All File Changes
v294_preview2 to v294_base (2014-01-06 to 2014-01-13) v294
- src/hg/encode/getTrackReferences/getTrackReferences
- lines changed 13, context: html, text, full: html, text
Fix for sometimes reporting no original paper link when really NCBI's page didn't serve up properly
- src/hg/encode3/encodeDataWarehouse/edwWebXSendFile/edwWebXSendFile.c
- lines changed 28, context: html, text, full: html, text
Changes made per Jim's feedback inhttp://redmine.soe.ucsc.edu/issues/12422#note-2
- src/hg/encode3/encodeDataWarehouse/makefile
- lines changed 7, context: html, text, full: html, text
Taking edwFinishAnalysis out of UTIL_DIRS if we're on a Mac because XCode doesn't come with -luuid;it has to be obtained separately by using homebrew or macports etc. Also, Jim confirms that Mac
users are extremely unlikely to need encodeDataWarehouse programs.
- src/hg/hgTracks/gencodeTracks.c
- src/hg/htdocs/FAQ/FAQformat.html
- lines changed 1, context: html, text, full: html, text
code review corrections, refs #12418
- src/hg/htdocs/goldenPath/help/blatSpec.html
- lines changed 4, context: html, text, full: html, text
Trying to fix disappearing menubar. Works on dev but not beta. RM #12382.
- src/hg/htdocs/goldenPath/help/hgRegMotifHelp.html
- lines changed 1, context: html, text, full: html, text
Removing a confusing text line, code review refs #12429
- src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
- lines changed 7, context: html, text, full: html, text
Fixed up format of Raney et al., per Matt code review.
- src/hg/htdocs/goldenPath/help/hgTracksHelp.html
- lines changed 5, context: html, text, full: html, text
code review corrections, refs #12418
- src/hg/htdocs/goldenPath/help/trackDb/README.txt
- lines changed 3, context: html, text, full: html, text
adding trackDb documentation for the iframeUrl and iframeOptions trackDbstatements. Also adding an HTML helper page that is required for dynamic
resizing of iframed pages. Sample HTML code is in the iframeOptions
doc. (The dynamic resizing option is probably overkill, I guess very few
users will need it. I got carried away and Mark asked for it a few
months ago). Also adding a tiny README file for trackDbDoc editing,
as I keep forgetting how the doc files are structured.
- src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html
- lines changed 6, context: html, text, full: html, text
adding trackDb documentation for the iframeUrl and iframeOptions trackDbstatements. Also adding an HTML helper page that is required for dynamic
resizing of iframed pages. Sample HTML code is in the iframeOptions
doc. (The dynamic resizing option is probably overkill, I guess very few
users will need it. I got carried away and Mark asked for it a few
months ago). Also adding a tiny README file for trackDbDoc editing,
as I keep forgetting how the doc files are structured.
- src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.html
- lines changed 6, context: html, text, full: html, text
adding trackDb documentation for the iframeUrl and iframeOptions trackDbstatements. Also adding an HTML helper page that is required for dynamic
resizing of iframed pages. Sample HTML code is in the iframeOptions
doc. (The dynamic resizing option is probably overkill, I guess very few
users will need it. I got carried away and Mark asked for it a few
months ago). Also adding a tiny README file for trackDbDoc editing,
as I keep forgetting how the doc files are structured.
- src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
- lines changed 66, context: html, text, full: html, text
adding trackDb documentation for the iframeUrl and iframeOptions trackDbstatements. Also adding an HTML helper page that is required for dynamic
resizing of iframed pages. Sample HTML code is in the iframeOptions
doc. (The dynamic resizing option is probably overkill, I guess very few
users will need it. I got carried away and Mark asked for it a few
months ago). Also adding a tiny README file for trackDbDoc editing,
as I keep forgetting how the doc files are structured.
