All File Changes
v255_preview to v255_preview2 (2011-07-26 to 2011-08-02) v255
- src/blat/version.doc
- src/hg/dbTrash/cleanLostTables.sh
- lines changed 44, context: html, text, full: html, text
controlling cron job script for lostTables.pl with logging information
- src/hg/dbTrash/lostTables.pl
- lines changed 193, context: html, text, full: html, text
initial source from running cron job on hgcustom
- src/hg/encode/antibodyWikiParser.py
- lines changed 1, context: html, text, full: html, text
Changed the include structure to be consistent with Morgan's new library structure
- lines changed 295, context: html, text, full: html, text
moved cellTypeParser and antibodyWikiParser into separate subdirs, with makefiles that copy them into the bin directory. For both files, added a -noDownload option
- src/hg/encode/antibodyWikiParser/antibodyWikiParser.py
- lines changed 306, context: html, text, full: html, text
moved cellTypeParser and antibodyWikiParser into separate subdirs, with makefiles that copy them into the bin directory. For both files, added a -noDownload option
- src/hg/encode/antibodyWikiParser/makefile
- lines changed 18, context: html, text, full: html, text
moved cellTypeParser and antibodyWikiParser into separate subdirs, with makefiles that copy them into the bin directory. For both files, added a -noDownload option
- src/hg/encode/cellTypeParser.py
- lines changed 196, context: html, text, full: html, text
moved cellTypeParser and antibodyWikiParser into separate subdirs, with makefiles that copy them into the bin directory. For both files, added a -noDownload option
- src/hg/encode/cellTypeParser/cellTypeParser.py
- lines changed 201, context: html, text, full: html, text
moved cellTypeParser and antibodyWikiParser into separate subdirs, with makefiles that copy them into the bin directory. For both files, added a -noDownload option
- src/hg/encode/cellTypeParser/makefile
- lines changed 18, context: html, text, full: html, text
moved cellTypeParser and antibodyWikiParser into separate subdirs, with makefiles that copy them into the bin directory. For both files, added a -noDownload option
- src/hg/encode/encodeDownloadReadme/downloadsReadmeTemplate.txt
- lines changed 45, context: html, text, full: html, text
made a script to push README file to the download directories
- src/hg/encode/encodeDownloadReadme/encodeDownloadReadme.pl
- lines changed 160, context: html, text, full: html, text
made a script to push README file to the download directories
- src/hg/encode/encodeDownloadReadme/makefile
- lines changed 47, context: html, text, full: html, text
made a script to push README file to the download directories
- src/hg/encode/encodeDownloadsPage/encodeDownloadsPage.pl
- lines changed 3, context: html, text, full: html, text
removed the double slashes that broke things in ie
- src/hg/encode/encodeMkChangeNotes/encodeMkChangeNotes
- lines changed 1, context: html, text, full: html, text
added pdf.gz support to mkchangenotes
- lines changed 1, context: html, text, full: html, text
added in matrix to files only list
- src/hg/encode/encodeValidate/config/downloadsReadmeTemplate.txt
- lines changed 45, context: html, text, full: html, text
Adding the downloads README.txt template into the config directory.
- src/hg/encode/encodeValidate/doEncodeValidate.pl
- lines changed 18, context: html, text, full: html, text
removed any readme references from doEncodeValidate.pl
- src/hg/hgGateway/hgGateway.c
- lines changed 1, context: html, text, full: html, text
change "import tracks" button to "track hubs" button. Make disconnects in hgHubConnect return to myHubs tab
- src/hg/hgHubConnect/hgHubConnect.c
- lines changed 11, context: html, text, full: html, text
disconnects from myHub just delete the cart variable, not the line in the hubStaus table
- lines changed 6, context: html, text, full: html, text
change "import tracks" button to "track hubs" button. Make disconnects in hgHubConnect return to myHubs tab
- lines changed 3, context: html, text, full: html, text
Added a much more visible link to hub documentation.
