All File Changes

v248_base to v249_preview (2011-03-08 to 2011-03-15) v249

• src/hg/autoXml/makefile
  • lines changed 2, context: html, text, full: html, text
    eliminate use of HOME in MYLIBDIR
• src/hg/bedOverlap/makefile
  • lines changed 1, context: html, text, full: html, text
    eliminate use of HOME in MYLIBDIR
• src/hg/chimpStuff/chimpHiQualDiffs/makefile
  • lines changed 1, context: html, text, full: html, text
    eliminate use of HOME in MYLIBDIR
• src/hg/chimpStuff/chimpSuperQuals/makefile
  • lines changed 1, context: html, text, full: html, text
    eliminate use of HOME in MYLIBDIR
• src/hg/encode/DAFs/2.0/stanfordMm9Hist.daf
  • lines changed 2, context: html, text, full: html, text
    Added validation setting that verifies that at least 99.9% of the bams have at most 3 mismatches.
  • lines changed 1, context: html, text, full: html, text
    Added matchFirst and nmatch options that lab requested.
• src/hg/encode/DAFs/2.0/stanfordMm9Tfbs.daf
  • lines changed 2, context: html, text, full: html, text
    Added validation setting that verifies that at least 99.9% of the bams have at most 3 mismatches.
  • lines changed 1, context: html, text, full: html, text
    Added matchFirst and nmatch options that lab requested.
• src/hg/encode/DAFs/2.0/uMassDekker5c.daf
  • lines changed 23, context: html, text, full: html, text
    Wrangling UW 5C track
• src/hg/encode/DAFs/2.0/uw5c.daf
  • lines changed 28, context: html, text, full: html, text
    Wrangling UW 5C track
• src/hg/encode/autoSql/bedRrbs.as
  • lines changed 15, context: html, text, full: html, text
    Haib MethylRrbs data
  • lines changed 2, context: html, text, full: html, text
    oops... score field has to be named score
• src/hg/encode/autoSql/bedRrbs.sql
  • lines changed 23, context: html, text, full: html, text
    Haib MethylRrbs data
  • lines changed 1, context: html, text, full: html, text
    oops... score field has to be named score
• src/hg/encode/encodeMkChangeNotes/encodeMkChangeNotes
  • lines changed 1, context: html, text, full: html, text
    Added bedRrbs as a file type to handle
• src/hg/encode/encodeMkChangeNotes/makefile
  • lines changed 3, context: html, text, full: html, text
    install and alpha put it in /cluster/bin/scripts, otherwise $HOME/bin/scripts
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • lines changed 1, context: html, text, full: html, text
    Added fileType txt
• src/hg/encode/encodeValidate/makefile
  • lines changed 3, context: html, text, full: html, text
    copy the alpha cv.ra file into the downloads directory if we're doing a make install. This allows the labs to grab the same cv.ra we're using in the pipeline.
• src/hg/encode/metaCheck/README.txt
  • lines changed 26, context: html, text, full: html, text
    a little more detail about what metaCheck does
• src/hg/encode/metaCheck/metaCheck.c
  • lines changed 6, context: html, text, full: html, text
    a little more detail about what metaCheck does
• src/hg/geneBounds/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    eliminate use of HOME in MYLIBDIR
• src/hg/geneOverlap/makefile
  • lines changed 2, context: html, text, full: html, text
    eliminate use of HOME in MYLIBDIR
• src/hg/hgApi/hgApi.c
  • lines changed 24, context: html, text, full: html, text
    Moved a few functions common to track search and file search into library code. Redesigned a few things to standardize on slPair lists of vals and labels.
  • lines changed 6, context: html, text, full: html, text
    Changed mdb API required this change.
• src/hg/hgFileSearch/hgFileSearch.c
  • lines changed 310, context: html, text, full: html, text
    Moved a few functions common to track search and file search into library code. Redesigned a few things to standardize on slPair lists of vals and labels.
  • lines changed 1, context: html, text, full: html, text
    Fixing Ubuntu gcc warnings by using puts instead of printf-without-format.
• src/hg/hgFileUi/hgFileUi.c
  • lines changed 8, context: html, text, full: html, text
    Added NAFV link to track description at bottom of page.
• src/hg/hgGene/hgGene.c
  • lines changed 2, context: html, text, full: html, text
    Adding hgBotDelay call to hgGene to avoid bot damage like we got yesterday.
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 2, context: html, text, full: html, text
    SuperTracks offer links to hgFileUi CGI if the tdb says downloadsOnly
  • lines changed 10, context: html, text, full: html, text
    Added support for showing downloadsOnly tracks in hgTracks (but only if they are part of a superTrack with other visible tracks). Also standardized links for downloadsOnly tacks between hgTracks and hgTrackUi
  • lines changed 60, context: html, text, full: html, text
    Added filters for new OMIM tracks.
  • lines changed 6, context: html, text, full: html, text
    Feature/Bug #3148 (DGV description page refs): fixing bug found by b0b:the filter on PubMed references was set to "include" by default, but all checkboxes were empty by default. Fix: if the checkbox group variable is not defined in the cart, then set all checkboxes.
• src/hg/hgTracks/bamTrack.c
  • lines changed 36, context: html, text, full: html, text
    put out one mapBox per row if there are too many individual items #1279
• src/hg/hgTracks/bedTrack.c
  • lines changed 28, context: html, text, full: html, text
    Track #34 (dbVar for human): Hooked up next/prev exon methodfor simple bed tracks, which simply hops to right edge/left edge of items hanging off the end of the window.
• src/hg/hgTracks/config.c
  • lines changed 43, context: html, text, full: html, text
    Added support for showing downloadsOnly tracks in hgTracks (but only if they are part of a superTrack with other visible tracks). Also standardized links for downloadsOnly tacks between hgTracks and hgTrackUi
• src/hg/hgTracks/searchTracks.c
  • lines changed 353, context: html, text, full: html, text
    Moved a few functions common to track search and file search into library code. Redesigned a few things to standardize on slPair lists of vals and labels.
  • lines changed 1, context: html, text, full: html, text
    Fixing Ubuntu gcc warnings by using puts instead of printf-without-format.
