All File Changes

v250_base to v251_preview (2011-04-19 to 2011-04-26) v251

• src/blat/version.doc
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    blat segfault fix for maxIntron <= 11 when tileSize <= 11
• src/hg/encode/encodePatchTdb/encodePatchTdb.c
  • lines changed 639, context: html, text, full: html, text
    Encode Rename Object utility. Helps when a submission has gone too far to easily change the metadata and re-run the pipeline. Squashed for easier git-reports reviewing.
• src/hg/encode/encodePatchTdb/makefile
  • lines changed 1, context: html, text, full: html, text
    Encode Rename Object utility. Helps when a submission has gone too far to easily change the metadata and re-run the pipeline. Squashed for easier git-reports reviewing.
• src/hg/encode/encodeRenameObj/encodeRenameObj.c
  • lines changed 1309, context: html, text, full: html, text
    Encode Rename Object utility. Helps when a submission has gone too far to easily change the metadata and re-run the pipeline. Squashed for easier git-reports reviewing.
• src/hg/encode/encodeRenameObj/encodeRenamerLog.as
  • lines changed 13, context: html, text, full: html, text
    Encode Rename Object utility. Helps when a submission has gone too far to easily change the metadata and re-run the pipeline. Squashed for easier git-reports reviewing.
• src/hg/encode/encodeRenameObj/encodeRenamerLog.sql
  • lines changed 21, context: html, text, full: html, text
    Encode Rename Object utility. Helps when a submission has gone too far to easily change the metadata and re-run the pipeline. Squashed for easier git-reports reviewing.
• src/hg/encode/encodeRenameObj/makefile
  • lines changed 20, context: html, text, full: html, text
    Encode Rename Object utility. Helps when a submission has gone too far to easily change the metadata and re-run the pipeline. Squashed for easier git-reports reviewing.
• src/hg/encode/lib/encodePatchTdb.c
  • lines changed 891, context: html, text, full: html, text
    Encode Rename Object utility. Helps when a submission has gone too far to easily change the metadata and re-run the pipeline. Squashed for easier git-reports reviewing.
• src/hg/encode/lib/makefile
  • lines changed 20, context: html, text, full: html, text
    Encode Rename Object utility. Helps when a submission has gone too far to easily change the metadata and re-run the pipeline. Squashed for easier git-reports reviewing.
• src/hg/hgGateway/hgGateway.c
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    Insignificant change from FONT tags to CSS.
• src/hg/hgSuggest/hgSuggest.c
  • lines changed 12, context: html, text, full: html, text
    use connGeneSuggestTable to generalize code
• src/hg/hgTables/filterFields.c
  • lines changed 4, context: html, text, full: html, text
    Bug #3537 (edit of filter in table browser truncates Free-form query string):the free-form query string needs to be htmlEncoded so that quotes don't mess up the HTML parsing of the text input box.
• src/hg/hgTables/usage.c
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    Removed a <P> tag to keep line spacing the same as when we used DOCTYPE 3.2.
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 21, context: html, text, full: html, text
    add specific Ensembl gene version string in longLabel for hgTracks and hgTrackUi
  • lines changed 0, context: html, text, full: html, text
    Fixed indentation on one line.
  • lines changed 3, context: html, text, full: html, text
    Checking in CGI usage of DOCTYPE 4.01 Transitional (instead of 3.2). Also removed some minor FONT tags that should be replaced by CSS.
• src/hg/hgTracks/bamTrack.c
  • lines changed 9, context: html, text, full: html, text
    Refactoring in hopes of making auto-scale work as you'd hope with multiwigs. That still isn't there, this is just preliminaries.
  • lines changed 1, context: html, text, full: html, text
    Making autoscale work as you'd hope for multiWigs - where all the wigs have a common scale.
• src/hg/hgTracks/bedGraph.c
  • lines changed 25, context: html, text, full: html, text
    Refactoring in hopes of making auto-scale work as you'd hope with multiwigs. That still isn't there, this is just preliminaries.
  • lines changed 6, context: html, text, full: html, text
    Making autoscale work as you'd hope for multiWigs - where all the wigs have a common scale.
• src/hg/hgTracks/bedTrack.c
  • lines changed 4, context: html, text, full: html, text
    Feature #3476 (zap-to-edge arrows for OMIM tracks): toggle "Left Edge"and "Right Edge" default labels when display is in reverse mode.