- src/hg/hgTables/mainPage.c
- lines changed 1, context: html, text, full: html, text
change "import tracks" button to "track hubs" button. Make disconnects in hgHubConnect return to myHubs tab
- src/hg/hgTrackUi/hgTrackUi.c
- lines changed 4, context: html, text, full: html, text
Feature #3710 (vcfTabix UI options): Added controls for selection of centervariant for haplotype clustering/sorting. Also, some hgc improvements:
made the Genotype Details table into a collapsible section; better display
of QUAL and FILTER column values, which also involved improving the
representation of those columns in src/inc/vcf.h.
- src/hg/hgTracks/bamTrack.c
- lines changed 2, context: html, text, full: html, text
MLQ #4765: User translated BED6 to BAM, with '*' (placeholder) for the querysequence and quality scores, and our BAM display code didn't anticipate
missing seq & base quals. Handle that case since it is legal BAM, albeit an
unusual use of BAM. :)
- src/hg/hgTracks/hgTracks.c
- lines changed 1, context: html, text, full: html, text
change "import tracks" button to "track hubs" button. Make disconnects in hgHubConnect return to myHubs tab
- lines changed 7, context: html, text, full: html, text
possible fix for default visibility of tdb->parent
- lines changed 7, context: html, text, full: html, text
Revert "possible fix for default visibility of tdb->parent"
This reverts commit 11f921f0e73765335b4d9f4b95dcf9045e2972b5.
- lines changed 4, context: html, text, full: html, text
fixing detecting visibility of remote bigDataUrl tracks and subtracks for parallel-loading
- lines changed 21, context: html, text, full: html, text
switch to using in-memory json; refactor trackDbJson so it is part of hgTracks global in the client (redmine #4550)
- lines changed 10, context: html, text, full: html, text
suppress printing of css and js includes when trackImgOnly is true
- lines changed 1, context: html, text, full: html, text
add and use hgTracks.cgiVersion
- src/hg/hgTracks/hgTracks.h
- lines changed 1, context: html, text, full: html, text
switch to using in-memory json; refactor trackDbJson so it is part of hgTracks global in the client (redmine #4550)
- src/hg/hgTracks/imageV2.c
- lines changed 46, context: html, text, full: html, text
switch to using in-memory json; refactor trackDbJson so it is part of hgTracks global in the client (redmine #4550)
- lines changed 13, context: html, text, full: html, text
Integrate my dragScroll with Larry's new json hash code.
- src/hg/hgTracks/imageV2.h
- lines changed 3, context: html, text, full: html, text
change jsonTdbSettings declarations
- lines changed 25, context: html, text, full: html, text
Integrate my dragScroll with Larry's new json hash code.
- src/hg/hgTracks/searchTracks.c
- lines changed 3, context: html, text, full: html, text
switch to using in-memory json; refactor trackDbJson so it is part of hgTracks global in the client (redmine #4550)
- src/hg/hgTracks/simpleTracks.c
- lines changed 4, context: html, text, full: html, text
Consolidated OMIM related declarations.
- src/hg/hgTracks/vcfTrack.c
- lines changed 29, context: html, text, full: html, text
Feature #3710 (vcfTabix UI options): Added controls for selection of centervariant for haplotype clustering/sorting. Also, some hgc improvements:
made the Genotype Details table into a collapsible section; better display
of QUAL and FILTER column values, which also involved improving the
representation of those columns in src/inc/vcf.h.
- lines changed 9, context: html, text, full: html, text
Feature #3711 (VCF haplotype sorting display): fixed goof in genotype summary mouseover text;corrected off-by-1 pixel outline that affected < base-level display.
- src/hg/hgc/bamClick.c
- lines changed 5, context: html, text, full: html, text
MLQ #4765: User translated BED6 to BAM, with '*' (placeholder) for the querysequence and quality scores, and our BAM display code didn't anticipate
missing seq & base quals. Handle that case since it is legal BAM, albeit an
unusual use of BAM. :)
- src/hg/hgc/hgc.c
- lines changed 5, context: html, text, full: html, text
Consolidated OMIM related declarations.