• src/hg/hgTracks/simpleTracks.c
  • lines changed 264, context: html, text, full: html, text
    Updated functions for new OMIM tracks.
• src/hg/hgTracks/variation.c
  • lines changed 14, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): oops, overwriting snp125->name whenchimp allele is added (in dbb7cbfd) caused the name+allele string to be passed to hgc as the item name, which causes an errAbort because the item can't be found. So now we need a mapItemName that strips off the allele string if any is added.
• src/hg/hgc/bamClick.c
  • lines changed 3, context: html, text, full: html, text
    put out one mapBox per row if there are too many individual items #1279
• src/hg/hgc/hgc.c
  • lines changed 29, context: html, text, full: html, text
    Updated funtions for new OMIM tracks.
• src/hg/hgc/hgdpClick.c
  • lines changed 7, context: html, text, full: html, text
    Bug #3208 (hg19 HGDP Allele Freq hgc position links are broken):doh, using a *StaticLoad and then immediately doing a sqlFreeResult is a bad idea. No need to scrounge for memory w/StaticLoad in hgc.
• src/hg/hgcentralTidy/hgcentralTidy.c
  • lines changed 412, context: html, text, full: html, text
    adding new hgcentralTidy; apologies to code reviewers that there are still comments in the code. this has been a work in progress but has reached the point of being useful for production.
• src/hg/htdocs/goldenPath/help/hgWiggleTrackHelp.html
  • lines changed 3, context: html, text, full: html, text
    fixed misspelling
• src/hg/htdocs/images/Meleagris_gallopavo.jpg
  • lines changed 0, context: html, text, full: html, text
    Shrink Turkey jpg a bit
• src/hg/htdocs/makefile
  • lines changed 1, context: html, text, full: html, text
    don't update the styles with make beta in htdocs
• src/hg/htdocs/style/HGStyle.css
  • lines changed 2, context: html, text, full: html, text
    The filterBy multi-selects that use ui-dropdownchecklist.js must be initially hidden.
• src/hg/htdocs/style/cpAndLinkToResourceFiles.pl
  • lines changed 94, context: html, text, full: html, text
    coallesce cpAndLinkToResourceFiles.pl
• src/hg/htdocs/style/makefile
  • lines changed 1, context: html, text, full: html, text
    add jquery.ui.autocomplete.css
  • lines changed 1, context: html, text, full: html, text
    change path to cpAndLinkToResourceFiles (which has been moved)
• src/hg/inc/cart.h
  • lines changed 6, context: html, text, full: html, text
    While working on something else, I realized that when cartRemove iscalled on a list variable, it should remove the list's multShadow variable in addition to all values, because the list variable is no longer defined in the cart. If the multShadow is left around, it will look like the variable is in the cart, set to empty.
• src/hg/inc/hdb.h
  • lines changed 4, context: html, text, full: html, text
    For download file lookup, beta should look on hgdownloads-test but in beta/ subdirectory.
• src/hg/inc/mdb.h
  • lines changed 5, context: html, text, full: html, text
    Subtle change to the mdbValLabelSearch() API to put the required val in the pair->name and the optional label in the pair->val. This helps standardize other code that deals with val/label pairs, and enables using slPairFind().
  • lines changed 11, context: html, text, full: html, text
    Added const to a couple of APIs and changed some stuff to aid fleUi filterFiles functionality
• src/hg/inc/searchTracks.h
  • lines changed 27, context: html, text, full: html, text
    Moved a few functions common to track search and file search into library code. Redesigned a few things to standardize on slPair lists of vals and labels.
• src/hg/js/hgTracks.js
  • lines changed 1, context: html, text, full: html, text
    redmine 2916. IE is finiky about extra commas.
• src/hg/js/makefile
  • lines changed 5, context: html, text, full: html, text
    make the DOCUMENTROOT logic match that in kent/src/hg/htodcs/style/makefile to handle user-specific htdocs sandboxes
  • lines changed 1, context: html, text, full: html, text
    cpJsFiles => cpAndLinkToResourceFiles.pl
• src/hg/js/ui.dropdownchecklist.js
  • lines changed 5, context: html, text, full: html, text
    Added filterBy boxes to hgFileUi to allow slimiting the number of files seen on the page
• src/hg/js/utils.js
  • lines changed 169, context: html, text, full: html, text
    Added filterBy boxes to hgFileUi to allow slimiting the number of files seen on the page
  • lines changed 1, context: html, text, full: html, text
    Empty multi-select resulted in browser errors.
• src/hg/lib/cart.c
  • lines changed 49, context: html, text, full: html, text
    While working on something else, I realized that when cartRemove iscalled on a list variable, it should remove the list's multShadow variable in addition to all values, because the list variable is no longer defined in the cart. If the multShadow is left around, it will look like the variable is in the cart, set to empty.
• src/hg/lib/clusterInputTrackTable2.as
  • lines changed 8, context: html, text, full: html, text
    More work on new TFBS clustering stuff.
• src/hg/lib/clusterInputTrackTable2.sql
  • lines changed 17, context: html, text, full: html, text
    More work on new TFBS clustering stuff.
• src/hg/lib/fileUi.c
  • lines changed 108, context: html, text, full: html, text
    For download file lookup, beta should look on hgdownloads-test but in beta/ subdirectory.
  • lines changed 152, context: html, text, full: html, text
    Added filterBy boxes to hgFileUi to allow slimiting the number of files seen on the page
  • lines changed 1, context: html, text, full: html, text
    filterFiles boxes should have bold titles. We want people to notice.
  • lines changed 1, context: html, text, full: html, text
    Preview host should not rsync but should use ls into it's filesystem. What about hgwbeta?
• src/hg/lib/hdb.c
  • lines changed 7, context: html, text, full: html, text
    For download file lookup, beta should look on hgdownloads-test but in beta/ subdirectory.
  • lines changed 1, context: html, text, full: html, text
    Kate suggested that 'genome-test' would be retargeted to 'genome-preview' but this hasn't happened yet.
• src/hg/lib/hui.c
  • lines changed 2, context: html, text, full: html, text
    Removing from metadata mdb vars defined as hidden by cvv.ra
  • lines changed 3, context: html, text, full: html, text
    Should be retiring ui.code.js as jquery-ui.js is a superset.