• src/hg/hgTracks/bigWigTrack.c
  • lines changed 10, context: html, text, full: html, text
    Refactoring in hopes of making auto-scale work as you'd hope with multiwigs. That still isn't there, this is just preliminaries.
  • lines changed 42, context: html, text, full: html, text
    Making autoscale work as you'd hope for multiWigs - where all the wigs have a common scale.
• src/hg/hgTracks/container.c
  • lines changed 4, context: html, text, full: html, text
    Refactoring in hopes of making auto-scale work as you'd hope with multiwigs. That still isn't there, this is just preliminaries.
• src/hg/hgTracks/gvfTrack.c
  • lines changed 9, context: html, text, full: html, text
    Track #34 (dbVar): oops, forgot NULL check -> segv when boringaggregate variants (sv) are excluded.
• src/hg/hgTracks/hgTracks.c
  • lines changed 6, context: html, text, full: html, text
    anoCar2 works for Ensembl due to ucscToEnsembl table
  • lines changed 1, context: html, text, full: html, text
    calJac3 also now has a ucscToEnsembl table, this needs to be a trackDb variable ...
  • lines changed 4, context: html, text, full: html, text
    oryCun2 now has a proper ucscToEnsembl translation table
  • lines changed 22, context: html, text, full: html, text
    add specific Ensembl gene version string in longLabel for hgTracks and hgTrackUi
  • lines changed 11, context: html, text, full: html, text
    Insignificant change from FONT tags to CSS.
• src/hg/hgTracks/hgTracks.h
  • lines changed 4, context: html, text, full: html, text
    Refactoring in hopes of making auto-scale work as you'd hope with multiwigs. That still isn't there, this is just preliminaries.
  • lines changed 1, context: html, text, full: html, text
    Making autoscale work as you'd hope for multiWigs - where all the wigs have a common scale.
• src/hg/hgTracks/multiWig.c
  • lines changed 21, context: html, text, full: html, text
    Refactoring in hopes of making auto-scale work as you'd hope with multiwigs. That still isn't there, this is just preliminaries.
  • lines changed 65, context: html, text, full: html, text
    Making autoscale work as you'd hope for multiWigs - where all the wigs have a common scale.
• src/hg/hgTracks/searchTracks.c
  • lines changed 95, context: html, text, full: html, text
    Removed a lot of ifdef'd out code. We are not going to revive fileSearch as a tab on trackSearch (unfortunately)
  • lines changed 2, context: html, text, full: html, text
    Checking in CGI usage of DOCTYPE 4.01 Transitional (instead of 3.2). Also removed some minor FONT tags that should be replaced by CSS.
• src/hg/hgTracks/simpleTracks.c
  • lines changed 953, context: html, text, full: html, text
    Feature #3476 (next block arrows for OMIM tracks): refactored sharedcode from several tracks (Superfamily, GAD, DECIPHER, OMIM*) with similar drawing and mouseover features, made the shared code compatible with nextPrevExon code (which for simple bed tracks like these is more like zap-to-edge), and added simpleBedNextPrevEdge to their *Methods.
  • lines changed 19, context: html, text, full: html, text
    add specific Ensembl gene version string in longLabel for hgTracks and hgTrackUi
• src/hg/hgTracks/variation.c
  • lines changed 1, context: html, text, full: html, text
    Fixed typo that broke snp132's coloring by bitfields.
• src/hg/hgTracks/wigCommon.h
  • lines changed 8, context: html, text, full: html, text
    Refactoring in hopes of making auto-scale work as you'd hope with multiwigs. That still isn't there, this is just preliminaries.
  • lines changed 4, context: html, text, full: html, text
    Making autoscale work as you'd hope for multiWigs - where all the wigs have a common scale.
• src/hg/hgTracks/wigTrack.c
  • lines changed 60, context: html, text, full: html, text
    Refactoring in hopes of making auto-scale work as you'd hope with multiwigs. That still isn't there, this is just preliminaries.
  • lines changed 37, context: html, text, full: html, text
    Making autoscale work as you'd hope for multiWigs - where all the wigs have a common scale.
• src/hg/htdocs/ENCODE/dataStandards.html
  • lines changed 8, context: html, text, full: html, text
    Removing a link to old standards doc that Barb Wold said was bad bad bad.