- src/hg/hgc/rnaFoldClick.c
- lines changed 41, context: html, text, full: html, text
Renamed htmlPrintSecStrDrawing to htmlPrintSecStrEvofoldDrawing for clarity. And added function for evofoldV2.
- src/hg/hgc/vcfClick.c
- lines changed 52, context: html, text, full: html, text
Feature #3710 (vcfTabix UI options): Added controls for selection of centervariant for haplotype clustering/sorting. Also, some hgc improvements:
made the Genotype Details table into a collapsible section; better display
of QUAL and FILTER column values, which also involved improving the
representation of those columns in src/inc/vcf.h.
- lines changed 3, context: html, text, full: html, text
Feature #2823 (VCF track handler): in hgc, let the user know when wecan't access the file (instead of just displaying nothing) and include
custom url.
- src/hg/htdocs/ENCODE/downloads.html
- lines changed 5, context: html, text, full: html, text
adding Stanf Nucleosome to downloads page
- src/hg/htdocs/FAQ/FAQformat.html
- lines changed 5, context: html, text, full: html, text
Updated ENCODE format titles
- src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
- lines changed 657, context: html, text, full: html, text
First draft of help documentation for the track hub utility. Ideally we will link to this from the Help button on the hgHubConnect page.
- lines changed 2, context: html, text, full: html, text
Fixed a few typos found via spellcheck.
- lines changed 2, context: html, text, full: html, text
Fixed section header for viewing track hubs
- lines changed 12, context: html, text, full: html, text
changed 'private' to 'unlisted'; added suggested max lengths for labels
- lines changed 3, context: html, text, full: html, text
Added suggested max lengths to step 7
- src/hg/inc/cv.h
- lines changed 19, context: html, text, full: html, text
Fixed some hash sizes, moved some validation code from mdb.c to cv.c, added numeric sort of hgFileUi filerBy and track/file search of terms defined in cv validation as integer.
- src/hg/inc/hui.h
- lines changed 6, context: html, text, full: html, text
Feature #3710 (vcfTabix UI options): Added controls for selection of centervariant for haplotype clustering/sorting. Also, some hgc improvements:
made the Genotype Details table into a collapsible section; better display
of QUAL and FILTER column values, which also involved improving the
representation of those columns in src/inc/vcf.h.
- src/hg/inc/jsHelper.h
- lines changed 59, context: html, text, full: html, text
add JSON Element code to represent JSON in memory and print out to html (redmine #4550)
- src/hg/inc/omim.h
- lines changed 7, context: html, text, full: html, text
Added omim.h for OMIM related declations.
- src/hg/inc/trackDb.h
- lines changed 1, context: html, text, full: html, text
Feature #3710 (vcfTabix UI options): Added controls for selection of centervariant for haplotype clustering/sorting. Also, some hgc improvements:
made the Genotype Details table into a collapsible section; better display
of QUAL and FILTER column values, which also involved improving the
representation of those columns in src/inc/vcf.h.
- lines changed 13, context: html, text, full: html, text
Cleaned up the tdbExtras a little. Jim recommended always allocating. Currently leaving in an assert, but will remove it on next check-in
- lines changed 3, context: html, text, full: html, text
Temporarily reverting a change because Angie sees the assert popping. Will fix this Monday.
- lines changed 54, context: html, text, full: html, text
Backtracking on tdbExtras. I don't think it should be defined for every tdb, but only defined when needed. I do think there should be getters and setters, because of create on use and because encapsulating object knowledge/assumptions makes sense long term.
- src/hg/inc/vcfUi.h
- lines changed 18, context: html, text, full: html, text
Feature #3710 (vcfTabix UI options): Added controls for selection of centervariant for haplotype clustering/sorting. Also, some hgc improvements:
made the Genotype Details table into a collapsible section; better display
of QUAL and FILTER column values, which also involved improving the
representation of those columns in src/inc/vcf.h.