- lines changed 1, context: html, text, full: html, text
little clarification of the parent setting in trackDbDoc
- src/hg/htdocs/goldenPath/pubs.html
- lines changed 14, context: html, text, full: html, text
Added Braney pub on elephant shark, added PMID to 2013 Brennan citation.
- src/hg/htdocs/inc/iframeHelper.html
- lines changed 31, context: html, text, full: html, text
adding trackDb documentation for the iframeUrl and iframeOptions trackDbstatements. Also adding an HTML helper page that is required for dynamic
resizing of iframed pages. Sample HTML code is in the iframeOptions
doc. (The dynamic resizing option is probably overkill, I guess very few
users will need it. I got carried away and Mark asked for it a few
months ago). Also adding a tiny README file for trackDbDoc editing,
as I keep forgetting how the doc files are structured.
- src/hg/inc/versionInfo.h
- src/hg/js/hgTracks.js
- lines changed 1, context: html, text, full: html, text
Fixed hgTracks image track sorting bug reported in redmine #12455
- src/hg/js/utils.js
- lines changed 1, context: html, text, full: html, text
Fixed hgTracks image track sorting bug reported in redmine #12455
- src/hg/lib/bed.c
- lines changed 2, context: html, text, full: html, text
removed condition that always evaulates to false and generates warnings with LLVM cc
- src/hg/lib/pubsBingArticle.sql
- lines changed 19, context: html, text, full: html, text
adding field descriptions, rm #12212
- src/hg/lib/pubsBingBlat.sql
- lines changed 21, context: html, text, full: html, text
adding field descriptions, rm #12212
- src/hg/lib/pubsBingBlatPsl.sql
- lines changed 28, context: html, text, full: html, text
adding field descriptions, rm #12212
- src/hg/lib/pubsBingSequenceAnnot.sql
- lines changed 15, context: html, text, full: html, text
adding field descriptions, rm #12212
- src/hg/lib/tableList.sql
- lines changed 5, context: html, text, full: html, text
modifying table field names to kent style as suggested by angie, code review rm #12431
- lines changed 1, context: html, text, full: html, text
fixing one field name from a previous commit
- src/hg/makeDb/doc/bosTau7.txt
- lines changed 12, context: html, text, full: html, text
Starting loading of QTL tracks for 3 farm animals refs #10954
- lines changed 6, context: html, text, full: html, text
Adding entries for animal QTL tracks. refs #10954
- src/hg/makeDb/doc/galGal4.txt
- lines changed 11, context: html, text, full: html, text
Starting loading of QTL tracks for 3 farm animals refs #10954
- lines changed 2, context: html, text, full: html, text
Adding entry to make QTL track appear on chicken refs #10954
- lines changed 6, context: html, text, full: html, text
animalQtl reloading refs #10954
- lines changed 5, context: html, text, full: html, text
Adding entries for animal QTL tracks. refs #10954
- src/hg/makeDb/doc/hg19.txt
- lines changed 26, context: html, text, full: html, text
liftOver to hg38 done refs #11681
- src/hg/makeDb/doc/hg38.txt
- lines changed 688, context: html, text, full: html, text
up to date repeat masker procedures, trf simple repeats and genscan refs #11681
- lines changed 9, context: html, text, full: html, text
Adding entry for liftover of temporary cytoband data from hg19.