• src/hg/htdocs/ENCODE/index.html
  • lines changed 45, context: html, text, full: html, text
    adding new news item about March/April track releases and archiving news items as needed
• src/hg/htdocs/ENCODE/newsarch.html
  • lines changed 38, context: html, text, full: html, text
    adding new news item about March/April track releases and archiving news items as needed
• src/hg/htdocs/admin/mirror.html
  • lines changed 5, context: html, text, full: html, text
    Replace Redhat 9 with CentOS 5.5
• src/hg/htdocs/style/HGStyle.css
  • lines changed 4, context: html, text, full: html, text
    Checking in CGI usage of DOCTYPE 4.01 Transitional (instead of 3.2). Also removed some minor FONT tags that should be replaced by CSS.
• src/hg/inc/cv.h
  • lines changed 3, context: html, text, full: html, text
    Support for cv.ra typeOfTerm hidden being alpha,beta,public
• src/hg/inc/ensFace.h
  • lines changed 4, context: html, text, full: html, text
    add specific Ensembl gene version string in longLabel for hgTracks and hgTrackUi
• src/hg/inc/hui.h
  • lines changed 1, context: html, text, full: html, text
    Refactoring in hopes of making auto-scale work as you'd hope with multiwigs. That still isn't there, this is just preliminaries.
• src/hg/inc/mdb.h
  • lines changed 1, context: html, text, full: html, text
    Changed encodeExp option to take table name and diverged mdbPrint and mdbUpdate requirements for encodeExp as per Cricket's request.
• src/hg/inc/suggest.h
  • lines changed 3, context: html, text, full: html, text
    make connGeneSuggestTable public so I can use it in hgSuggest.c
• src/hg/inc/tfbsConsFactors.h
  • lines changed 4, context: html, text, full: html, text
    some changes in table labels requested by Luvina #2713
• src/hg/inc/wiggle.h
  • lines changed 7, context: html, text, full: html, text
    Refactoring in hopes of making auto-scale work as you'd hope with multiwigs. That still isn't there, this is just preliminaries.
• src/hg/js/cpJsFiles.pl
  • lines changed 94, context: html, text, full: html, text
    delete obsolete file (3170)delete obsolete file (see 3170)
• src/hg/js/hui.js
  • lines changed 9, context: html, text, full: html, text
    redmine 1411. One more tweek to martix CB graying. This was found by Katrina when already on beta.
• src/hg/lib/cv.c
  • lines changed 42, context: html, text, full: html, text
    Support for cv.ra typeOfTerm hidden being alpha,beta,public
• src/hg/lib/ensFace.c
  • lines changed 25, context: html, text, full: html, text
    add specific Ensembl gene version string in longLabel for hgTracks and hgTrackUi
• src/hg/lib/fileUi.c
  • lines changed 313, context: html, text, full: html, text
    Adding CGI support for mdb fimeName being a comma delimited list. Also includes support for md5sum as comma delimited list.
• src/hg/lib/hui.c
  • lines changed 16, context: html, text, full: html, text
    Adding CGI support for mdb fimeName being a comma delimited list. Also includes support for md5sum as comma delimited list.
  • lines changed 1, context: html, text, full: html, text
    Support for cv.ra typeOfTerm hidden being alpha,beta,public
  • lines changed 10, context: html, text, full: html, text
    Checking in CGI usage of DOCTYPE 4.01 Transitional (instead of 3.2). Also removed some minor FONT tags that should be replaced by CSS.
• src/hg/lib/jsHelper.c
  • lines changed 1, context: html, text, full: html, text
    Checking in CGI usage of DOCTYPE 4.01 Transitional (instead of 3.2). Also removed some minor FONT tags that should be replaced by CSS.
• src/hg/lib/mdb.c
  • lines changed 13, context: html, text, full: html, text
    When in doubt, should always prefer the sandbox table.
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    Temprarily block experimentify from creating expId's in encodeExp table. Cricket will manage expId creation with Kate's tool for now. mdbUpdate can still create accessions in encodeExp table when expId already exists.
  • lines changed 16, context: html, text, full: html, text
    Changes so that -accession -test will work. Also made some experimentify errors more prominent.