- src/hg/js/hgTracks.js
- lines changed 38, context: html, text, full: html, text
switch to using in-memory json; refactor trackDbJson so it is part of hgTracks global in the client (redmine #4550)
- lines changed 42, context: html, text, full: html, text
Integrate my dragScroll with Larry's new json hash code.
- lines changed 1, context: html, text, full: html, text
Oops. Left a 'curly' bracket. Is no 'mo'. Sorry 'Larry'.
- lines changed 17, context: html, text, full: html, text
add and use hgTracks.cgiVersion
- src/hg/js/utils.js
- lines changed 1, context: html, text, full: html, text
switch to using in-memory json; refactor trackDbJson so it is part of hgTracks global in the client (redmine #4550)
- src/hg/lib/customFactory.c
- lines changed 1, context: html, text, full: html, text
Cleaned up the tdbExtras a little. Jim recommended always allocating. Currently leaving in an assert, but will remove it on next check-in
- src/hg/lib/cv.c
- lines changed 214, context: html, text, full: html, text
Fixed some hash sizes, moved some validation code from mdb.c to cv.c, added numeric sort of hgFileUi filerBy and track/file search of terms defined in cv validation as integer.
- src/hg/lib/fileUi.c
- lines changed 6, context: html, text, full: html, text
Fixed some hash sizes, moved some validation code from mdb.c to cv.c, added numeric sort of hgFileUi filerBy and track/file search of terms defined in cv validation as integer.
- src/hg/lib/hdb.c
- lines changed 2, context: html, text, full: html, text
Cleaned up the tdbExtras a little. Jim recommended always allocating. Currently leaving in an assert, but will remove it on next check-in
- lines changed 13, context: html, text, full: html, text
Checking in a solution to hgApi/ajax call to get hub track metadata (redmine 3280). The fix is ifdef'd out until we are clear what we want.
- lines changed 3, context: html, text, full: html, text
Backtracking on tdbExtras. I don't think it should be defined for every tdb, but only defined when needed. I do think there should be getters and setters, because of create on use and because encapsulating object knowledge/assumptions makes sense long term.
- src/hg/lib/hui.c
- lines changed 5, context: html, text, full: html, text
Feature #3710 (vcfTabix UI options): Added controls for selection of centervariant for haplotype clustering/sorting. Also, some hgc improvements:
made the Genotype Details table into a collapsible section; better display
of QUAL and FILTER column values, which also involved improving the
representation of those columns in src/inc/vcf.h.
- lines changed 4, context: html, text, full: html, text
Rearranged order of encode peak filters in hgTrackUi as per Katrina and redmine 4720.
- src/hg/lib/jsHelper.c
- lines changed 152, context: html, text, full: html, text
add JSON Element code to represent JSON in memory and print out to html (redmine #4550)
- src/hg/lib/makefile
- lines changed 1, context: html, text, full: html, text
Feature #3710 (vcfTabix UI options): Added controls for selection of centervariant for haplotype clustering/sorting. Also, some hgc improvements:
made the Genotype Details table into a collapsible section; better display
of QUAL and FILTER column values, which also involved improving the
representation of those columns in src/inc/vcf.h.
- src/hg/lib/mdb.c
- lines changed 167, context: html, text, full: html, text
Fixed some hash sizes, moved some validation code from mdb.c to cv.c, added numeric sort of hgFileUi filerBy and track/file search of terms defined in cv validation as integer.
- src/hg/lib/trackDb.c
- lines changed 1, context: html, text, full: html, text
Cleaned up the tdbExtras a little. Jim recommended always allocating. Currently leaving in an assert, but will remove it on next check-in
- src/hg/lib/trackDbCustom.c
- lines changed 19, context: html, text, full: html, text
Cleaned up the tdbExtras a little. Jim recommended always allocating. Currently leaving in an assert, but will remove it on next check-in
- lines changed 2, context: html, text, full: html, text
I need to init tdbExtras in hgTrackDb too.
