fdeeaf8f Fri Dec 18 16:28:29 2020 -0800
    Adding utility to help pull out genes positions from a bunch of transcripts and a gene/transcript table.
• src/hg/txGraph/txgToGeneBed/txgToGeneBed.c
  • lines changed 75, context: html, text, full: html, text
    f6ef041a6fa43e86f7b0c17f79371cb0fdeeaf8f Fri Dec 18 16:28:29 2020 -0800
    Adding utility to help pull out genes positions from a bunch of transcripts and a gene/transcript table.
  • lines changed 10, context: html, text, full: html, text
    8b7a946061426398e6c6253e3478dd1ac84450ff Fri Dec 18 16:42:59 2020 -0800
    Adding geneName parameter
• src/hg/utils/automation/asmHubChromAlias.pl
  • lines changed 3, context: html, text, full: html, text
    123fabea3a7c3d2877818bfe27bcfaf49bbf0c58 Mon Dec 14 22:52:47 2020 -0800
    beware blanks in sequence names refs #23891
• src/hg/utils/gencodeGeneSymVerTx/gencodeGeneSymVerTx.c
  • lines changed 310, context: html, text, full: html, text
    68efbf55fbd3a55194ef24ca5e21d4bb09221c22 Sat Dec 26 13:07:43 2020 -0800
    First version of something to make file to help assign gencode genes and symbols to best transcripts is done.
• src/hg/utils/gencodeGeneSymVerTx/makefile
  • lines changed 3, context: html, text, full: html, text
    68efbf55fbd3a55194ef24ca5e21d4bb09221c22 Sat Dec 26 13:07:43 2020 -0800
    First version of something to make file to help assign gencode genes and symbols to best transcripts is done.
• src/hg/utils/gencodeVersionForGenes/gencodeVersionForGenes.c
  • lines changed 225, context: html, text, full: html, text
    0787a6e99b0df048ce46baccf261948c5ba10c7a Sat Dec 26 14:45:30 2020 -0800
    Utility to look through ucsc genome directories for best gencode to use.
  • lines changed 13, context: html, text, full: html, text
    761fffb81a48ba6ee7596f43a90c9e5069271adc Sat Dec 26 15:07:46 2020 -0800
    Adding ucscDb to output, and making optional bed output include full geneset, not just bits that our particular input matrix uses.
  • lines changed 86, context: html, text, full: html, text
    98eab6403a6627259fbbf38b1abc19d2d42387c2 Sat Dec 26 16:09:51 2020 -0800
    Making bed option just give genes we use, and reorder name/name2 to fit data use. Made allBed output to get data dump in Max's cellBrowser gene bed format.
  • lines changed 68, context: html, text, full: html, text
    4602afa7547202518272b4b49c3b188960c538dc Tue Dec 29 10:27:30 2020 -0800
    Making it strip .versions from gencode names if they are stripped in user gene list.
  • lines changed 2, context: html, text, full: html, text
    7b22e08d678f2e36efc345de2dcc850ca8840bcb Thu Dec 31 14:58:29 2020 -0800
    Hopefully getting rid of mixup between gene name and symbol.
• src/hg/utils/gencodeVersionForGenes/makefile
  • lines changed 3, context: html, text, full: html, text
    0787a6e99b0df048ce46baccf261948c5ba10c7a Sat Dec 26 14:45:30 2020 -0800
    Utility to look through ucsc genome directories for best gencode to use.
• src/hg/utils/hubCheck/hubCheck.c
  • lines changed 1, context: html, text, full: html, text
    cff0a237099d06f16896ec781a85cccb1a663849 Mon Dec 21 14:21:59 2020 -0800
    make sure that trackDb cache on hubs keeps track of files that are included in the trackDb.txt file
• src/hg/utils/otto/clinGen/clinGenWrapper.sh
  • lines changed 1, context: html, text, full: html, text
    7dea7c645f8ce8892d6d4d162a3cf8295309062f Fri Dec 11 11:22:24 2020 -0800
    Bringing repo copies of omim scripts up to date with the working versions, refs #18151
• src/hg/utils/otto/decipher/decipherWrapper.sh
  • lines changed 1, context: html, text, full: html, text
    7dea7c645f8ce8892d6d4d162a3cf8295309062f Fri Dec 11 11:22:24 2020 -0800
    Bringing repo copies of omim scripts up to date with the working versions, refs #18151
• src/hg/utils/otto/decipher/makefile
  • lines changed 1, context: html, text, full: html, text
    7dea7c645f8ce8892d6d4d162a3cf8295309062f Fri Dec 11 11:22:24 2020 -0800
    Bringing repo copies of omim scripts up to date with the working versions, refs #18151
• src/hg/utils/otto/geneReviews/geneReviewsWrapper.sh
  • lines changed 1, context: html, text, full: html, text
    7dea7c645f8ce8892d6d4d162a3cf8295309062f Fri Dec 11 11:22:24 2020 -0800
    Bringing repo copies of omim scripts up to date with the working versions, refs #18151
• src/hg/utils/otto/geneReviews/makefile
  • lines changed 3, context: html, text, full: html, text
    7dea7c645f8ce8892d6d4d162a3cf8295309062f Fri Dec 11 11:22:24 2020 -0800
    Bringing repo copies of omim scripts up to date with the working versions, refs #18151
• src/hg/utils/otto/gwas/checkGwas.sh
  • lines changed 5, context: html, text, full: html, text
    7dea7c645f8ce8892d6d4d162a3cf8295309062f Fri Dec 11 11:22:24 2020 -0800
    Bringing repo copies of omim scripts up to date with the working versions, refs #18151
• src/hg/utils/otto/gwas/gwasWrapper.sh
  • lines changed 1, context: html, text, full: html, text
    7dea7c645f8ce8892d6d4d162a3cf8295309062f Fri Dec 11 11:22:24 2020 -0800
    Bringing repo copies of omim scripts up to date with the working versions, refs #18151
• src/hg/utils/otto/gwas/makefile
  • lines changed 5, context: html, text, full: html, text
    7dea7c645f8ce8892d6d4d162a3cf8295309062f Fri Dec 11 11:22:24 2020 -0800
    Bringing repo copies of omim scripts up to date with the working versions, refs #18151
• src/hg/utils/otto/gwas/perlParser.pl
  • lines changed 3, context: html, text, full: html, text
    7dea7c645f8ce8892d6d4d162a3cf8295309062f Fri Dec 11 11:22:24 2020 -0800
    Bringing repo copies of omim scripts up to date with the working versions, refs #18151
• src/hg/utils/otto/isca/buildISCA.csh
  • lines changed 39, context: html, text, full: html, text
    7dea7c645f8ce8892d6d4d162a3cf8295309062f Fri Dec 11 11:22:24 2020 -0800