  • lines changed 6, context: html, text, full: html, text
    Support for cv.ra typeOfTerm hidden being alpha,beta,public
  • lines changed 30, context: html, text, full: html, text
    Cleaned up some mesages in experimentify mdbPrint command
• src/hg/lib/suggest.c
  • lines changed 1, context: html, text, full: html, text
    make connGeneSuggestTable public so I can use it in hgSuggest.c
• src/hg/lib/tfbsConsFactors.as
  • lines changed 4, context: html, text, full: html, text
    some changes in table labels requested by Luvina #2713
• src/hg/lib/tfbsConsFactors.c
  • lines changed 7, context: html, text, full: html, text
    some changes in table labels requested by Luvina #2713
• src/hg/lib/tfbsConsFactors.sql
  • lines changed 4, context: html, text, full: html, text
    some changes in table labels requested by Luvina #2713
• src/hg/lib/web.c
  • lines changed 130, context: html, text, full: html, text
    Checking in CGI usage of DOCTYPE 4.01 Transitional (instead of 3.2). Also removed some minor FONT tags that should be replaced by CSS.
• src/hg/lib/wiggleCart.c
  • lines changed 49, context: html, text, full: html, text
    Refactoring in hopes of making auto-scale work as you'd hope with multiwigs. That still isn't there, this is just preliminaries.
• src/hg/makeDb/doc/anoCar1.txt
  • lines changed 25, context: html, text, full: html, text
    constructed liftOver from anoCar1 to anoCar2
• src/hg/makeDb/doc/anoCar2.txt
  • lines changed 73, context: html, text, full: html, text
    in the pushQ and now with Ensembl v61 genes
  • lines changed 18, context: html, text, full: html, text
    adding hg19 human lastz chain net
  • lines changed 36, context: html, text, full: html, text
    added blat servers and set default positon and ensGene v62 done
  • lines changed 6, context: html, text, full: html, text
    setting current for dateReference v62 trackVersion for ensGenes
  • lines changed 57, context: html, text, full: html, text
    starting lastz runs with Lizard anoCar2
• src/hg/makeDb/doc/calJac3.txt
  • lines changed 53, context: html, text, full: html, text
    add the ucscToEnsembl table
  • lines changed 33, context: html, text, full: html, text
    adding ensGene v62
  • lines changed 138, context: html, text, full: html, text
    multiz13way rework done.
  • lines changed 42, context: html, text, full: html, text
    Multiz 13way rework done.
• src/hg/makeDb/doc/danRer7.txt
  • lines changed 98, context: html, text, full: html, text
    Added U Mass ChIP-Seq tracks.
• src/hg/makeDb/doc/encodeDccHg18/broadBernstein.txt
  • lines changed 75, context: html, text, full: html, text
    Some old doc, and a lot of new stuff to get expIds and dccAccessions in
• src/hg/makeDb/doc/encodeDccHg18/dukeUtaUncCrawford.txt
  • lines changed 46, context: html, text, full: html, text
    Some old doc, and a lot of new stuff to get expIds and dccAccessions in
• src/hg/makeDb/doc/encodeDccHg19/broadHistoneBernstein.hg19.txt
  • lines changed 76, context: html, text, full: html, text
    Some old doc, and a lot of new stuff to get expIds and dccAccessions in
• src/hg/makeDb/doc/encodeDccHg19/openChromCrawford.hg19.txt
  • lines changed 194, context: html, text, full: html, text
    Some old doc, and a lot of new stuff to get expIds and dccAccessions in
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeHaibMethylRrbs.release2.notes
  • lines changed 657, context: html, text, full: html, text
    New submissions added
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeUchicagoTfbs.release1.notes
  • lines changed 21, context: html, text, full: html, text
    Added files, which are symbolic links to the same file, for inputcontrol rep 1 which is shared by all experiments. Removed the Initial file name and added the 6 duplicates of the file for each experiment.
• src/hg/makeDb/doc/galGal3.txt
  • lines changed 57, context: html, text, full: html, text
    starting lastz runs with Lizard anoCar2
• src/hg/makeDb/doc/hg18.txt
  • lines changed 4, context: html, text, full: html, text
    Track #34 (dbVar): reloaded iscaRetrospective track to drop the boringaggregate variants (sv) and to keep only the better-annotated supporting variants (ssv).
• src/hg/makeDb/doc/hg19.txt
  • lines changed 57, context: html, text, full: html, text
    adding lastz anoCar2
  • lines changed 56, context: html, text, full: html, text
    patch3 naming business on hg19 and adding ensGene v62
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    Adding an unfortunately long line that describes how the metadata was faked for the pooled RNA track.