- lines changed 86, context: html, text, full: html, text
Backtracking on tdbExtras. I don't think it should be defined for every tdb, but only defined when needed. I do think there should be getters and setters, because of create on use and because encapsulating object knowledge/assumptions makes sense long term.
- src/hg/lib/vcfUi.c
- lines changed 182, context: html, text, full: html, text
Feature #3710 (vcfTabix UI options): Added controls for selection of centervariant for haplotype clustering/sorting. Also, some hgc improvements:
made the Genotype Details table into a collapsible section; better display
of QUAL and FILTER column values, which also involved improving the
representation of those columns in src/inc/vcf.h.
- src/hg/lib/web.c
- lines changed 2, context: html, text, full: html, text
make help in blue bar go to track hub help when in hgHubConnect
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeCaltechRnaSeq.release2.notes
- lines changed 281, context: html, text, full: html, text
updated notes file after loading submission
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeCshlLongRnaSeq.release1.notes
- lines changed 865, context: html, text, full: html, text
release 1 notes for cshl long
- lines changed 658, context: html, text, full: html, text
errors in notes file, duplicates, and some extra files
- lines changed 64, context: html, text, full: html, text
removed transcriptgencv7 and corrected amount of new tables
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeSydhNsome.release1.notes
- src/hg/makeDb/doc/hg18.txt
- lines changed 75, context: html, text, full: html, text
adding new decode recombination map data
- lines changed 15, context: html, text, full: html, text
tuning up the final set of tracks for decode data
- lines changed 74, context: html, text, full: html, text
Track #4533 (High Seq Depth): loaded files into hg18 & hg19;initial trackDb & track description in place.
- lines changed 4, context: html, text, full: html, text
Track #1656 (GWAS Catalog): bi-monthly update on hgwdev.
- src/hg/makeDb/doc/hg19.txt
- lines changed 68, context: html, text, full: html, text
Track #4533 (High Seq Depth): loaded files into hg18 & hg19;initial trackDb & track description in place.
- lines changed 3, context: html, text, full: html, text
Track #1656 (GWAS Catalog): bi-monthly update on hgwdev.
- src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh
- lines changed 12, context: html, text, full: html, text
Added a new switch to hgMapToGene to override any derived mapping with a known value, if that value is known in advance. Used that switch to make sure that the values in the knownToRefSeq table are consistent with the UCSC Genes - RefSeq assignments in the kgXref table. This means that if a UCSC Genes transcript is derived (in part) from a RefSeq transcript, that RefSeq transcript will be listed in the knownToRefSeq table. UCSC Genes transcripts that are NOT derived from RefSeq transcripts will have entries in the knownToRefSeq table that identify the most-overlapping RefSeq
- src/hg/makeDb/trackDb/README
- lines changed 6, context: html, text, full: html, text
subGroup is actually subGroups
- src/hg/makeDb/trackDb/cv/alpha/cv.ra
- lines changed 1, context: html, text, full: html, text
Added an order URL for the Wold lab for the C2C12 cell line
- lines changed 4, context: html, text, full: html, text
Changing descriptions for the views that affect CSHL and Caltech to apply to both
- src/hg/makeDb/trackDb/human/hg18/decode.rmap.ra
- lines changed 75, context: html, text, full: html, text
adding views and default visibilities
- lines changed 37, context: html, text, full: html, text
adjusting colors and adding two tracks for hot spots
- src/hg/makeDb/trackDb/human/hg18/decodeRmap.html
- src/hg/makeDb/trackDb/human/hg18/evofoldV2.html
- lines changed 112, context: html, text, full: html, text
Added human/hg18/evofoldV2.html.
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaMethylSeq.ra
- lines changed 57, context: html, text, full: html, text
removed parentTable to get methyl seq to comply with CV
- src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeUwDnaseSeq.ra
- lines changed 193, context: html, text, full: html, text
Added UW Validation data successfully as attic submission through beta pipeline.