• src/hg/lib/knownCanonical.as
  • lines changed 1, context: html, text, full: html, text
    Updating protein column description in knownCanonical to reflect UCSC IDs instead of SwissProt.
• src/hg/lib/mdb.c
  • lines changed 73, context: html, text, full: html, text
    Subtle change to the mdbValLabelSearch() API to put the required val in the pair->name and the optional label in the pair->val. This helps standardize other code that deals with val/label pairs, and enables using slPairFind().
  • lines changed 2, context: html, text, full: html, text
    Fix a couple of small bugs I just introduced to track/file searches
  • lines changed 65, context: html, text, full: html, text
    Added const to a couple of APIs and changed some stuff to aid fleUi filterFiles functionality
• src/hg/lib/searchTracks.c
  • lines changed 241, context: html, text, full: html, text
    Moved a few functions common to track search and file search into library code. Redesigned a few things to standardize on slPair lists of vals and labels.
  • lines changed 3, context: html, text, full: html, text
    Fix a couple of small bugs I just introduced to track/file searches
  • lines changed 10, context: html, text, full: html, text
    Changed mdb API required this change.
• src/hg/lib/trackDbCustom.c
  • lines changed 1, context: html, text, full: html, text
    Track #34 (dbVar for human): new track type gvf needs to be made packable in trackDbCustom.c. I forget this every time I make a new track type.
• src/hg/lib/web.c
  • lines changed 7, context: html, text, full: html, text
    use CGI version based softlinks for js and css files in production sites (see redmine 3170
• src/hg/logCrawl/hgAccessCrawl/makefile
  • lines changed 1, context: html, text, full: html, text
    eliminate use of HOME in MYLIBDIR
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeGisChiaPet.release1.notes
  • lines changed 0, context: html, text, full: html, text
    Release notes for GisChiaPet
  • lines changed 176, context: html, text, full: html, text
    Added better release notes for Chia Pet
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeHaibMethylRrbs.release2.notes
  • lines changed 342, context: html, text, full: html, text
    Updated file type from .bed9 to .bedRrbs
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeSunyAlbanyGeneSt.release1.notes
  • lines changed 4, context: html, text, full: html, text
    removed extra / in 4 places
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeSunySwitchgear.release1.notes
  • lines changed 48, context: html, text, full: html, text
    New notes files for 2 files
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeUwTfbs.release1.notes
  • lines changed 2, context: html, text, full: html, text
    Removed 2 fastq files that were accidently left in notes file.
  • lines changed 2, context: html, text, full: html, text
    Updated the total file counts with accurate number of files available in download files.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 51, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): regenerated snp132 with updatedsnpNcbiToUcsc's -par option. Tweaked singly-mapped PAR SNPs' weights to 1 (dbSNP agrees they should be 1 not 3 and plans to fix). Regenerated subset tracks snp132{Common,Patient,NonUnique}.
  • lines changed 99, context: html, text, full: html, text
    Documented build process for new OMIM tracks.
  • lines changed 119, context: html, text, full: html, text
    Work on wgEncodeReg track.
  • lines changed 79, context: html, text, full: html, text
    Further work on wgEncodeReg.
• src/hg/makeDb/doc/melGal1.txt
  • lines changed 207, context: html, text, full: html, text
    Add melGal1 to pushQ
• src/hg/makeDb/doc/panTro3.txt
  • lines changed 83, context: html, text, full: html, text
    only monDom5 and mm9 chain net left to go
• src/hg/makeDb/doc/ucscGenes/mm9.ucscGenes12.csh
  • lines changed 63, context: html, text, full: html, text
    Some last bits of mouse UCSC genes redo I hope.
• src/hg/makeDb/genbank/etc/align-genbank
  • lines changed 2, context: html, text, full: html, text
    switch build to hgwdev
• src/hg/makeDb/genbank/etc/align.dbs
  • lines changed 2, context: html, text, full: html, text
    removed databases that are not needed
• src/hg/makeDb/genbank/etc/build.crontab
  • lines changed 3, context: html, text, full: html, text
    switch build to hgwdev
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 2, context: html, text, full: html, text
    switch build to hgwdev
• src/hg/makeDb/genbank/etc/hgwdev.crontab
  • lines changed 5, context: html, text, full: html, text
    switch build to hgwdev
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • lines changed 2, context: html, text, full: html, text
    removed databases that are not needed
• src/hg/makeDb/genbank/src/align/gbAlignCommon.h
  • lines changed 5, context: html, text, full: html, text
    avoid need to recheck indices when installing alignments if there is nothing to migrate or align
• src/hg/makeDb/genbank/src/align/gbAlignGet.c
  • lines changed 14, context: html, text, full: html, text
    avoid need to recheck indices when installing alignments if there is nothing to migrate or align
• src/hg/makeDb/genbank/src/align/gbAlignRSync
  • lines changed 48, context: html, text, full: html, text
    allow multiple databases to be run in parallel
• src/hg/makeDb/genbank/src/align/gbAlignSetup
  • lines changed 1, context: html, text, full: html, text
    avoid need to recheck indices when installing alignments if there is nothing to migrate or align
• src/hg/makeDb/genbank/src/align/gbAlignStep
  • lines changed 155, context: html, text, full: html, text
    allow multiple databases to be run in parallel
• src/hg/makeDb/genbank/src/align/makefile
  • lines changed 1, context: html, text, full: html, text
    allow multiple databases to be run in parallel
• src/hg/makeDb/genbank/src/lib/gbCommon.pm
  • lines changed 13, context: html, text, full: html, text
    allow multiple databases to be run in parallel
• src/hg/makeDb/hgTrackDb/hgTrackDb.c
  • lines changed 28, context: html, text, full: html, text
    Extended hgTrackDb's new #insert syntax: optionally it may be precededby a conditional on the database, e.g. <!-- #if (db==hg19) #insert file="human/hg19/specialNote.html" -->
• src/hg/makeDb/mdbUpdate/mdbPrint.c
  • lines changed 19, context: html, text, full: html, text
    Slight change to allow -composite -vars and -var to all work simultaneously to create a single selection.