    Bringing repo copies of omim scripts up to date with the working versions, refs #18151
• src/hg/utils/otto/isca/checkISCA.sh
  • lines changed 1, context: html, text, full: html, text
    7dea7c645f8ce8892d6d4d162a3cf8295309062f Fri Dec 11 11:22:24 2020 -0800
    Bringing repo copies of omim scripts up to date with the working versions, refs #18151
• src/hg/utils/otto/isca/iscaWrapper.sh
  • lines changed 1, context: html, text, full: html, text
    7dea7c645f8ce8892d6d4d162a3cf8295309062f Fri Dec 11 11:22:24 2020 -0800
    Bringing repo copies of omim scripts up to date with the working versions, refs #18151
• src/hg/utils/otto/isca/makefile
  • lines changed 5, context: html, text, full: html, text
    7dea7c645f8ce8892d6d4d162a3cf8295309062f Fri Dec 11 11:22:24 2020 -0800
    Bringing repo copies of omim scripts up to date with the working versions, refs #18151
• src/hg/utils/otto/isca/validateISCA.sh
  • lines changed 1, context: html, text, full: html, text
    7dea7c645f8ce8892d6d4d162a3cf8295309062f Fri Dec 11 11:22:24 2020 -0800
    Bringing repo copies of omim scripts up to date with the working versions, refs #18151
• src/hg/utils/otto/omim/buildOmimTracks.sh
  • lines changed 17, context: html, text, full: html, text
    7dea7c645f8ce8892d6d4d162a3cf8295309062f Fri Dec 11 11:22:24 2020 -0800
    Bringing repo copies of omim scripts up to date with the working versions, refs #18151
• src/hg/utils/otto/omim/checkOmim.sh
  • lines changed 4, context: html, text, full: html, text
    7dea7c645f8ce8892d6d4d162a3cf8295309062f Fri Dec 11 11:22:24 2020 -0800
    Bringing repo copies of omim scripts up to date with the working versions, refs #18151
• src/hg/utils/otto/omim/makefile
  • lines changed 4, context: html, text, full: html, text
    7dea7c645f8ce8892d6d4d162a3cf8295309062f Fri Dec 11 11:22:24 2020 -0800
    Bringing repo copies of omim scripts up to date with the working versions, refs #18151
• src/hg/utils/otto/omim/omimUploadWrapper.sh
  • lines changed 1, context: html, text, full: html, text
    7dea7c645f8ce8892d6d4d162a3cf8295309062f Fri Dec 11 11:22:24 2020 -0800
    Bringing repo copies of omim scripts up to date with the working versions, refs #18151
• src/hg/utils/otto/omim/omimWrapper.sh
  • lines changed 1, context: html, text, full: html, text
    7dea7c645f8ce8892d6d4d162a3cf8295309062f Fri Dec 11 11:22:24 2020 -0800
    Bringing repo copies of omim scripts up to date with the working versions, refs #18151
• src/hg/utils/otto/sarscov2phylo/cladeLineageColors.pl
  • lines changed 3, context: html, text, full: html, text
    0018392edd796d5e02beecaf8482e3e905d9ef94 Thu Dec 10 09:47:54 2020 -0800
    Nextstrain clades now include subclades; for now, ignore subclades for coloring.
• src/hg/utils/otto/sarscov2phylo/extractUnmappedPublic.sh
  • lines changed 1, context: html, text, full: html, text
    70e001e0f7a71f53c7a70b45feabac07d9d3751b Mon Dec 14 16:35:16 2020 -0800
    Update sarscov2phylo process to use tree and multi-seq ali's downloaded from GISAID instead of tree from github and aligning nextfasta locally.
• src/hg/utils/otto/sarscov2phylo/installSarsCov2Phylo.sh
  • lines changed 80, context: html, text, full: html, text
    7124216a15d1239d897a2cc77888ff8640bd207c Mon Dec 14 17:05:04 2020 -0800
    Automate linking of sarsCov2Phylo and sarsCov2PhyloPub /gbdb/ files.
• src/hg/utils/otto/sarscov2phylo/mapPublic.sh
  • lines changed 22, context: html, text, full: html, text
    f2690b5f40e7e33dc355782853e812c76f4736ea Fri Dec 4 09:11:41 2020 -0800
    Add minimal metadata file for public sequences for use by hgPhyloPlace.
  • lines changed 19, context: html, text, full: html, text
    70e001e0f7a71f53c7a70b45feabac07d9d3751b Mon Dec 14 16:35:16 2020 -0800
    Update sarscov2phylo process to use tree and multi-seq ali's downloaded from GISAID instead of tree from github and aligning nextfasta locally.
• src/hg/utils/otto/sarscov2phylo/processGisaid.sh
  • lines changed 150, context: html, text, full: html, text
    70e001e0f7a71f53c7a70b45feabac07d9d3751b Mon Dec 14 16:35:16 2020 -0800
    Update sarscov2phylo process to use tree and multi-seq ali's downloaded from GISAID instead of tree from github and aligning nextfasta locally.
• src/hg/utils/otto/sarscov2phylo/updateSarsCov2Phylo.sh
  • lines changed 9, context: html, text, full: html, text
    70e001e0f7a71f53c7a70b45feabac07d9d3751b Mon Dec 14 16:35:16 2020 -0800
    Update sarscov2phylo process to use tree and multi-seq ali's downloaded from GISAID instead of tree from github and aligning nextfasta locally.
• src/inc/common.h
  • lines changed 4, context: html, text, full: html, text
    d1a9d0f8693e766b2214e65c1bcd6942a4718d5a Sat Dec 19 11:28:13 2020 -0800
    Adding a sortStrings function as a little wrapper around qsort for an array of char *'s. Also added microoptimization to doubleSort
• src/inc/common.mk
  • lines changed 5, context: html, text, full: html, text
    880d0ccc0f725d16e5b6ed9405bec57d766f0b23 Sun Dec 13 12:23:27 2020 -0800
    updated snake tracks to use latest HAL, which has some perforemance improvements
  • lines changed 6, context: html, text, full: html, text
    01a64f9d63b8d29bee782ced4e5ce16260089649 Fri Dec 18 15:37:24 2020 -0800
    fix hgTracks bring in uncommon shared library with HAL/HDF5, make CGIs less portable
• src/inc/fieldedTable.h
  • lines changed 8, context: html, text, full: html, text
    e41713ca26a553b4fe04ba1e4bc311d92c4e6654 Sun Dec 27 19:11:34 2020 -0800
    Adding a new routine, fieldedTableReadTabHeader, to allow matrix reading code to reuse some of fielded table
  • lines changed 13, context: html, text, full: html, text
    7d421618af20105240d24be483214c4259d45601 Mon Dec 28 15:07:59 2020 -0800
    Reordered definition of new function.