- src/hg/makeDb/trackDb/human/hg18/trackDb.ra
- src/hg/makeDb/trackDb/human/hg18/wgEncodeSangerGencode.html
- lines changed 4, context: html, text, full: html, text
added a reference that was recently published
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra
- lines changed 480, context: html, text, full: html, text
updated rate unrestricted in boradhistone mdb beta and alpha
- lines changed 319, context: html, text, full: html, text
reremoved fileindex after syncing the metaDb for date unrestricted required a restore of an earlier version of histone
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
- lines changed 37, context: html, text, full: html, text
added replacement submissions
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
- lines changed 89, context: html, text, full: html, text
Removing a V2 file and changing TranscriptV7 to file not table
- lines changed 60, context: html, text, full: html, text
Removing a V2 file and changing TranscriptV7 to file not table
- lines changed 1, context: html, text, full: html, text
incorrect treatment value for SK-N-SH_RA
- lines changed 382, context: html, text, full: html, text
added geo accession #s for 20 more samples. CshlLong should be done for now
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
- lines changed 4, context: html, text, full: html, text
removed parentTable from affected tracks
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromFaire.ra
- lines changed 8, context: html, text, full: html, text
removed parentTable from affected tracks
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromSynth.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra
- lines changed 7, context: html, text, full: html, text
corrected dateReSubmitted to dateResubmitted
- lines changed 5, context: html, text, full: html, text
removed parentTable from affected tracks
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
- lines changed 158, context: html, text, full: html, text
renamed control for gm12878 + igg-rab to have treatment TNFa
- lines changed 75, context: html, text, full: html, text
added missing control to tfbs
- lines changed 17, context: html, text, full: html, text
fixed control metadata issues
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUmassDekker5C.ra
- lines changed 8, context: html, text, full: html, text
removed parentTable from affected tracks
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUw5C.ra
- lines changed 107, context: html, text, full: html, text
added stanzas for primer files
- lines changed 18, context: html, text, full: html, text
redid the compressed files for matrix gz > tgz
- lines changed 1, context: html, text, full: html, text
forgot to generate magic number
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
- lines changed 2, context: html, text, full: html, text
removed parentTable from affected tracks
- lines changed 1309, context: html, text, full: html, text
added new tracks for UWTFBS and Histone
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra
- lines changed 2362, context: html, text, full: html, text
added new tracks for UWTFBS and Histone
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/makefile
- lines changed 1, context: html, text, full: html, text
staging Stanf Nucleosome on beta, redmine #131
- lines changed 1, context: html, text, full: html, text
accidentally copied the wrong .ra file name when staging on beta, fixed, redmine #131
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeBroadHistone.ra
- lines changed 77, context: html, text, full: html, text
updated rate unrestricted in boradhistone mdb beta and alpha
- src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeSydhNsome.ra
- lines changed 1248, context: html, text, full: html, text
staging Stanf Nucleosome on beta, redmine #131
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/makefile
- lines changed 1, context: html, text, full: html, text
preparing metadata for release of Stanf Nucleosome, redmine # 131
- src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeSydhNsome.ra
- lines changed 1248, context: html, text, full: html, text
preparing metadata for release of Stanf Nucleosome, redmine # 131
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra
- lines changed 6, context: html, text, full: html, text
Track #1656 (GWAS Catalog): removing outdated release alpha,betaoverride for hg19.