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    starting lastz runs with Lizard anoCar2
  • lines changed 22, context: html, text, full: html, text
    Added hg19 GERP track.
• src/hg/makeDb/doc/makeEnsembl.txt
  • lines changed 24, context: html, text, full: html, text
    adding anoCar2 v61 genes
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    update v62 documented
  • lines changed 34, context: html, text, full: html, text
    patch3 naming business on hg19 and adding ensGene v62
• src/hg/makeDb/doc/melGal1.txt
  • lines changed 162, context: html, text, full: html, text
    add human proteins
• src/hg/makeDb/doc/mm9.txt
  • lines changed 185, context: html, text, full: html, text
    Initial Nuclear Lamina track work
  • lines changed 55, context: html, text, full: html, text
    starting lastz runs with Lizard anoCar2
  • lines changed 22, context: html, text, full: html, text
    Added mm9 GERP track.
• src/hg/makeDb/doc/nomLeu1.txt
  • lines changed 20, context: html, text, full: html, text
    adding ensGene v62
  • lines changed 3, context: html, text, full: html, text
    setting current for dateReference v62 trackVersion for ensGenes
• src/hg/makeDb/doc/oryCun2.txt
  • lines changed 103, context: html, text, full: html, text
    adding ensGene v62 and ucscToEnsembl name translation table
• src/hg/makeDb/doc/panTro3.txt
  • lines changed 25, context: html, text, full: html, text
    clean up some comments on 12way bigWig processing
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh
  • lines changed 75, context: html, text, full: html, text
    Generate PSL files for the Rfam and tRNA input data, add them to the input to txInfoAssemble.
• src/hg/makeDb/doc/ucscGenes/mm9.ucscGenes12.csh
  • lines changed 21, context: html, text, full: html, text
    Updating blastTabs
• src/hg/makeDb/mdbUpdate/mdbPrint.c
  • lines changed 20, context: html, text, full: html, text
    Changed encodeExp option to take table name and diverged mdbPrint and mdbUpdate requirements for encodeExp as per Cricket's request.
  • lines changed 9, context: html, text, full: html, text
    Simplified the encodeExp table option
• src/hg/makeDb/mdbUpdate/mdbUpdate.c
  • lines changed 21, context: html, text, full: html, text
    Changed encodeExp option to take table name and diverged mdbPrint and mdbUpdate requirements for encodeExp as per Cricket's request.
  • lines changed 1, context: html, text, full: html, text
    Changes so that -accession -test will work. Also made some experimentify errors more prominent.
  • lines changed 9, context: html, text, full: html, text
    Simplified the encodeExp table option
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 2, context: html, text, full: html, text
    Added two new Stam lab protocol documents
  • lines changed 16, context: html, text, full: html, text
    Changed the BTO numbers for Cell lines as specified by the NHGRI. Melissa should review this
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    added the url for Jennifer Condon
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    Extended typeOfTerm hidden var to hide from beta,public
  • lines changed 1, context: html, text, full: html, text
    Hopefully fixed a bad regex on dccAccession
  • lines changed 28, context: html, text, full: html, text
    Adding GeneSt and Tiling as dataTypes
  • lines changed 40, context: html, text, full: html, text
    Checking in a new header comment for Morgan
  • lines changed 3, context: html, text, full: html, text
    Revised the tag for term BaseOverlapSignal so it will pass Morgan's validator
  • lines changed 8, context: html, text, full: html, text
    Accepting some provisional changes, with slight modifications to shorten the tags
  • lines changed 4, context: html, text, full: html, text
    Changed dataType GeneSt to RipGeneSt at request of CV maven
  • lines changed 20, context: html, text, full: html, text
    Started reviewing the karyotype information compared to vendor, Jeff is taking over
  • lines changed 4, context: html, text, full: html, text
    Changing the Methyl27 to MethylArray for dataType. This should be reviewed by Melissa. The reasoning is that we also will have some data from Methyl450 and these data are to be considered together.
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    Added 4 cell lines and 2 strains. Updated the catergory for 2 cell lines
• src/hg/makeDb/trackDb/gibbon/nomLeu1/description.html
  • lines changed 1, context: html, text, full: html, text
    Added the common name of this cute little fellow.