• src/inc/hash.h
  • lines changed 2, context: html, text, full: html, text
    4bd8d0793488ed896bf604d1ce7252fd601df161 Sat Dec 19 11:25:30 2020 -0800
    Making hashIncInt return the value (after increment, rather than be void.
• src/inc/linefile.h
  • lines changed 2, context: html, text, full: html, text
    a7e2892242a5f79a05b0c2ac6b9230058fc4b97c Thu Dec 31 14:55:36 2020 -0800
    Added lineFileTellSize to get size of current line.
• src/inc/matrixMarket.h
  • lines changed 47, context: html, text, full: html, text
    b0118c2f9d714a1913c16443c6684943497509ad Sun Dec 27 21:27:17 2020 -0800
    Adding matrixMarket file routine that helps handle row-at-a-time access in sorted files
• src/inc/obscure.h
  • lines changed 3, context: html, text, full: html, text
    9cb00c4f07c40b647094f0d03b2bcce00e535d9c Thu Dec 31 14:56:48 2020 -0800
    Added hashTsvBy since I needed it in two places, and it seems pretty general, but not common.
• src/inc/psGfx.h
  • lines changed 1, context: html, text, full: html, text
    77041cdec2060274397a745305d0b575aa7ac731 Sat Dec 19 10:00:28 2020 -0800
    re-connect the postscript output to the font setting, which had disappeared a while back. #26681
• src/lib/common.c
  • lines changed 16, context: html, text, full: html, text
    d1a9d0f8693e766b2214e65c1bcd6942a4718d5a Sat Dec 19 11:28:13 2020 -0800
    Adding a sortStrings function as a little wrapper around qsort for an array of char *'s. Also added microoptimization to doubleSort
• src/lib/fieldedTable.c
  • lines changed 58, context: html, text, full: html, text
    e41713ca26a553b4fe04ba1e4bc311d92c4e6654 Sun Dec 27 19:11:34 2020 -0800
    Adding a new routine, fieldedTableReadTabHeader, to allow matrix reading code to reuse some of fielded table
• src/lib/hash.c
  • lines changed 7, context: html, text, full: html, text
    4bd8d0793488ed896bf604d1ce7252fd601df161 Sat Dec 19 11:25:30 2020 -0800
    Making hashIncInt return the value (after increment, rather than be void.
• src/lib/makefile
  • lines changed 2, context: html, text, full: html, text
    b0118c2f9d714a1913c16443c6684943497509ad Sun Dec 27 21:27:17 2020 -0800
    Adding matrixMarket file routine that helps handle row-at-a-time access in sorted files
• src/lib/matrixMarket.c
  • lines changed 130, context: html, text, full: html, text
    b0118c2f9d714a1913c16443c6684943497509ad Sun Dec 27 21:27:17 2020 -0800
    Adding matrixMarket file routine that helps handle row-at-a-time access in sorted files
• src/lib/obscure.c
  • lines changed 28, context: html, text, full: html, text
    9cb00c4f07c40b647094f0d03b2bcce00e535d9c Thu Dec 31 14:56:48 2020 -0800
    Added hashTsvBy since I needed it in two places, and it seems pretty general, but not common.
• src/lib/psGfx.c
  • lines changed 3, context: html, text, full: html, text
    77041cdec2060274397a745305d0b575aa7ac731 Sat Dec 19 10:00:28 2020 -0800
    re-connect the postscript output to the font setting, which had disappeared a while back. #26681
• src/lib/pscmGfx.c
  • lines changed 6, context: html, text, full: html, text
    77041cdec2060274397a745305d0b575aa7ac731 Sat Dec 19 10:00:28 2020 -0800
    re-connect the postscript output to the font setting, which had disappeared a while back. #26681
• src/product/installer/README.md
  • lines changed 78, context: html, text, full: html, text
    062cabd2609425fd657324214ee55857d6b44440 Wed Dec 23 16:43:06 2020 -0800
    Updating the README.md file to catch up the help doc for GBiC on GitHub. Is currently missing the embedded youtube link that is currently on the gbic.html page, refs #23297
  • lines changed 5, context: html, text, full: html, text
    e06433e5a691534449ed3cb9ec070b2be6cf07b7 Mon Dec 28 15:09:39 2020 -0800
    Catching up the github README for GBiC to match the gbic.html documentation. refs #23297
  • lines changed 1, context: html, text, full: html, text
    ec7a214792ae943389d82a2d32d1774acf211b0b Mon Dec 28 15:28:30 2020 -0800
    Escaping a single quote, refs #23297
  • lines changed 1, context: html, text, full: html, text
    1a5e0c8a18a754369662bac65abca9b1f64fee64 Tue Dec 29 11:37:29 2020 -0800
    Escaping a period that gets encoded differently on the HTML page, refs #23297
• src/product/installer/browserSetup.sh
  • lines changed 2, context: html, text, full: html, text
    c8bef32e9a011410ae03ed0b44316085c8df86ff Thu Dec 10 01:58:41 2020 -0800
    add the fonts packages to gbic installer script, refs #25525
• src/product/mirrorDocs/staticPage.lua
  • lines changed 8, context: html, text, full: html, text
    b119f2db427a7199b97e8060054a38bbcc1a5d72 Mon Dec 28 14:19:44 2020 -0800
    Adding a RawBlock function to the staticPage.lua file so pandoc can convert the embedded YouTube link on the markdown file to HTML, refs #23297
• src/tabFile/tabToTabDir/tabToTabDir.c
  • lines changed 2, context: html, text, full: html, text
    d858704add16d24efbcc1a83ddc110a76a72d857 Sat Oct 3 09:57:23 2020 -0700
    Improving usage statement.
  • lines changed 1, context: html, text, full: html, text
    a8287907aff5a8e7b783da53fc9e26a3d2a989a6 Sat Oct 3 09:58:11 2020 -0700
    Improving usage statement.
  • lines changed 83, context: html, text, full: html, text
    44221bac6c8204e4f2549139877b9ad42d7e6f0a Sat Oct 3 20:16:09 2020 -0700
    Fixing a bug where you couldn't have a single line use of a defined variable if it's name should match name of output field. Also added first cut of aggregation - count, to be expanded soon.
  • lines changed 104, context: html, text, full: html, text
    46cbe5852e09da1ac8f78402722f7cd74229dcb1 Sat Oct 3 22:13:29 2020 -0700
    Adding way to create a field that aggregates unique values.