- src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
- lines changed 1, context: html, text, full: html, text
staging Stanf Nucleosome on beta, redmine #131
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.ra
- lines changed 1, context: html, text, full: html, text
removed PAM from default checked
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.html
- lines changed 6, context: html, text, full: html, text
added miltuview instructions
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibShRnaSeq.html
- lines changed 14, context: html, text, full: html, text
Added general description header
- lines changed 57, context: html, text, full: html, text
Removing redundancies in description
- src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.ra
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhNsome.html
- lines changed 18, context: html, text, full: html, text
fixed stuff according to redmine #131(QA requests)
- lines changed 5, context: html, text, full: html, text
added periods to references
- lines changed 2, context: html, text, full: html, text
html cleanup and added line about pooled data
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhNsome.ra
- lines changed 2, context: html, text, full: html, text
changed cv line, and added tier 1 to cell lines
- lines changed 1, context: html, text, full: html, text
fixed stuff according to redmine #131(QA requests)
- lines changed 1, context: html, text, full: html, text
changed view limit to match new signal files
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra
- lines changed 2, context: html, text, full: html, text
renamed control for gm12878 + igg-rab to have treatment TNFa
- lines changed 11, context: html, text, full: html, text
added missing control to tfbs
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUw5C.html
- lines changed 3, context: html, text, full: html, text
put in a line about how primer data must be downloaded to make sense of the matrix
- lines changed 6, context: html, text, full: html, text
added release notes for 5c data
- lines changed 3, context: html, text, full: html, text
cleaned up filesortorder and correct some html mistakes
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUw5C.ra
- lines changed 1, context: html, text, full: html, text
added view to filesortorder
- lines changed 1, context: html, text, full: html, text
cleaned up filesortorder and correct some html mistakes
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.new.ra
- lines changed 7, context: html, text, full: html, text
changed wi-28 with ohtam treatment to have it's own tag
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.new.ra
- lines changed 18, context: html, text, full: html, text
filled in missing controls
- lines changed 424, context: html, text, full: html, text
added new tracks for UWTFBS and Histone
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.new.ra
- lines changed 9, context: html, text, full: html, text
filled in missing controls
- lines changed 536, context: html, text, full: html, text
added new tracks for UWTFBS and Histone
- src/hg/makeDb/trackDb/human/hiSeqDepth.html
- lines changed 39, context: html, text, full: html, text
Track #4533 (High Seq Depth): loaded files into hg18 & hg19;initial trackDb & track description in place.
- src/hg/makeDb/trackDb/human/mrna.html
- lines changed 92, context: html, text, full: html, text
removed html text about re-including the Invitrogen mRNAs
- src/hg/makeDb/trackDb/human/trackDb.ra
- lines changed 41, context: html, text, full: html, text
Track #4533 (High Seq Depth): loaded files into hg18 & hg19;initial trackDb & track description in place.
- src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra
- lines changed 172, context: html, text, full: html, text
added LicrHistone Geo Accession numbers. It is now fully submitted
- src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrRnaSeq.html
- lines changed 3, context: html, text, full: html, text
capitalized and added commas, redmine #3629
- src/hg/near/hgMapToGene/hgMapToGene.c
- lines changed 1, context: html, text, full: html, text
On closer examination, I see that this 'bug fix' that I made a while ago actually introduced a bug. Consequently, I'm un-fixing the 'fix'
- lines changed 30, context: html, text, full: html, text
Added a new switch to hgMapToGene to override any derived mapping with a known value, if that value is known in advance. Used that switch to make sure that the values in the knownToRefSeq table are consistent with the UCSC Genes - RefSeq assignments in the kgXref table. This means that if a UCSC Genes transcript is derived (in part) from a RefSeq transcript, that RefSeq transcript will be listed in the knownToRefSeq table. UCSC Genes transcripts that are NOT derived from RefSeq transcripts will have entries in the knownToRefSeq table that identify the most-overlapping RefSeq
- src/hg/oneShot/doEvoFoldV2/doEvoFoldV2.c
- src/hg/oneShot/doEvoFoldV2/makefile
- src/inc/common.h
- lines changed 6, context: html, text, full: html, text
Fixed some hash sizes, moved some validation code from mdb.c to cv.c, added numeric sort of hgFileUi filerBy and track/file search of terms defined in cv validation as integer.
- src/inc/vcf.h
- lines changed 3, context: html, text, full: html, text
Feature #3710 (vcfTabix UI options): Added controls for selection of centervariant for haplotype clustering/sorting. Also, some hgc improvements:
made the Genotype Details table into a collapsible section; better display
of QUAL and FILTER column values, which also involved improving the
representation of those columns in src/inc/vcf.h.