• src/hg/makeDb/schema/all.joiner
  • lines changed 4, context: html, text, full: html, text
    Add melGal1 to pushQ
  • lines changed 3, context: html, text, full: html, text
    added ncbiIncidentDb to tablesIgnored for hg19,mm9,danRer7
• src/hg/makeDb/trackDb/README
  • lines changed 3, context: html, text, full: html, text
    Extended hgTrackDb's new #insert syntax: optionally it may be precededby a conditional on the database, e.g. <!-- #if (db==hg19) #insert file="human/hg19/specialNote.html" -->
• src/hg/makeDb/trackDb/chicken/trackDb.chainNet.ra
  • lines changed 5, context: html, text, full: html, text
    adding chain net overrides for all panTro3 related chain net combinations
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 35, context: html, text, full: html, text
    Wrangling UW 5C track
  • lines changed 7, context: html, text, full: html, text
    Accepted several provisional stanzas
  • lines changed 5, context: html, text, full: html, text
    More 5C data agreement work
  • lines changed 7, context: html, text, full: html, text
    Added SNP dataTye
  • lines changed 20, context: html, text, full: html, text
    Commented out submitPath and docId for now
  • lines changed 29, context: html, text, full: html, text
    Removed the , in the treatment description, replaced with a with
  • lines changed 6, context: html, text, full: html, text
    Accepted a couple provisional stanzas
• src/hg/makeDb/trackDb/cv/public/cv.ra
  • lines changed 18, context: html, text, full: html, text
    pushing cv.ra with multiSelect instead of select to public since the v248 CGIs have been released and can support multiSelect, Redmine Issue 3085
• src/hg/makeDb/trackDb/dog/trackDb.chainNet.ra
  • lines changed 5, context: html, text, full: html, text
    adding chain net overrides for all panTro3 related chain net combinations
• src/hg/makeDb/trackDb/horse/trackDb.chainNet.ra
  • lines changed 6, context: html, text, full: html, text
    adding chain net overrides for all panTro3 related chain net combinations
• src/hg/makeDb/trackDb/human/affyExonArray.html
  • lines changed 50, context: html, text, full: html, text
    Updated the page for the Affy Exon array track, to reflect its new content
  • lines changed 6, context: html, text, full: html, text
    Added a short paragraph to the affy exon array track details page, describing what the identifiers represent. Added separate views for the probe and probeset subtracks, so that their iews can be set independently.
• src/hg/makeDb/trackDb/human/encodeEgaspSuper.html
  • lines changed 1, context: html, text, full: html, text
    Fixed link to Reymond 'Nineteen...' article
• src/hg/makeDb/trackDb/human/hg18/description.html
  • lines changed 1, context: html, text, full: html, text
    Fixed a typo.
• src/hg/makeDb/trackDb/human/hg18/encodeNhgriDukeDnaseHs.html
  • lines changed 1, context: html, text, full: html, text
    Fixed link for McArthur article
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • lines changed 20, context: html, text, full: html, text
    added some hyphens
• src/hg/makeDb/trackDb/human/hg19/description.html
  • lines changed 1, context: html, text, full: html, text
    Fixed a typo.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra
  • lines changed 6, context: html, text, full: html, text
    Added experimental variables to all composites
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBuOrchid.ra
  • lines changed 36, context: html, text, full: html, text
    Added experimental variables to all composites
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
  • lines changed 4537, context: html, text, full: html, text
    Added the new elements data and some of the replacement data
  • lines changed 578, context: html, text, full: html, text
    Added experimental variables to all composites
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 6, context: html, text, full: html, text
    Added experimental variables to all composites
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
  • lines changed 2, context: html, text, full: html, text
    Added experimental variables to all composites
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeDukeAffyExon.ra
  • lines changed 6, context: html, text, full: html, text
    Added experimental variables to all composites
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisChiaPet.ra
  • lines changed 6, context: html, text, full: html, text
    Added experimental variables to all composites
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisDnaPet.ra
  • lines changed 6, context: html, text, full: html, text
    Added experimental variables to all composites
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra
  • lines changed 6, context: html, text, full: html, text
    Added experimental variables to all composites
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaSeq.ra
  • lines changed 2, context: html, text, full: html, text
    Added experimental variables to all composites
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibGenotype.ra
  • lines changed 298, context: html, text, full: html, text
    Changed to have the one with a treatment show as a cell type, for Tier 1 and Tier 2 to filter to the top
  • lines changed 6, context: html, text, full: html, text
    Added experimental variables to all composites
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethyl27.ra
  • lines changed 147, context: html, text, full: html, text
    Cleaned up the meta data and the downloads display
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylArray.ra
  • lines changed 1466, context: html, text, full: html, text
    Added experimental variables to all composites
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra
  • lines changed 2, context: html, text, full: html, text
    Corrected file names, .bed.gz > .bed9.gz
  • lines changed 198, context: html, text, full: html, text
    Changed file extensions from .bed9.gz to .bedRrbs.gz
  • lines changed 2, context: html, text, full: html, text
    added exp vars
  • lines changed 198, context: html, text, full: html, text
    Added experimental variables to all composites
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylSeq.ra
  • lines changed 230, context: html, text, full: html, text
    Added experimental variables to all composites
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibRnaSeq.ra
  • lines changed 6, context: html, text, full: html, text
    Added experimental variables to all composites
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 24, context: html, text, full: html, text
    Removed wgEncodeHaibTfbsGm12892Pol24h8V0416102RawRep1 from metaDb, on recommendation of Flo.
  • lines changed 24, context: html, text, full: html, text
    Removed reference to file wgEncodeHaibTfbsT47dCtcfV0416102Dmso2RawRep2, as per Flo.
  • lines changed 1992, context: html, text, full: html, text
    Added 8 submissions that included missing data and resubmitted files with updated meta-data.