• src/hg/makeDb/trackDb/human/hg18/ceuBcellComposite.html
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    "Trying git commit to get rid of symbolic links."
• src/hg/makeDb/trackDb/human/hg18/ceuBcellRNASeqBW.html
  • lines changed 1, context: html, text, full: html, text
    "Trying git commit to get rid of symbolic links."
• src/hg/makeDb/trackDb/human/hg18/ceuBcellSuper.html
  • lines changed 1, context: html, text, full: html, text
    "Trying git commit to get rid of symbolic links."
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeBroadChipSeq.ra
  • lines changed 1099, context: html, text, full: html, text
    Added expId's and dccAccessions to Broad Histone hg18 and hg19
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeBroadHmm.ra
  • lines changed 19, context: html, text, full: html, text
    Added expIds and dccAccessions for Broad HMM hg18 and hg19
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeBuOrchid.ra
  • lines changed 5, context: html, text, full: html, text
    Added the ver first accession number and exp ID
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    Issue 1440 Note 15. I am changing to add fileSortOrder to display the new accession numbers for both hg18 and hg19.
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeChromatinMap.ra
  • lines changed 1067, context: html, text, full: html, text
    Added expIds and dccAccessions for Open Chrom hg18 and hg19
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaCnv.ra
  • lines changed 7, context: html, text, full: html, text
    Changing Cnv to Genotype for dataType
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaMethyl27.ra
  • lines changed 13, context: html, text, full: html, text
    Changed the dataType to be MethylArray instead of Methyl27 and added labVersion to indicate that Methyl27 was used
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeHudsonalphaMethylSeq.ra
  • lines changed 2, context: html, text, full: html, text
    Remove restrictionEnzyme from expVars
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeNhgriBip.ra
  • lines changed 2, context: html, text, full: html, text
    Changed the lab name to comply with the cv.ra
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeNhgriNRE.ra
  • lines changed 5, context: html, text, full: html, text
    Changed the lab name to comply with the cv.ra
• src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeYaleRNAseq.ra
  • lines changed 20, context: html, text, full: html, text
    Added rnaExtract=polyA for all tracks not certain if it is right
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • lines changed 4, context: html, text, full: html, text
    Added fileSortOrder to some hg18 tracks which will be reved some day with dccAccessions
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadChipSeq.new.ra
  • lines changed 1, context: html, text, full: html, text
    Added fileSortOrder to some hg18 tracks which will be reved some day with dccAccessions
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadHmm.ra
  • lines changed 1, context: html, text, full: html, text
    Added fileSortOrder to some hg18 tracks which will be reved some day with dccAccessions
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBuOrchid.ra
  • lines changed 5, context: html, text, full: html, text
    Issue 1440 Note 15. I am changing to add fileSortOrder to display the new accession numbers for both hg18 and hg19.
  • lines changed 1, context: html, text, full: html, text
    commented out fileSortOrder line so that this change doesn't leak out to the RR, redmine #1440
• src/hg/makeDb/trackDb/human/hg18/wgEncodeChromatinMap.new.ra
  • lines changed 2, context: html, text, full: html, text
    Added fileSortOrder to some hg18 tracks which will be reved some day with dccAccessions
• src/hg/makeDb/trackDb/human/hg19/allHg19RS_BW.html
  • lines changed 71, context: html, text, full: html, text
    Created allHg19RS_BW.html.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/makefile
  • lines changed 1, context: html, text, full: html, text
    Adding metadata for pooled Caltech signals used in wgEncodeReg.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra
  • lines changed 1861, context: html, text, full: html, text
    Added expId's and dccAccessions to Broad Histone hg18 and hg19
  • lines changed 211, context: html, text, full: html, text
    Changed antibody=Control to the standard antibody=Input. Removed expIds and dccAccessions for those as well.
  • lines changed 91, context: html, text, full: html, text
    45 of 70 antobody=Input experiment objects got proper expId's matching hg18.
  • lines changed 41, context: html, text, full: html, text
    Revived the legitimate hg19 only antibody=Input experiments which had been screwed up by antibody=Control.
  • lines changed 11, context: html, text, full: html, text
    One more exp where antibody should not have been Control
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHmm.ra
  • lines changed 19, context: html, text, full: html, text
    Added expIds and dccAccessions for Broad HMM hg18 and hg19
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBuOrchid.ra
  • lines changed 5, context: html, text, full: html, text
    Added the ver first accession number and exp ID
  • lines changed 3, context: html, text, full: html, text
    Issue 1440 Note 15. I am changing to add fileSortOrder to display the new accession numbers for both hg18 and hg19.