- src/lib/common.c
- lines changed 13, context: html, text, full: html, text
Fixed some hash sizes, moved some validation code from mdb.c to cv.c, added numeric sort of hgFileUi filerBy and track/file search of terms defined in cv validation as integer.
- src/lib/internet.c
- lines changed 18, context: html, text, full: html, text
use thread-safe getaddrinfo() instead of gethostbyname() which was getting the dns-looked-up remote host IP clobbered on hgw0
- src/lib/linefile.c
- lines changed 2, context: html, text, full: html, text
Feature #3710 (vcfTabix UI options): Added controls for selection of centervariant for haplotype clustering/sorting. Also, some hgc improvements:
made the Genotype Details table into a collapsible section; better display
of QUAL and FILTER column values, which also involved improving the
representation of those columns in src/inc/vcf.h.
- src/lib/ra.c
- lines changed 1, context: html, text, full: html, text
Fixed some hash sizes, moved some validation code from mdb.c to cv.c, added numeric sort of hgFileUi filerBy and track/file search of terms defined in cv validation as integer.
- src/lib/tests/expected/vcfParse1kGNoGenotypes.out
- lines changed 5, context: html, text, full: html, text
Feature #3710 (vcfTabix UI options): Added controls for selection of centervariant for haplotype clustering/sorting. Also, some hgc improvements:
made the Genotype Details table into a collapsible section; better display
of QUAL and FILTER column values, which also involved improving the
representation of those columns in src/inc/vcf.h.
- src/lib/tests/expected/vcfParse1kGWithGenotypes.out
- lines changed 6, context: html, text, full: html, text
Feature #3710 (vcfTabix UI options): Added controls for selection of centervariant for haplotype clustering/sorting. Also, some hgc improvements:
made the Genotype Details table into a collapsible section; better display
of QUAL and FILTER column values, which also involved improving the
representation of those columns in src/inc/vcf.h.
- src/lib/tests/expected/vcfParseOldV3.out
- lines changed 14, context: html, text, full: html, text
Feature #3710 (vcfTabix UI options): Added controls for selection of centervariant for haplotype clustering/sorting. Also, some hgc improvements:
made the Genotype Details table into a collapsible section; better display
of QUAL and FILTER column values, which also involved improving the
representation of those columns in src/inc/vcf.h.
- src/lib/tests/vcfParseTest.c
- lines changed 1, context: html, text, full: html, text
Feature #3710 (vcfTabix UI options): Added controls for selection of centervariant for haplotype clustering/sorting. Also, some hgc improvements:
made the Genotype Details table into a collapsible section; better display
of QUAL and FILTER column values, which also involved improving the
representation of those columns in src/inc/vcf.h.
- src/lib/vcf.c
- lines changed 21, context: html, text, full: html, text
Feature #3710 (vcfTabix UI options): Added controls for selection of centervariant for haplotype clustering/sorting. Also, some hgc improvements:
made the Genotype Details table into a collapsible section; better display
of QUAL and FILTER column values, which also involved improving the
representation of those columns in src/inc/vcf.h.
- lines changed 9, context: html, text, full: html, text
Feature #2821 (VCF parser): correctly handle an INFO column that is just a"." placeholder.
- src/utils/bedCollapse.pl
- lines changed 50, context: html, text, full: html, text
adding a bedCollapse.pl command to the scripts
- src/utils/git-reports/git-reports.c
- lines changed 7, context: html, text, full: html, text
putting period to separate filename from commit-hashID to avoid ambiguity
- src/utils/makefile
- lines changed 1, context: html, text, full: html, text
adding a bedCollapse.pl command to the scripts
- src/utils/qa/checkSync.csh
- lines changed 1, context: html, text, full: html, text
Made a grep check for a whole word match. The hg19Patch5 database was wreaking havoc when this was run on hg19.
- src/utils/qa/weeklybld/buildEnv.csh
- src/utils/qa/weeklybld/buildHgCentralSql.csh
- lines changed 2, context: html, text, full: html, text
adding hubPublic and hubStatus tables to hgcentral.sql
- lines changed: 16582
- files changed: 213