  • lines changed 6, context: html, text, full: html, text
    Added experimental variables to all composites
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
  • lines changed 6, context: html, text, full: html, text
    Added experimental variables to all composites
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
  • lines changed 6, context: html, text, full: html, text
    Added experimental variables to all composites
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromFaire.ra
  • lines changed 6, context: html, text, full: html, text
    Fixed 5 invalid lab vars
  • lines changed 6, context: html, text, full: html, text
    Added experimental variables to all composites
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromSynth.ra
  • lines changed 6, context: html, text, full: html, text
    Added experimental variables to all composites
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
  • lines changed 6, context: html, text, full: html, text
    Added experimental variables to all composites
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyAlbanyGeneSt.ra
  • lines changed 6, context: html, text, full: html, text
    Added experimental variables to all composites
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyAlbanyTiling.ra
  • lines changed 6, context: html, text, full: html, text
    Added experimental variables to all composites
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyRipSeq.ra
  • lines changed 6, context: html, text, full: html, text
    Added experimental variables to all composites
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunySwitchgear.ra
  • lines changed 6, context: html, text, full: html, text
    Added experimental variables to all composites
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra
  • lines changed 6, context: html, text, full: html, text
    Added experimental variables to all composites
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhNsome.ra
  • lines changed 6, context: html, text, full: html, text
    Added experimental variables to all composites
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 6, context: html, text, full: html, text
    Added experimental variables to all composites
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUchicagoTfbs.ra
  • lines changed 275, context: html, text, full: html, text
    Added experimental variables to all composites
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwAffyExonArray.ra
  • lines changed 119, context: html, text, full: html, text
    resubmitted data so the metaData Changed
  • lines changed 6, context: html, text, full: html, text
    Added experimental variables to all composites
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwChIPSeq.ra
  • lines changed 6, context: html, text, full: html, text
    Added experimental variables to all composites
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra
  • lines changed 2, context: html, text, full: html, text
    Added experimental variables to all composites
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 6, context: html, text, full: html, text
    Added experimental variables to all composites
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwHistone.ra
  • lines changed 178, context: html, text, full: html, text
    Added experimental variables to all composites
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra
  • lines changed 144, context: html, text, full: html, text
    Added experimental variables to all composites
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeYaleChIPseq.ra
  • lines changed 6, context: html, text, full: html, text
    Added experimental variables to all composites
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeYaleRnaSeq.ra
  • lines changed 66, context: html, text, full: html, text
    Changed the polyA+ to polyA- for K562
  • lines changed 2, context: html, text, full: html, text
    Changed two typos in the fileNames
  • lines changed 6, context: html, text, full: html, text
    Added experimental variables to all composites
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeUwAffyExonArray.ra
  • lines changed 119, context: html, text, full: html, text
    updated metaDb for UWAffyExon, redmine# 59 note# 34
• src/hg/makeDb/trackDb/human/hg19/omimLocation.html
  • lines changed 1, context: html, text, full: html, text
    Updated human/hg19/omimLocation.html.
• src/hg/makeDb/trackDb/human/hg19/snp132ParTweak.html
  • lines changed 13, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): At Brooke's suggestion, added a noteto the #Weight section about the tweaking of weights in the PAR region.
• src/hg/makeDb/trackDb/human/hg19/tfbsConsSites.html
  • lines changed 195, context: html, text, full: html, text
    updated HTML.
  • lines changed 0, context: html, text, full: html, text
    dos2unix this puppy
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 100, context: html, text, full: html, text
    Added a newly-reworked Affy Exon track
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    releasing the the sunyAlbany track with the corresponding super track, redmine issue# 460
  • lines changed 16, context: html, text, full: html, text
    Wrangling UW 5C track
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.new.ra
  • lines changed 1, context: html, text, full: html, text
    Added the new elements data and some of the replacement data
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.ra
  • lines changed 61, context: html, text, full: html, text
    Changed type from bedElements to bed6
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisChiaPet.html
  • lines changed 10, context: html, text, full: html, text
    Added a subheader and explained where you could get downloads
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.ra
  • lines changed 284, context: html, text, full: html, text
    Changed to have the one with a treatment show as a cell type, for Tier 1 and Tier 2 to filter to the top
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl27.ra
  • lines changed 24, context: html, text, full: html, text
    Removed the colors and the itemRGB
  • lines changed 8, context: html, text, full: html, text
    Cleaned up the meta data and the downloads display
  • lines changed 6, context: html, text, full: html, text
    Fixed long labels for six entries
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra
  • lines changed 18, context: html, text, full: html, text
    Removed signal: wgEncodeHaibTfbsGm12892Pol24h8V0416102RawRep1 and wgEncodeHaibTfbsT47dCtcfV0416102Dmso2RawRep2, according to Flo.
  • lines changed 508, context: html, text, full: html, text
    Added 8 submissions that included missing data and resubmitted files with updated meta-data.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.html
  • lines changed 11, context: html, text, full: html, text
    Minute change to methods and links to genome-preview as cascade of open chrom composites are released.
  • lines changed 1, context: html, text, full: html, text
    Be been botched.
  • lines changed 5, context: html, text, full: html, text
    Requested by Kate is explicit mention that replicates of alignments and raw data are available in downloads. Also noticed that downloads links should have been to hgFileUi
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.html
  • lines changed 7, context: html, text, full: html, text
    Minute change to methods and links to genome-preview as cascade of open chrom composites are released.
  • lines changed 1, context: html, text, full: html, text
    Be been botched.
  • lines changed 8, context: html, text, full: html, text
    Requested by Kate is explicit mention that replicates of alignments and raw data are available in downloads. Also noticed that downloads links should have been to hgFileUi
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.html
  • lines changed 9, context: html, text, full: html, text
    Minute change to methods and links to genome-preview as cascade of open chrom composites are released.
  • lines changed 1, context: html, text, full: html, text
    Be been botched.