  • lines changed 38, context: html, text, full: html, text
    5d0b7bb9098685d0a547b24328de982f090b9100 Sun Oct 4 09:23:46 2020 -0700
    Adding first cut at stats aggregator
  • lines changed 28, context: html, text, full: html, text
    5deadb92cd2d8ddc11d8e11fee61d5f8faf304d6 Sun Oct 4 09:48:11 2020 -0700
    Made stats output sort so most common occurs first in list.
  • lines changed 24, context: html, text, full: html, text
    7e420071260c119b5917eb52a2aa20edf4bc1d94 Tue Oct 6 17:45:55 2020 -0700
    Adding percentage after count in stats output. Moving doc mostly from usage to new tabToTabDir.doc file.
  • lines changed 5, context: html, text, full: html, text
    b3834f9b6ec64e8b6018eca2c0c737cbd394484c Sat Dec 19 11:24:16 2020 -0800
    Handling some syntax errors with meaningful error messages rather than program crashes.
• src/tabFile/tabToTabDir/tabToTabDir.doc
  • lines changed 91, context: html, text, full: html, text
    8d70270630439dce0f7b3f5a06d0a2a4f74e395f Tue Oct 6 17:42:17 2020 -0700
    tabToTabDir.doc
  • lines changed 16, context: html, text, full: html, text
    9fc4a45a0bc85ef2d4c397a557fd1d9cd7dee535 Thu Oct 29 11:11:51 2020 -0700
    Documenting 'unroll' stanzas
• src/tabFile/tabToTabDir/tests/expected/donor_organ_cells.tsv
  • lines changed 13, context: html, text, full: html, text
    3cbb4b9933f89be56be960e16e2cce7a94b37ec8 Sun Oct 4 19:29:16 2020 -0700
    Updating test set to include new features of agregating by list
  • lines changed 13, context: html, text, full: html, text
    cfcd633ac84929aca1dca0656cd92e8381a35d68 Sun Oct 4 19:31:49 2020 -0700
    Adding test set for count type field.
• src/tabFile/tabToTabDir/tests/expected/lab_submitters.tsv
  • lines changed 2, context: html, text, full: html, text
    3cbb4b9933f89be56be960e16e2cce7a94b37ec8 Sun Oct 4 19:29:16 2020 -0700
    Updating test set to include new features of agregating by list
  • lines changed 2, context: html, text, full: html, text
    bee3b5304bafb04498dd966ca167a7fbbc9b0e8c Sun Oct 4 19:46:04 2020 -0700
    Adding stats field type to test suite.
• src/tabFile/tabToTabDir/tests/expected/unroll_test.tsv
  • lines changed 1, context: html, text, full: html, text
    3cbb4b9933f89be56be960e16e2cce7a94b37ec8 Sun Oct 4 19:29:16 2020 -0700
    Updating test set to include new features of agregating by list
• src/tabFile/tabToTabDir/tests/input/spec.txt
  • lines changed 15, context: html, text, full: html, text
    3cbb4b9933f89be56be960e16e2cce7a94b37ec8 Sun Oct 4 19:29:16 2020 -0700
    Updating test set to include new features of agregating by list
  • lines changed 1, context: html, text, full: html, text
    cfcd633ac84929aca1dca0656cd92e8381a35d68 Sun Oct 4 19:31:49 2020 -0700
    Adding test set for count type field.
  • lines changed 1, context: html, text, full: html, text
    bee3b5304bafb04498dd966ca167a7fbbc9b0e8c Sun Oct 4 19:46:04 2020 -0700
    Adding stats field type to test suite.
• src/tabFile/tabToTabDir/tests/test.x
  • lines changed 13, context: html, text, full: html, text
    cfcd633ac84929aca1dca0656cd92e8381a35d68 Sun Oct 4 19:31:49 2020 -0700
    Adding test set for count type field.
• src/tagStorm/tagStormFromTab/100.divSpec
  • lines changed 5, context: html, text, full: html, text
    7c06824caee59a83b81af4fc02bca7705e6263f9 Mon Feb 10 15:30:35 2020 -0800
    Adding new test sets.
• src/tagStorm/tagStormFromTab/100.tab
  • lines changed 100, context: html, text, full: html, text
    7c06824caee59a83b81af4fc02bca7705e6263f9 Mon Feb 10 15:30:35 2020 -0800
    Adding new test sets.
• src/tagStorm/tagStormFromTab/100.tag
  • lines changed 517, context: html, text, full: html, text
    7c06824caee59a83b81af4fc02bca7705e6263f9 Mon Feb 10 15:30:35 2020 -0800
    Adding new test sets.
• src/utils/chromToUcsc/chromToUcsc
  • lines changed 2, context: html, text, full: html, text
    cf1446a79ba6729f0d88f1ccca523d9604d758ca Tue Dec 15 02:09:54 2020 -0800
    fixing up the chromToUcsc test case to use a more realistic vcf.gz file, refs #26672
  • lines changed 3, context: html, text, full: html, text
    572f8e2a5e67250ee2802f039a8b97d2322cc99a Tue Dec 15 02:16:25 2020 -0800
    documenting supported file formats, refs #26689
• src/utils/chromToUcsc/tests/expected/hg19.vcf
  • lines changed 500, context: html, text, full: html, text
    231229599259249d0b0a00be9dd95b64d9d9a48c Tue Dec 15 01:58:10 2020 -0800
    adding VCF test case to chromToUcsc, no new feature or code change, so no redmine
• src/utils/chromToUcsc/tests/in/hg19.vcf
  • lines changed 500, context: html, text, full: html, text
    231229599259249d0b0a00be9dd95b64d9d9a48c Tue Dec 15 01:58:10 2020 -0800
    adding VCF test case to chromToUcsc, no new feature or code change, so no redmine
  • lines changed 500, context: html, text, full: html, text
    cf1446a79ba6729f0d88f1ccca523d9604d758ca Tue Dec 15 02:09:54 2020 -0800
    fixing up the chromToUcsc test case to use a more realistic vcf.gz file, refs #26672
• src/utils/chromToUcsc/tests/in/hg19.vcf.gz
  • lines changed 0, context: html, text, full: html, text
    cf1446a79ba6729f0d88f1ccca523d9604d758ca Tue Dec 15 02:09:54 2020 -0800
    fixing up the chromToUcsc test case to use a more realistic vcf.gz file, refs #26672
• src/utils/chromToUcsc/tests/makefile
  • lines changed 1, context: html, text, full: html, text
    231229599259249d0b0a00be9dd95b64d9d9a48c Tue Dec 15 01:58:10 2020 -0800
    adding VCF test case to chromToUcsc, no new feature or code change, so no redmine
• src/utils/clusterMatrixToBarChartBed/clusterMatrixToBarChartBed.c
  • lines changed 297, context: html, text, full: html, text
    47c764d7fd7d2538ccc1d0eacdf19bf0949ab225 Sun Dec 20 18:11:14 2020 -0800
    Fixing camel casing to be like most of our barChart C code.