  • lines changed 2, context: html, text, full: html, text
    fixed a weird error of expVars showing up in a table object
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 229, context: html, text, full: html, text
    Removed fileIndex and changed the Denovo and Exon to files not tables
  • lines changed 113, context: html, text, full: html, text
    Changed the TranscriptGencV3c from tables into files
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlShortRnaSeq.ra
  • lines changed 12, context: html, text, full: html, text
    Removed fileIndex from composites where it was only in some of the stanzas
  • lines changed 44, context: html, text, full: html, text
    Added attic=auxExp for auxillary experiments
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisDnaPet.ra
  • lines changed 7, context: html, text, full: html, text
    Removed fileIndex from composites where it was only in some of the stanzas
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaPet.ra
  • lines changed 3, context: html, text, full: html, text
    Removed fileIndex from composites where it was only in some of the stanzas
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisRnaSeq.ra
  • lines changed 5, context: html, text, full: html, text
    Removed fileIndex from composites where it was only in some of the stanzas
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylArray.ra
  • lines changed 147, context: html, text, full: html, text
    Changed the dataType to be MethylArray instead of Methyl27 and added labVersion to indicate that Methyl27 was used
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra
  • lines changed 107, context: html, text, full: html, text
    Hand changed the attic files that the renamer could not do so that growprot was not in the object name and that Yale became Stanford
  • lines changed 27, context: html, text, full: html, text
    2 more files renamed to add Duke, using renamer
  • lines changed 20, context: html, text, full: html, text
    Revoking labExpID SL941 as it should have been SL1914. Waiting for replacement data.
  • lines changed 448, context: html, text, full: html, text
    New submissions updated
  • lines changed 15, context: html, text, full: html, text
    Labeled with the attic=auxExp for auxiallary experminets
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylSeq.ra
  • lines changed 45, context: html, text, full: html, text
    Removed fileIndex from composites where it was only in some of the stanzas
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibRnaSeq.ra
  • lines changed 168, context: html, text, full: html, text
    Changed rnaExtract at request of the lab. Will need to run renamer
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 577, context: html, text, full: html, text
    This was a test of the renamer. There was a list of files to rename in issue 3011. Venkat should be asked to double check this check in.
  • lines changed 3, context: html, text, full: html, text
    Correct meta-data for fastq for Sl14 and SL167.
  • lines changed 25, context: html, text, full: html, text
    Updated protocol for wgEncodeHaibTfbsGm12892ControlV0416101AlnRep1 to match CV. Removed wgEncodeHaibTfbsGm12892ControlPcr1xAlnRep2 from submission 3877, which had wrong meta-data and was advised by lab they would like me to revoke.
  • lines changed 33, context: html, text, full: html, text
    Added 4 missing or updated files to complete experiments.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromChip.ra
  • lines changed 555, context: html, text, full: html, text
    Added expIds and dccAccessions for Open Chrom hg18 and hg19
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromDnase.ra
  • lines changed 657, context: html, text, full: html, text
    Added expIds and dccAccessions for Open Chrom hg18 and hg19
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeOpenChromFaire.ra
  • lines changed 363, context: html, text, full: html, text
    Added expIds and dccAccessions for Open Chrom hg18 and hg19
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeReg.ra
  • lines changed 154, context: html, text, full: html, text
    Adding metadata for pooled Caltech signals used in wgEncodeReg.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
  • lines changed 630, context: html, text, full: html, text
    Removed fileIndex from composites where it was only in some of the stanzas
  • lines changed 12, context: html, text, full: html, text
    added attic=auxExp for attic files
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyAlbanyGeneSt.ra
  • lines changed 97, context: html, text, full: html, text
    Issue 37, Note 48, Items: 8,9,10 and 17, as well as the addition of md5sums and the changing of dataType to GeneST, these changes are all being reviewed by Katrina
  • lines changed 49, context: html, text, full: html, text
    Issue 37, removing dccaccession and expId from mdb, adding clarifications in .html about the signal value and score, fixing ripInput to RIP-Input
  • lines changed 48, context: html, text, full: html, text
    Changed dataType GeneSt to RipGeneSt at request of CV maven
  • lines changed 24, context: html, text, full: html, text
    Issue 37 note 58 and 59, changed the dataType, updated the md5sums, fixed the greyValue by adding a min
  • lines changed 49, context: html, text, full: html, text
    The magic number is uptodate now
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyAlbanyTiling.ra
  • lines changed 9, context: html, text, full: html, text
    Changed datatype from RipChip to RipTiling
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra
  • lines changed 24, context: html, text, full: html, text
    Removed fileIndex reference from meta-data.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 267, context: html, text, full: html, text
    This was a test of the renamer. There was a list of files to rename in issue 3011. Venkat should be asked to double check this check in.