- lines changed 83, context: html, text, full: html, text
rerunning repeat masking refs #11682
- lines changed 59, context: html, text, full: html, text
adding par and centromere tracks refs #11681
- lines changed 159, context: html, text, full: html, text
the alternate/haplotype sequence lastz chain net psl track refs #11681
- lines changed 90, context: html, text, full: html, text
done with rmskHmmer and added hg38.contigs.2bit build refs #11681
- lines changed 56, context: html, text, full: html, text
add repeat masker analysis refs #11681
- lines changed 98, context: html, text, full: html, text
fixup gc5BaseBw bbi directory path, and running cpgIslands on contig sequence refs #11681
- src/hg/makeDb/doc/susScr3.txt
- lines changed 11, context: html, text, full: html, text
Starting loading of QTL tracks for 3 farm animals refs #10954
- lines changed 5, context: html, text, full: html, text
Adding entries for animal QTL tracks. refs #10954
- src/hg/makeDb/genbank/etc/genbank.conf
- lines changed 25, context: html, text, full: html, text
preparing for GRCh38/hg38 genbank run refs #11681
- lines changed 1, context: html, text, full: html, text
comment out ccds build for hg38
- src/hg/makeDb/genbank/src/ccds/createKeys.sql
- src/hg/makeDb/genbank/src/ccds/createTables.sql
- src/hg/makeDb/genbank/src/ccds/ncbiSql/createKeys.sql
- src/hg/makeDb/genbank/src/ccds/ncbiSql/createTables.sql
- src/hg/makeDb/hgLoadOut/hgLoadOut.c
- lines changed 7, context: html, text, full: html, text
ignore the noSplit arguments to make it become the default refs #11681
- src/hg/makeDb/schema/all.joiner
- src/hg/makeDb/trackDb/animalQtl.html
- lines changed 80, context: html, text, full: html, text
Adding description page for QTL tracks. refs#10954
- src/hg/makeDb/trackDb/chicken/galGal4/trackDb.ra
- lines changed 4, context: html, text, full: html, text
Adding entries for animal QTL tracks. refs #10954
- src/hg/makeDb/trackDb/cow/bosTau7/trackDb.ra
- lines changed 4, context: html, text, full: html, text
Adding entries for animal QTL tracks. refs #10954
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra
- lines changed 14, context: html, text, full: html, text
Moved 5 repeats tracks to new repeats group. refs #12284
- lines changed 4, context: html, text, full: html, text
Resetting priorities to move pubs to top and impose alpha order for rest of tracks. refs #12362
- lines changed 5, context: html, text, full: html, text
Putting settings for new combined phen+lit group down at assembly level - see note 11 refs #12362
- lines changed 3, context: html, text, full: html, text
Removing unneccesary lines. refs #12425
- src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeSuper.html
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV18.ra
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV19.html
- lines changed 1, context: html, text, full: html, text
Changing PI foreign character name to fix display in GENCODE V19 html refs #12452
- src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV19.ra
- src/hg/makeDb/trackDb/human/hg38/altSequences.ra
- lines changed 91, context: html, text, full: html, text
adding alternate haplotype sequences chain net psl locations track refs #11681
- src/hg/makeDb/trackDb/human/hg38/centromeres.html
- lines changed 6, context: html, text, full: html, text
documentation for the centromere track refs #11681
- src/hg/makeDb/trackDb/human/hg38/rmskBlastn.html
- lines changed 26, context: html, text, full: html, text
update the featureBits and add the class summary refs #11681
- src/hg/makeDb/trackDb/human/hg38/rmskCM.html
- lines changed 105, context: html, text, full: html, text
adding RepeatMasker cross-match documentation refs #11681
- lines changed 25, context: html, text, full: html, text
add the class summary refs #11681
- lines changed 0, context: html, text, full: html, text
adding HMMER rmsk documentation refs #11681
- src/hg/makeDb/trackDb/human/hg38/rmskGenbank.html
- lines changed 25, context: html, text, full: html, text
add the class summary refs #11681
- src/hg/makeDb/trackDb/human/hg38/rmskHmmer.html
- lines changed 127, context: html, text, full: html, text
adding HMMER rmsk documentation refs #11681
- src/hg/makeDb/trackDb/human/hg38/trackDb.ra