  • lines changed 55, context: html, text, full: html, text
    992541b9ac7cdc7f292bc6cc35b8c471e15ffaea Tue Dec 22 10:07:00 2020 -0800
    Adding name2 option. Making mean the default and median a flag.
  • lines changed 2, context: html, text, full: html, text
    3f2b8e9bd546eadd2883cbd2aecadd998496f334 Sat Dec 26 17:33:37 2020 -0800
    Reducing verbosity and adding percentage missed to output
  • lines changed 2, context: html, text, full: html, text
    0f37bc93a62d4e0b25336becb089f7c42ceef160 Sat Dec 26 17:38:35 2020 -0800
    Reducing verbosity
  • lines changed 6, context: html, text, full: html, text
    45b9bd3fd9a066cb2515629b23c3eef5a10eeb74 Sat Dec 26 20:22:29 2020 -0800
    Making outputting position in expMatrix part of default output.
  • lines changed 41, context: html, text, full: html, text
    b3291f717be7ee6ce33882e0c07cf815d7ac40c5 Thu Dec 31 15:05:10 2020 -0800
    Moved hashTsvBy() to obscure.c. Removed some debugging uglyfs.
• src/utils/clusterMatrixToBarChartBed/clusterMatrixToBarchartBed.c
  • lines changed 297, context: html, text, full: html, text
    8bb6956fbfc0b789de4c76938878dd3a4399b3d0 Sun Dec 20 18:09:04 2020 -0800
    Fixing camel casing to be like most of our barChart C code.
  • lines changed 297, context: html, text, full: html, text
    47c764d7fd7d2538ccc1d0eacdf19bf0949ab225 Sun Dec 20 18:11:14 2020 -0800
    Fixing camel casing to be like most of our barChart C code.
• src/utils/clusterMatrixToBarChartBed/makefile
  • lines changed 4, context: html, text, full: html, text
    8bb6956fbfc0b789de4c76938878dd3a4399b3d0 Sun Dec 20 18:09:04 2020 -0800
    Fixing camel casing to be like most of our barChart C code.
  • lines changed 4, context: html, text, full: html, text
    47c764d7fd7d2538ccc1d0eacdf19bf0949ab225 Sun Dec 20 18:11:14 2020 -0800
    Fixing camel casing to be like most of our barChart C code.
• src/utils/clusterMatrixToBarChartBed/tests/hub.conf
  • lines changed 23, context: html, text, full: html, text
    866a89e5704f4bde33de441b72016347a0cdd180 Tue Dec 22 06:01:02 2020 -0800
    adding hub.conf to Jim's new tool test directory
• src/utils/clusterMatrixToBarChartBed/tests/makefile
  • lines changed 7, context: html, text, full: html, text
    8bb6956fbfc0b789de4c76938878dd3a4399b3d0 Sun Dec 20 18:09:04 2020 -0800
    Fixing camel casing to be like most of our barChart C code.
  • lines changed 1, context: html, text, full: html, text
    15b999a555451debea863862c67b7b0784cdb20c Sun Dec 20 18:11:46 2020 -0800
    Fixing camel casing to be like most of our barChart C code.
  • lines changed 5, context: html, text, full: html, text
    f8f44ba39e3c8a4c1c92f5332d22d2a3e1f83e2a Tue Dec 22 10:05:53 2020 -0800
    Adding new cases to test set
  • lines changed 2, context: html, text, full: html, text
    4d18f275081580118e24c54d96caaf93c7963452 Mon Dec 28 20:57:05 2020 -0800
    Updating test set for new command line options setup.
• src/utils/clusterMatrixToBarChartBed/tests/mean.expected
  • lines changed 10, context: html, text, full: html, text
    f8f44ba39e3c8a4c1c92f5332d22d2a3e1f83e2a Tue Dec 22 10:05:53 2020 -0800
    Adding new cases to test set
• src/utils/clusterMatrixToBarChartBed/tests/median.expected
  • lines changed 10, context: html, text, full: html, text
    f8f44ba39e3c8a4c1c92f5332d22d2a3e1f83e2a Tue Dec 22 10:05:53 2020 -0800
    Adding new cases to test set
  • lines changed 10, context: html, text, full: html, text
    4d18f275081580118e24c54d96caaf93c7963452 Mon Dec 28 20:57:05 2020 -0800
    Updating test set for new command line options setup.
• src/utils/clusterMatrixToBarChartBed/tests/name2.expected
  • lines changed 10, context: html, text, full: html, text
    f8f44ba39e3c8a4c1c92f5332d22d2a3e1f83e2a Tue Dec 22 10:05:53 2020 -0800
    Adding new cases to test set
• src/utils/clusterMatrixToBarChartBed/tests/test.coords
  • lines changed 10, context: html, text, full: html, text
    8bb6956fbfc0b789de4c76938878dd3a4399b3d0 Sun Dec 20 18:09:04 2020 -0800
    Fixing camel casing to be like most of our barChart C code.
• src/utils/clusterMatrixToBarChartBed/tests/test.expected
  • lines changed 10, context: html, text, full: html, text
    8bb6956fbfc0b789de4c76938878dd3a4399b3d0 Sun Dec 20 18:09:04 2020 -0800
    Fixing camel casing to be like most of our barChart C code.
  • lines changed 10, context: html, text, full: html, text
    f8f44ba39e3c8a4c1c92f5332d22d2a3e1f83e2a Tue Dec 22 10:05:53 2020 -0800
    Adding new cases to test set
• src/utils/clusterMatrixToBarChartBed/tests/test.groupOrder
  • lines changed 4, context: html, text, full: html, text
    8bb6956fbfc0b789de4c76938878dd3a4399b3d0 Sun Dec 20 18:09:04 2020 -0800
    Fixing camel casing to be like most of our barChart C code.
• src/utils/clusterMatrixToBarChartBed/tests/test.matrix
  • lines changed 11, context: html, text, full: html, text
    8bb6956fbfc0b789de4c76938878dd3a4399b3d0 Sun Dec 20 18:09:04 2020 -0800
    Fixing camel casing to be like most of our barChart C code.
• src/utils/clusterMatrixToBarChartBed/tests/test.meta
  • lines changed 8, context: html, text, full: html, text
    8bb6956fbfc0b789de4c76938878dd3a4399b3d0 Sun Dec 20 18:09:04 2020 -0800
    Fixing camel casing to be like most of our barChart C code.