  • lines changed 8, context: html, text, full: html, text
    Requested by Kate is explicit mention that replicates of alignments and raw data are available in downloads. Also noticed that downloads links should have been to hgFileUi
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyTiling.ra
  • lines changed 2, context: html, text, full: html, text
    releasing the the sunyAlbany track with the corresponding super track, redmine issue# 460
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyRipSeq.html
  • lines changed 1, context: html, text, full: html, text
    Fixed copyright html tag
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.html
  • lines changed 2, context: html, text, full: html, text
    Removed max-width reference as this doesn't work and is not needed anymore. Redmine issue 486 note 15.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUchicagoTfbs.html
  • lines changed 256, context: html, text, full: html, text
    New description page, requires refs and contacts
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUw5C.html
  • lines changed 114, context: html, text, full: html, text
    Wrangling UW 5C track
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUw5C.ra
  • lines changed 8, context: html, text, full: html, text
    Wrangling UW 5C track
  • lines changed 6, context: html, text, full: html, text
    More 5C data agreement work
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.ra
  • lines changed 1, context: html, text, full: html, text
    Changed windowing function from mean to mean+whiskers as requested by QA.
  • lines changed 1, context: html, text, full: html, text
    Added fileSortOrder to track.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeYaleRnaSeq.ra
  • lines changed 8, context: html, text, full: html, text
    Changed the polyA+ to polyA- for K562
• src/hg/makeDb/trackDb/human/hg19Patch2/description.html
  • lines changed 1, context: html, text, full: html, text
    Fixed a typo.
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 11, context: html, text, full: html, text
    Added omimGene2 track to human/trackDb.ra.
  • lines changed 19, context: html, text, full: html, text
    Updated new OMIM tracks entries.
• src/hg/makeDb/trackDb/marmoset/trackDb.chainNet.ra
  • lines changed 3, context: html, text, full: html, text
    adding chain net overrides for all panTro3 related chain net combinations
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.html
  • lines changed 2, context: html, text, full: html, text
    Removed max-width reference as this doesn't work and is not needed anymore. Redmine issue 486 note 15.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.html
  • lines changed 2, context: html, text, full: html, text
    Removed max-width reference as this doesn't work and is not needed anymore. Redmine issue 486 note 15.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.html
  • lines changed 2, context: html, text, full: html, text
    Removed max-width reference as this doesn't work and is not needed anymore. Redmine issue 486 note 15.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.html
  • lines changed 2, context: html, text, full: html, text
    Removed max-width reference as this doesn't work and is not needed anymore. Redmine issue 486 note 15.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhHist.html
  • lines changed 2, context: html, text, full: html, text
    Removed max-width reference as this doesn't work and is not needed anymore. Redmine issue 486 note 15.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.html
  • lines changed 2, context: html, text, full: html, text
    Removed max-width reference as this doesn't work and is not needed anymore. Redmine issue 486 note 15.
• src/hg/makeDb/trackDb/mouse/trackDb.chainNet.ra
  • lines changed 5, context: html, text, full: html, text
    adding chain net overrides for all panTro3 related chain net combinations
• src/hg/makeDb/trackDb/opossum/trackDb.chainNet.ra
  • lines changed 5, context: html, text, full: html, text
    adding chain net overrides for all panTro3 related chain net combinations
• src/hg/makeDb/trackDb/orangutan/trackDb.chainNet.ra
  • lines changed 3, context: html, text, full: html, text
    adding chain net overrides for all panTro3 related chain net combinations
• src/hg/makeDb/trackDb/rhesus/trackDb.chainNet.ra
  • lines changed 3, context: html, text, full: html, text
    adding chain net overrides for all panTro3 related chain net combinations
• src/hg/makeDb/trackDb/snp132.shared.html
  • lines changed 8, context: html, text, full: html, text
    Added text at the top pointing out that the rest of the page is the same for all 4 snp132 tracks.
  • lines changed 1, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): At Brooke's suggestion, added a noteto the #Weight section about the tweaking of weights in the PAR region.
• src/hg/makeDb/trackDb/turkey/melGal1/ctgPos2.html
  • lines changed 15, context: html, text, full: html, text
    add ctgPos2 for melGal1
• src/hg/makeDb/trackDb/turkey/melGal1/description.html
  • lines changed 89, context: html, text, full: html, text
    Edit turkey description page
  • lines changed 56, context: html, text, full: html, text
    Add html for gap, gold, and descrition
• src/hg/makeDb/trackDb/turkey/melGal1/gap.html
  • lines changed 45, context: html, text, full: html, text
    Add html for gap, gold, and descrition
• src/hg/makeDb/trackDb/turkey/melGal1/gold.html
  • lines changed 13, context: html, text, full: html, text
    Add html for gap, gold, and descrition
• src/hg/makeDb/trackDb/turkey/melGal1/trackDb.ra
  • lines changed 30, context: html, text, full: html, text
    Add melGal1 to pushQ
• src/hg/makeDb/trackDb/zebrafish/trackDb.chainNet.ra
  • lines changed 16, context: html, text, full: html, text
    adding chain net overrides for all panTro3 related chain net combinations
• src/hg/oneShot/doOmimAv/makefile
  • lines changed 30, context: html, text, full: html, text
    Cleaned up makefile.
  • lines changed 1, context: html, text, full: html, text
    eliminate use of HOME in MYLIBDIR
• src/hg/oneShot/dupedInTable/makefile
  • lines changed 1, context: html, text, full: html, text
    eliminate use of HOME in MYLIBDIR
• src/hg/oneShot/kgName/makefile
  • lines changed 1, context: html, text, full: html, text
    eliminate use of HOME in MYLIBDIR
• src/hg/oneShot/makefile
  • lines changed 1, context: html, text, full: html, text
    eliminate use of HOME in MYLIBDIR
• src/hg/oneShot/musAliAt/makefile
  • lines changed 1, context: html, text, full: html, text
    eliminate use of HOME in MYLIBDIR
• src/hg/oneShot/protDat/makefile
  • lines changed 1, context: html, text, full: html, text
    eliminate use of HOME in MYLIBDIR
• src/hg/oneShot/testCart/makefile
  • lines changed 1, context: html, text, full: html, text
    eliminate use of HOME in MYLIBDIR
• src/hg/oneShot/testTableExists/makefile
  • lines changed 1, context: html, text, full: html, text
    eliminate use of HOME in MYLIBDIR
• src/hg/oneShot/weedKnownBlastTab/makefile
  • lines changed 1, context: html, text, full: html, text
    eliminate use of HOME in MYLIBDIR
• src/hg/oneShot/weedTab/makefile
  • lines changed 1, context: html, text, full: html, text
    eliminate use of HOME in MYLIBDIR
• src/hg/pslToFa/makefile
  • lines changed 1, context: html, text, full: html, text
    eliminate use of HOME in MYLIBDIR
• src/hg/qaPushQ/formPushQ.html
  • lines changed 16, context: html, text, full: html, text
    added new dropdown column "importance" with values from Redmine issue, as requested by Ann
• src/hg/qaPushQ/pushQ.as
  • lines changed 1, context: html, text, full: html, text
    added new dropdown column "importance" with values from Redmine issue, as requested by Ann
• src/hg/qaPushQ/pushQ.sql
  • lines changed 52, context: html, text, full: html, text
    this file was only added accidentally in recent months; it does not need to be in the source code since it is easily and automatically generated using autoSql in the makefile
• src/hg/qaPushQ/qaPushQ.c
  • lines changed 34, context: html, text, full: html, text
    added new dropdown column "importance" with values from Redmine issue, as requested by Ann
• src/hg/regulate/regClusterAttachMetadataToTableOfTables/makefile
  • lines changed 18, context: html, text, full: html, text
    Work on wgEncodeReg track.