- lines changed 6, context: html, text, full: html, text
move the rmsk experments to experimental track group refs #11681
- lines changed 20, context: html, text, full: html, text
adding alternate haplotype sequences chain net psl locations track refs #11681
- src/hg/makeDb/trackDb/human/trackDb.ra
- lines changed 14, context: html, text, full: html, text
Resetting priorities to move pubs to top and impose alpha order for rest of tracks. refs #12362
- src/hg/makeDb/trackDb/pig/susScr3/trackDb.ra
- lines changed 5, context: html, text, full: html, text
Adding entries for animal QTL tracks. refs #10954
- src/hg/makeDb/trackDb/pubsBingBlat.html
- lines changed 1, context: html, text, full: html, text
Removing odd line break in the middle of the Display Convention and Configuration section
- src/hg/makeDb/trackDb/trackDb.ra
- lines changed 1, context: html, text, full: html, text
Folding pubs track into combined phen+lit group. refs #12362
- lines changed 1, context: html, text, full: html, text
Resetting priorities to move pubs to top and impose alpha order for rest of tracks. refs #12362
- lines changed 2, context: html, text, full: html, text
Putting settings for new combined phen+lit group down at assembly level - see note 11 refs #12362
- lines changed 10, context: html, text, full: html, text
Adding entry to make QTL track appear on chicken refs #10954
- lines changed 4, context: html, text, full: html, text
add url to animalQtl refs #10954
- lines changed 2, context: html, text, full: html, text
Adding entries for animal QTL tracks. refs #10954
- lines changed 3, context: html, text, full: html, text
Updating coloring for animal QTL tracks, removing lines moved to lower level. refs #10954
- lines changed 2, context: html, text, full: html, text
moved animalQtl track to expression and regulation group and expanded longLabel to spell out QTL. refs 10954
- lines changed 1, context: html, text, full: html, text
moved animalQtl back to map group. refs #10954
- src/hg/utils/automation/doRepeatMasker.pl
- lines changed 2, context: html, text, full: html, text
need to use 32Gb and 4 CPU limits on HMMER refs #11681
- src/hg/utils/automation/makeGenomeDb.pl
- lines changed 8, context: html, text, full: html, text
new convention for location of bbi files, in bbi/tableName/... refs #11681
- src/hg/utils/makeTableList/makeTableList.c
- lines changed 4, context: html, text, full: html, text
modifying table field names to kent style as suggested by angie, code review rm #12431
- lines changed 1, context: html, text, full: html, text
fixing one field name from a previous commit
- src/hg/utils/phyloTrees/dbCommonScientificCladeOrderkey.tab
- lines changed 14, context: html, text, full: html, text
adding other genomes found on the RR for completeness refs #10272
- src/lib/bamFile.c
- lines changed 1, context: html, text, full: html, text
Changing warn to errAbort as suggested by Jonathan (since that is more consistent with how bamFileAndIndexMustExist works).refs #12401
- src/lib/vcf.c
- lines changed 1, context: html, text, full: html, text
Tolerate missing '=' in metadata line for VCF3 because as Jonathan pointed out, the spec didn't demand key=val in 3.3.refs #12412
- lines changed 2, context: html, text, full: html, text
Oops, as Jonathan pointed out, VCF 4.0 can still have meta-information lineswithout '='. fixes #12417
- src/parasol/parasol/parasol.c
- lines changed 1, context: html, text, full: html, text
oops, Jim accidentally removed the -dir option.
- src/product/scripts/kentSrcUpdate.sh
- lines changed 15, context: html, text, full: html, text
add directory safety checks as it starts refs #9104
- src/utils/bigWigCat/bigWigCat.c
- lines changed 3, context: html, text, full: html, text
Fixing usage message. Daniel was supposed to have already fixed this. Originally the utility was called mergeBigWig instead of bigWigCat. Also fixed capitalization problem for one function name that neede to start with lower-case letter.
- lines changed 2, context: html, text, full: html, text
bigWigCat - adding helpful information to the usage statement about creating the right input files.
- src/utils/qa/weeklybld/buildEnv.csh
- lines changed 3, context: html, text, full: html, text
v294 final build refs #12191
- lines changed: 3161
- files changed: 101