• src/utils/clusterMatrixToBarChartBed/tests/test.name2
  • lines changed 10, context: html, text, full: html, text
    f8f44ba39e3c8a4c1c92f5332d22d2a3e1f83e2a Tue Dec 22 10:05:53 2020 -0800
    Adding new cases to test set
• src/utils/clusterMatrixToBarchartBed/clusterMatrixToBarchartBed.c
  • lines changed 276, context: html, text, full: html, text
    8d6aa83c01798ccb80e22f049c825369a3320c01 Fri Dec 18 11:24:50 2020 -0800
    First working cut of C program to convert gene expression and similar matrixes to barchart bed files using a 6 or 7 column bed file to describe gene positions.
  • lines changed 11, context: html, text, full: html, text
    f0c88ba99715e71d8868232507ddf166270e1e33 Fri Dec 18 18:19:57 2020 -0800
    Allowing a gene name to be multiply mapped.
  • lines changed 45, context: html, text, full: html, text
    8135446fb6a4c338e543585aa411808eef36ee10 Sun Dec 20 16:00:10 2020 -0800
    Optimizing speed and polishing comments.
  • lines changed 297, context: html, text, full: html, text
    8bb6956fbfc0b789de4c76938878dd3a4399b3d0 Sun Dec 20 18:09:04 2020 -0800
    Fixing camel casing to be like most of our barChart C code.
• src/utils/clusterMatrixToBarchartBed/makefile
  • lines changed 4, context: html, text, full: html, text
    8d6aa83c01798ccb80e22f049c825369a3320c01 Fri Dec 18 11:24:50 2020 -0800
    First working cut of C program to convert gene expression and similar matrixes to barchart bed files using a 6 or 7 column bed file to describe gene positions.
  • lines changed 4, context: html, text, full: html, text
    8bb6956fbfc0b789de4c76938878dd3a4399b3d0 Sun Dec 20 18:09:04 2020 -0800
    Fixing camel casing to be like most of our barChart C code.
• src/utils/clusterMatrixToBarchartBed/tests/makefile
  • lines changed 4, context: html, text, full: html, text
    8d6aa83c01798ccb80e22f049c825369a3320c01 Fri Dec 18 11:24:50 2020 -0800
    First working cut of C program to convert gene expression and similar matrixes to barchart bed files using a 6 or 7 column bed file to describe gene positions.
  • lines changed 3, context: html, text, full: html, text
    2d4ce573d9b6e9929d5c2c2481f64bf105b62031 Sun Dec 20 16:06:34 2020 -0800
    Adding making 'clean' rule work and adding to parent makefile again.
  • lines changed 7, context: html, text, full: html, text
    8bb6956fbfc0b789de4c76938878dd3a4399b3d0 Sun Dec 20 18:09:04 2020 -0800
    Fixing camel casing to be like most of our barChart C code.
• src/utils/clusterMatrixToBarchartBed/tests/test.coords
  • lines changed 10, context: html, text, full: html, text
    8d6aa83c01798ccb80e22f049c825369a3320c01 Fri Dec 18 11:24:50 2020 -0800
    First working cut of C program to convert gene expression and similar matrixes to barchart bed files using a 6 or 7 column bed file to describe gene positions.
  • lines changed 10, context: html, text, full: html, text
    8bb6956fbfc0b789de4c76938878dd3a4399b3d0 Sun Dec 20 18:09:04 2020 -0800
    Fixing camel casing to be like most of our barChart C code.
• src/utils/clusterMatrixToBarchartBed/tests/test.expected
  • lines changed 10, context: html, text, full: html, text
    8d6aa83c01798ccb80e22f049c825369a3320c01 Fri Dec 18 11:24:50 2020 -0800
    First working cut of C program to convert gene expression and similar matrixes to barchart bed files using a 6 or 7 column bed file to describe gene positions.
  • lines changed 10, context: html, text, full: html, text
    8bb6956fbfc0b789de4c76938878dd3a4399b3d0 Sun Dec 20 18:09:04 2020 -0800
    Fixing camel casing to be like most of our barChart C code.
• src/utils/clusterMatrixToBarchartBed/tests/test.groupOrder
  • lines changed 4, context: html, text, full: html, text
    8d6aa83c01798ccb80e22f049c825369a3320c01 Fri Dec 18 11:24:50 2020 -0800
    First working cut of C program to convert gene expression and similar matrixes to barchart bed files using a 6 or 7 column bed file to describe gene positions.
  • lines changed 4, context: html, text, full: html, text
    8bb6956fbfc0b789de4c76938878dd3a4399b3d0 Sun Dec 20 18:09:04 2020 -0800
    Fixing camel casing to be like most of our barChart C code.
• src/utils/clusterMatrixToBarchartBed/tests/test.matrix
  • lines changed 11, context: html, text, full: html, text
    8d6aa83c01798ccb80e22f049c825369a3320c01 Fri Dec 18 11:24:50 2020 -0800
    First working cut of C program to convert gene expression and similar matrixes to barchart bed files using a 6 or 7 column bed file to describe gene positions.
  • lines changed 11, context: html, text, full: html, text
    8bb6956fbfc0b789de4c76938878dd3a4399b3d0 Sun Dec 20 18:09:04 2020 -0800
    Fixing camel casing to be like most of our barChart C code.
• src/utils/clusterMatrixToBarchartBed/tests/test.meta
  • lines changed 8, context: html, text, full: html, text
    8d6aa83c01798ccb80e22f049c825369a3320c01 Fri Dec 18 11:24:50 2020 -0800
    First working cut of C program to convert gene expression and similar matrixes to barchart bed files using a 6 or 7 column bed file to describe gene positions.
  • lines changed 8, context: html, text, full: html, text
    8bb6956fbfc0b789de4c76938878dd3a4399b3d0 Sun Dec 20 18:09:04 2020 -0800
    Fixing camel casing to be like most of our barChart C code.
• src/utils/csvToTsv/csvToTsv.c
  • lines changed 71, context: html, text, full: html, text
    d13f1c8f1fada76cc569fc0c6f073f76fdeace92 Thu Oct 1 17:03:37 2020 -0700
    We have a shell script that does this so slowly on big files it is painful, so I wrote this in C.
• src/utils/csvToTsv/makefile
  • lines changed 3, context: html, text, full: html, text
    d13f1c8f1fada76cc569fc0c6f073f76fdeace92 Thu Oct 1 17:03:37 2020 -0700
    We have a shell script that does this so slowly on big files it is painful, so I wrote this in C.
• src/utils/faSize/faSize.c
  • lines changed 10, context: html, text, full: html, text
    b89ddcc7f8d37a686a917fd22a321b963821dfa5 Mon Dec 14 16:37:58 2020 -0800
    Added -veryDetailed option to show not only size, but also #Ns in each sequence.
• src/utils/makefile
  • lines changed 1, context: html, text, full: html, text
    21e481b8c5061e91f5e3abd49e92c9bee87be6ca Fri Dec 18 16:56:34 2020 -0800
    A little polishing and adding to parent makefile.