• src/hg/regulate/regClusterAttachMetadataToTableOfTables/regClusterAttachMetadataToTableOfTables.c
  • lines changed 177, context: html, text, full: html, text
    Work on wgEncodeReg track.
  • lines changed 5, context: html, text, full: html, text
    Adding some comments.
• src/hg/regulate/regClusterBedExpCfg/cellLetter2.tab
  • lines changed 95, context: html, text, full: html, text
    More work on new TFBS clustering stuff.
• src/hg/regulate/regClusterMakeTableOfTables/regClusterMakeTableOfTables.c
  • lines changed 147, context: html, text, full: html, text
    Work on wgEncodeReg track.
• src/hg/regulate/regClusterTreeCells/makefile
  • lines changed 18, context: html, text, full: html, text
    First cut of cell clusterer. Runs and produces output, but output isn't making a bunch of sense. Need to develop some test cases.
• src/hg/regulate/regClusterTreeCells/regClusterTreeCells.c
  • lines changed 349, context: html, text, full: html, text
    First cut of cell clusterer. Runs and produces output, but output isn't making a bunch of sense. Need to develop some test cases.
• src/hg/utils/cpAndLinkToResourceFiles.pl
  • lines changed 94, context: html, text, full: html, text
    coallesce cpAndLinkToResourceFiles.pl
  • lines changed 51, context: html, text, full: html, text
    Use version based links in production sites, mtime based links in dev sites (see redmine #3170)
• src/hg/utils/refSeqGet/makefile
  • lines changed 1, context: html, text, full: html, text
    Recurse to tests in the clean target.
• src/inc/cheapcgi.h
  • lines changed 9, context: html, text, full: html, text
    Added lib routine for creating a single/multiple drop down, where the multiple will be expected to be converted into a ui-dropdownchecklist.js type multi-select
• src/inc/common.h
  • lines changed 7, context: html, text, full: html, text
    fixing processing of last-modified header in udc; also setting the original time on the finished file in paraFetch (net.c); new helper function in common.c handles conversion to UTC time
• src/inc/linefile.h
  • lines changed 2, context: html, text, full: html, text
    Feature #2821 (VCF parser): works on a 1000 Genomes pilot release VCF+tabix file with genotypes.[Note: this is a squash of 6 commits, developed off in my vcf branch.]
• src/inc/vcf.h
  • lines changed 181, context: html, text, full: html, text
    Feature #2821 (VCF parser): works on a 1000 Genomes pilot release VCF+tabix file with genotypes.[Note: this is a squash of 6 commits, developed off in my vcf branch.]
• src/jkOwnLib/genoFind.c
  • lines changed 1, context: html, text, full: html, text
    Bug #3150 (blat is crashing): The gfPepTile logic assumes that aaValcontains either -1 or 0 to 19. Previously, aaVal['X'] was -1. Then in 1b5e64c4, 'X' was added to dnautil.c's aminoAcidTable and therefore to aaVal, with aaVal['X'] = 20. One of the peptide test sequences ends with "XXXXX", which caused gfPepTile to produce an out-of-range tile, leading to a SEGV in gfStraightFindHits. Fix: if aaVal[] is > 19, treat as if -1.
• src/lib/cheapcgi.c
  • lines changed 74, context: html, text, full: html, text
    Added lib routine for creating a single/multiple drop down, where the multiple will be expected to be converted into a ui-dropdownchecklist.js type multi-select
• src/lib/common.c
  • lines changed 26, context: html, text, full: html, text
    fixing processing of last-modified header in udc; also setting the original time on the finished file in paraFetch (net.c); new helper function in common.c handles conversion to UTC time
• src/lib/linefile.c
  • lines changed 9, context: html, text, full: html, text
    Feature #2821 (VCF parser): works on a 1000 Genomes pilot release VCF+tabix file with genotypes.[Note: this is a squash of 6 commits, developed off in my vcf branch.]
• src/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Feature #2821 (VCF parser): works on a 1000 Genomes pilot release VCF+tabix file with genotypes.[Note: this is a squash of 6 commits, developed off in my vcf branch.]
• src/lib/net.c
  • lines changed 38, context: html, text, full: html, text
    fixing processing of last-modified header in udc; also setting the original time on the finished file in paraFetch (net.c); new helper function in common.c handles conversion to UTC time
• src/lib/regexHelper.c
  • lines changed 9, context: html, text, full: html, text
    Build a more accurate description in regexMatchSubstrMaybeCase.
• src/lib/tests/expected/tabixFetch1kGNoGenotypes.out
  • lines changed 6, context: html, text, full: html, text
    Feature #2820 (tabix), #2821 (VCF parser): added basic test cases for VCF andtabix -- thanks Mark for the prod.
• src/lib/tests/expected/tabixFetch1kGWithGenotypes.out
  • lines changed 7, context: html, text, full: html, text
    Feature #2820 (tabix), #2821 (VCF parser): added basic test cases for VCF andtabix -- thanks Mark for the prod.