  • lines changed 1, context: html, text, full: html, text
    beb03835a67006b093a20746fcaf5b12a7a1156c Sat Dec 19 12:01:02 2020 -0800
    Taking clusterMatrixToBarchartBed out of build chain until I can figure out how to get make clean to work with it in.
  • lines changed 1, context: html, text, full: html, text
    2d4ce573d9b6e9929d5c2c2481f64bf105b62031 Sun Dec 20 16:06:34 2020 -0800
    Adding making 'clean' rule work and adding to parent makefile again.
• src/utils/matrixCat/makefile
  • lines changed 3, context: html, text, full: html, text
    2ec8e153f0b10f84aac7109840f6cab79d5f8902 Wed Dec 30 18:50:13 2020 -0800
    Pastes together matrices in the x-dimension while trimming duplicate row-labels.
  • lines changed 3, context: html, text, full: html, text
    a34abddf2f3f018f50f596632a4ba0b1fc6d718b Thu Dec 31 15:06:06 2020 -0800
    Renamed this to matrixPaste
• src/utils/matrixCat/matrixPaste.c
  • lines changed 103, context: html, text, full: html, text
    2ec8e153f0b10f84aac7109840f6cab79d5f8902 Wed Dec 30 18:50:13 2020 -0800
    Pastes together matrices in the x-dimension while trimming duplicate row-labels.
  • lines changed 103, context: html, text, full: html, text
    a34abddf2f3f018f50f596632a4ba0b1fc6d718b Thu Dec 31 15:06:06 2020 -0800
    Renamed this to matrixPaste
• src/utils/matrixCat/test.in
  • lines changed 6, context: html, text, full: html, text
    2ec8e153f0b10f84aac7109840f6cab79d5f8902 Wed Dec 30 18:50:13 2020 -0800
    Pastes together matrices in the x-dimension while trimming duplicate row-labels.
  • lines changed 6, context: html, text, full: html, text
    a34abddf2f3f018f50f596632a4ba0b1fc6d718b Thu Dec 31 15:06:06 2020 -0800
    Renamed this to matrixPaste
• src/utils/matrixCat/test.in2
  • lines changed 6, context: html, text, full: html, text
    2ec8e153f0b10f84aac7109840f6cab79d5f8902 Wed Dec 30 18:50:13 2020 -0800
    Pastes together matrices in the x-dimension while trimming duplicate row-labels.
  • lines changed 6, context: html, text, full: html, text
    a34abddf2f3f018f50f596632a4ba0b1fc6d718b Thu Dec 31 15:06:06 2020 -0800
    Renamed this to matrixPaste
• src/utils/matrixCat/test.long
  • lines changed 9, context: html, text, full: html, text
    2ec8e153f0b10f84aac7109840f6cab79d5f8902 Wed Dec 30 18:50:13 2020 -0800
    Pastes together matrices in the x-dimension while trimming duplicate row-labels.
  • lines changed 9, context: html, text, full: html, text
    a34abddf2f3f018f50f596632a4ba0b1fc6d718b Thu Dec 31 15:06:06 2020 -0800
    Renamed this to matrixPaste
• src/utils/matrixCat/test.remix
  • lines changed 6, context: html, text, full: html, text
    2ec8e153f0b10f84aac7109840f6cab79d5f8902 Wed Dec 30 18:50:13 2020 -0800
    Pastes together matrices in the x-dimension while trimming duplicate row-labels.
  • lines changed 6, context: html, text, full: html, text
    a34abddf2f3f018f50f596632a4ba0b1fc6d718b Thu Dec 31 15:06:06 2020 -0800
    Renamed this to matrixPaste
• src/utils/matrixCat/test.short
  • lines changed 3, context: html, text, full: html, text
    2ec8e153f0b10f84aac7109840f6cab79d5f8902 Wed Dec 30 18:50:13 2020 -0800
    Pastes together matrices in the x-dimension while trimming duplicate row-labels.
  • lines changed 3, context: html, text, full: html, text
    a34abddf2f3f018f50f596632a4ba0b1fc6d718b Thu Dec 31 15:06:06 2020 -0800
    Renamed this to matrixPaste
• src/utils/matrixClusterColumns/makefile
  • lines changed 3, context: html, text, full: html, text
    826d8721b1c1b0a8b1030056c90f14a8d319f5e8 Mon Dec 28 16:30:36 2020 -0800
    First cut of tool designed to cluster big matrices by column. This is a refactoring of clusterMatrixIntoBarchartBed to just handle the matrix shrinking part, whichis the most time consuming and perhaps useful elsewhere.
• src/utils/matrixClusterColumns/matrixClusterColumns.c
  • lines changed 420, context: html, text, full: html, text
    826d8721b1c1b0a8b1030056c90f14a8d319f5e8 Mon Dec 28 16:30:36 2020 -0800
    First cut of tool designed to cluster big matrices by column. This is a refactoring of clusterMatrixIntoBarchartBed to just handle the matrix shrinking part, whichis the most time consuming and perhaps useful elsewhere.
  • lines changed 36, context: html, text, full: html, text
    e2f20604e7a8eaaa06057a074466ee31c6642adc Thu Dec 31 13:05:18 2020 -0800
    Polishing a little, adding makeIndex option, fixing an off-by-one bug.
  • lines changed 54, context: html, text, full: html, text
    f6a7885f1bd5a869ced47dc1dfed6d03daec7c3a Thu Dec 31 16:15:46 2020 -0800
    Adding median flag and the start of a test set.
  • lines changed 63, context: html, text, full: html, text
    9e970884e47accc964b1fac1e9bd356be9202e84 Thu Dec 31 16:55:22 2020 -0800
    Rearranging command line. Sample is always col0. Added stats output file.
• src/utils/matrixClusterColumns/test.expected
  • lines changed 11, context: html, text, full: html, text
    f6a7885f1bd5a869ced47dc1dfed6d03daec7c3a Thu Dec 31 16:15:46 2020 -0800
    Adding median flag and the start of a test set.
• src/utils/matrixClusterColumns/test.matrix
  • lines changed 11, context: html, text, full: html, text
    f6a7885f1bd5a869ced47dc1dfed6d03daec7c3a Thu Dec 31 16:15:46 2020 -0800
    Adding median flag and the start of a test set.
• src/utils/matrixClusterColumns/test.meta
  • lines changed 9, context: html, text, full: html, text
    f6a7885f1bd5a869ced47dc1dfed6d03daec7c3a Thu Dec 31 16:15:46 2020 -0800
    Adding median flag and the start of a test set.
• src/utils/matrixPaste/makefile
  • lines changed 3, context: html, text, full: html, text
    2ec8e153f0b10f84aac7109840f6cab79d5f8902 Wed Dec 30 18:50:13 2020 -0800
    Pastes together matrices in the x-dimension while trimming duplicate row-labels.
• src/utils/matrixPaste/matrixPaste.c
  • lines changed 151, context: html, text, full: html, text
    2ec8e153f0b10f84aac7109840f6cab79d5f8902 Wed Dec 30 18:50:13 2020 -0800
    Pastes together matrices in the x-dimension while trimming duplicate row-labels.
• src/utils/matrixPaste/test.in
  • lines changed 6, context: html, text, full: html, text
    2ec8e153f0b10f84aac7109840f6cab79d5f8902 Wed Dec 30 18:50:13 2020 -0800
    Pastes together matrices in the x-dimension while trimming duplicate row-labels.
• src/utils/matrixPaste/test.in2
  • lines changed 6, context: html, text, full: html, text
    2ec8e153f0b10f84aac7109840f6cab79d5f8902 Wed Dec 30 18:50:13 2020 -0800
    Pastes together matrices in the x-dimension while trimming duplicate row-labels.
• src/utils/matrixPaste/test.long
  • lines changed 9, context: html, text, full: html, text
    2ec8e153f0b10f84aac7109840f6cab79d5f8902 Wed Dec 30 18:50:13 2020 -0800
    Pastes together matrices in the x-dimension while trimming duplicate row-labels.
• src/utils/matrixPaste/test.remix
  • lines changed 6, context: html, text, full: html, text
    2ec8e153f0b10f84aac7109840f6cab79d5f8902 Wed Dec 30 18:50:13 2020 -0800
    Pastes together matrices in the x-dimension while trimming duplicate row-labels.
• src/utils/matrixPaste/test.short
  • lines changed 3, context: html, text, full: html, text
    2ec8e153f0b10f84aac7109840f6cab79d5f8902 Wed Dec 30 18:50:13 2020 -0800
    Pastes together matrices in the x-dimension while trimming duplicate row-labels.
• src/utils/matrixRelabel/makefile
  • lines changed 3, context: html, text, full: html, text
    9186636eb6806a49e2e2cc5fd6b11d690ab729c1 Mon Dec 28 18:36:02 2020 -0800
    A little utility for changing labels in first row and or column of a tsv table.
• src/utils/matrixRelabel/matrixRelabel.c
  • lines changed 121, context: html, text, full: html, text
    9186636eb6806a49e2e2cc5fd6b11d690ab729c1 Mon Dec 28 18:36:02 2020 -0800
    A little utility for changing labels in first row and or column of a tsv table.
  • lines changed 10, context: html, text, full: html, text
    6aa2022b82fb742c780fec6dc197371c2f299f42 Mon Dec 28 20:49:54 2020 -0800
    Making it so first word is expected to be in the new lables
• src/utils/matrixRelabel/test.col
  • lines changed 4, context: html, text, full: html, text
    9186636eb6806a49e2e2cc5fd6b11d690ab729c1 Mon Dec 28 18:36:02 2020 -0800
    A little utility for changing labels in first row and or column of a tsv table.
• src/utils/matrixRelabel/test.in
  • lines changed 4, context: html, text, full: html, text
    9186636eb6806a49e2e2cc5fd6b11d690ab729c1 Mon Dec 28 18:36:02 2020 -0800
    A little utility for changing labels in first row and or column of a tsv table.
• src/utils/matrixRelabel/test.row
  • lines changed 3, context: html, text, full: html, text
    9186636eb6806a49e2e2cc5fd6b11d690ab729c1 Mon Dec 28 18:36:02 2020 -0800
    A little utility for changing labels in first row and or column of a tsv table.
• src/utils/matrixScale/makefile
  • lines changed 3, context: html, text, full: html, text
    26bdb2dad348ff9eae2a6846b4af6458a8893328 Sat Jan 2 21:16:12 2021 -0800
    Another little matrix utility.
• src/utils/matrixScale/matrixScale.c
  • lines changed 76, context: html, text, full: html, text
    26bdb2dad348ff9eae2a6846b4af6458a8893328 Sat Jan 2 21:16:12 2021 -0800
    Another little matrix utility.
• src/utils/matrixToBarChartBed/makefile
  • lines changed 3, context: html, text, full: html, text
    76bba8a5c8a2b584ac5cd9d0610395c0617cf7e6 Sun Jan 3 14:04:57 2021 -0800
    Program for attaching a barchart track to a matrix with option to make a trackDb stanza.
• src/utils/matrixToBarChartBed/matrixClusterStats.as
  • lines changed 7, context: html, text, full: html, text
    76bba8a5c8a2b584ac5cd9d0610395c0617cf7e6 Sun Jan 3 14:04:57 2021 -0800
    Program for attaching a barchart track to a matrix with option to make a trackDb stanza.
• src/utils/matrixToBarChartBed/matrixToBarChartBed.c
  • lines changed 262, context: html, text, full: html, text
    76bba8a5c8a2b584ac5cd9d0610395c0617cf7e6 Sun Jan 3 14:04:57 2021 -0800
    Program for attaching a barchart track to a matrix with option to make a trackDb stanza.
• src/utils/matrixTrim/makefile
  • lines changed 3, context: html, text, full: html, text
    f31aa864d2c8a8bedadffa47cf184f85724ee0d9 Wed Dec 30 15:20:00 2020 -0800
    A little matrix manipulation utility, not very general purpose yet.
• src/utils/matrixTrim/matrixTrim.c
  • lines changed 123, context: html, text, full: html, text
    f31aa864d2c8a8bedadffa47cf184f85724ee0d9 Wed Dec 30 15:20:00 2020 -0800
    A little matrix manipulation utility, not very general purpose yet.
• src/utils/matrixTrim/test.in
  • lines changed 6, context: html, text, full: html, text
    f31aa864d2c8a8bedadffa47cf184f85724ee0d9 Wed Dec 30 15:20:00 2020 -0800
    A little matrix manipulation utility, not very general purpose yet.
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    f673475f54b9ac05139b41a477048d7ca5f38599 Mon Jan 4 10:01:25 2021 -0800
    v409 preview1
• src/utils/subColumn/subColumn.c
  • lines changed 21, context: html, text, full: html, text
    2aa6eaa0d58ff2019e8719decafe720209d421cc Mon Nov 23 11:30:08 2020 -0800
    Making substitution file be tab separated as usage statement says.
• src/utils/wordLine/wordLine.c
  • lines changed 10, context: html, text, full: html, text
    901666d674b8e7147670eb2fd3f9e80f0c1d2fbd Thu Dec 31 14:59:45 2020 -0800
    Removed dependency on having less than 16k words/line.

• lines changed: 17534
• files changed: 422