• src/lib/tests/expected/vcfParse1kGNoGenotypes.out
  • lines changed 7, context: html, text, full: html, text
    Feature #2820 (tabix), #2821 (VCF parser): added basic test cases for VCF andtabix -- thanks Mark for the prod.
• src/lib/tests/expected/vcfParse1kGWithGenotypes.out
  • lines changed 8, context: html, text, full: html, text
    Feature #2820 (tabix), #2821 (VCF parser): added basic test cases for VCF andtabix -- thanks Mark for the prod.
• src/lib/tests/input/YRI.low_coverage.2010_07_excerpt.genotypes.vcf.gz
  • lines changed 0, context: html, text, full: html, text
    Feature #2820 (tabix), #2821 (VCF parser): added basic test cases for VCF andtabix -- thanks Mark for the prod.
• src/lib/tests/input/YRI.low_coverage.2010_07_excerpt.genotypes.vcf.gz.tbi
  • lines changed 0, context: html, text, full: html, text
    Feature #2820 (tabix), #2821 (VCF parser): added basic test cases for VCF andtabix -- thanks Mark for the prod.
• src/lib/tests/input/YRI.trio.2010_06.novelsequences.sites.vcf.gz
  • lines changed 0, context: html, text, full: html, text
    Feature #2820 (tabix), #2821 (VCF parser): added basic test cases for VCF andtabix -- thanks Mark for the prod.
• src/lib/tests/input/YRI.trio.2010_06.novelsequences.sites.vcf.gz.tbi
  • lines changed 0, context: html, text, full: html, text
    Feature #2820 (tabix), #2821 (VCF parser): added basic test cases for VCF andtabix -- thanks Mark for the prod.
• src/lib/tests/makefile
  • lines changed 37, context: html, text, full: html, text
    Feature #2820 (tabix), #2821 (VCF parser): added basic test cases for VCF andtabix -- thanks Mark for the prod.
• src/lib/tests/tabixFetch.c
  • lines changed 114, context: html, text, full: html, text
    Mark rightly pointed out that these programs I used for quick testingshould go in lib/tests with proper testcases, not in oneShot/. Test cases coming up...
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    Feature #2820 (tabix), #2821 (VCF parser): added basic test cases for VCF andtabix -- thanks Mark for the prod.
• src/lib/tests/vcfParseTest.c
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    Mark rightly pointed out that these programs I used for quick testingshould go in lib/tests with proper testcases, not in oneShot/. Test cases coming up...
• src/lib/udc.c
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    fixing processing of last-modified header in udc; also setting the original time on the finished file in paraFetch (net.c); new helper function in common.c handles conversion to UTC time
• src/lib/vcf.c
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    Feature #2821 (VCF parser): works on a 1000 Genomes pilot release VCF+tabix file with genotypes.[Note: this is a squash of 6 commits, developed off in my vcf branch.]
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    Feature #2821 (VCF parser): adding workaround for annoying non-ASCIIcharacters in the header of a file included in 1000 Genomes' pilot release, found when adding basic test case.
• src/oneShot/balancedTree/makefile
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    eliminate use of HOME in MYLIBDIR
• src/oneShot/findContigsWithClones/makefile
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    eliminate use of HOME in MYLIBDIR
• src/oneShot/foo2/makefile
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    eliminate use of HOME in MYLIBDIR
• src/oneShot/formatFastaSeq/makefile
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    eliminate use of HOME in MYLIBDIR
• src/oneShot/mafFindZero/makefile
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    eliminate use of HOME in MYLIBDIR
• src/oneShot/makefile
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    eliminate use of HOME in MYLIBDIR
• src/oneShot/newStitch4/makefile
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    eliminate use of HOME in MYLIBDIR
• src/oneShot/tabixFetch/makefile
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    Mark rightly pointed out that these programs I used for quick testingshould go in lib/tests with proper testcases, not in oneShot/. Test cases coming up...
• src/oneShot/tabixFetch/tabixFetch.c
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    Mark rightly pointed out that these programs I used for quick testingshould go in lib/tests with proper testcases, not in oneShot/. Test cases coming up...
• src/oneShot/test/makefile
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    eliminate use of HOME in MYLIBDIR
• src/oneShot/vcfParseTest/makefile
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    Feature #2821 (VCF parser): works on a 1000 Genomes pilot release VCF+tabix file with genotypes.[Note: this is a squash of 6 commits, developed off in my vcf branch.]
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    Mark rightly pointed out that these programs I used for quick testingshould go in lib/tests with proper testcases, not in oneShot/. Test cases coming up...
• src/oneShot/vcfParseTest/vcfParseTest.c
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    Feature #2821 (VCF parser): works on a 1000 Genomes pilot release VCF+tabix file with genotypes.[Note: this is a squash of 6 commits, developed off in my vcf branch.]
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    Mark rightly pointed out that these programs I used for quick testingshould go in lib/tests with proper testcases, not in oneShot/. Test cases coming up...
• src/parasol/dataSim/makefile
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    eliminate use of HOME in MYLIBDIR
• src/parasol/para/para.c
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    Doubling max queue size since we seem to actually sometimes be hitting limit and memory has more than doubled since this was set.
• src/product/scripts/fetchMinimalGbdb.sh
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    update to include trix and metaDb files and properly rsync js and style directories
• src/product/scripts/fetchMinimalGoldenPath.sh
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    update to include trix and metaDb files and properly rsync js and style directories
• src/product/scripts/updateHtml.sh
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    update to include trix and metaDb files and properly rsync js and style directories
• src/reformat/makeOrf2gene/makefile
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    eliminate use of HOME in MYLIBDIR
• src/utils/bigBedSummary/makefile
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    properly clean the executable
• src/utils/bigBedToBed/makefile
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    properly clean the executable
• src/utils/bigWigSummary/makefile
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    properly clean the executable
• src/utils/bigWigToBedGraph/makefile
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    properly clean the executable
• src/utils/git-reports/git-reports.c
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    adding note that 0 lines diff happens with binary files too
• src/utils/makefile
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    this clean target wasn't descending into USE_DIRS
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    properly clean the executable
• src/utils/qa/alertBqueue.csh
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    corrected donna's email address
• src/utils/qa/weeklybld/buildEnv.csh
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    v249 preview

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• files changed: 322