  • lines changed 445, context: html, text, full: html, text
    Removed fileIndex reference from meta-data.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUchicagoTfbs.ra
  • lines changed 276, context: html, text, full: html, text
    Input Control Replicate 1 was used as control for all Replicate 1's for each experiment. To correctly assign experiment Id's and groupings renamed the wgEncodeUchicagoTfbsK562InputControl*Rep1 files as wgEncodeUchicagoTfbsK562InputControlfos*Rep1. Then made symbolic links for all other experiments to wgEncodeUchicagoTfbsK562InputControlfos*Rep1 files following naming convention of inputs for replicate 2's. Added meta-data for this Rep1 input controls for each experiment. Also updated meta-data of control names for peaks and signals to explicitly state the control pairing used. Removed control as a sortable field in trackDb.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDgf.ra
  • lines changed 6, context: html, text, full: html, text
    Removed fileIndex reference from meta-data.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 77, context: html, text, full: html, text
    Removed fileIndex reference from meta-data.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUwTfbs.ra
  • lines changed 67, context: html, text, full: html, text
    Removed fileIndex reference from meta-data.
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/makefile
  • lines changed 1, context: html, text, full: html, text
    staging metaDb for BuOrchid, redmine #1440
  • lines changed 1, context: html, text, full: html, text
    staging Open Chrom Synth on beta, redmine #2881
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeBuOrchid.ra
  • lines changed 45, context: html, text, full: html, text
    staging metaDb for BuOrchid, redmine #1440
  • lines changed 4, context: html, text, full: html, text
    copied over new metaDb that contains the new accession stuff, redmine#1440 note-15
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeOpenChromSynth.ra
  • lines changed 132, context: html, text, full: html, text
    staging Open Chrom Synth on beta, redmine #2881
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 13, context: html, text, full: html, text
    Made snp131 hidden by default.
  • lines changed 1, context: html, text, full: html, text
    Fixed typo I made in last commit.
  • lines changed 11, context: html, text, full: html, text
    Fine tuned GERP track.
  • lines changed 6, context: html, text, full: html, text
    adding panTro3 into the primate chain/net for hg19
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    removed release tags from .ra file, staging on beta, redmine# 1440
  • lines changed 8, context: html, text, full: html, text
    Four composites which are released but need fileSortOrder update for dccAccession
  • lines changed 2, context: html, text, full: html, text
    Starting a Release 2 for Tiling
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.new.ra
  • lines changed 2767, context: html, text, full: html, text
    Four composites which are released but need fileSortOrder update for dccAccession
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHmm.ra
  • lines changed 1, context: html, text, full: html, text
    Updated fileSortOrder for dccAccession
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBuOrchid.html
  • lines changed 12, context: html, text, full: html, text
    alphabetized references, redmine# 1440
  • lines changed 12, context: html, text, full: html, text
    checking in this change again since I forgot to save :(, alphabetized references, redmine# 1440
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBuOrchid.ra
  • lines changed 2, context: html, text, full: html, text
    removed release tags from .ra file, staging on beta, redmine# 1440
  • lines changed 2, context: html, text, full: html, text
    Issue 1440 Note 15. I am changing to add fileSortOrder to display the new accession numbers for both hg18 and hg19.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.new.html
  • lines changed 99, context: html, text, full: html, text
    Merged Gingeras lab details with Hannon lab details
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.new.ra
  • lines changed 5, context: html, text, full: html, text
    Hand changed the attic files that the renamer could not do so that growprot was not in the object name and that Yale became Stanford
  • lines changed 4, context: html, text, full: html, text
    2 more files renamed to add Duke, using renamer
  • lines changed 81, context: html, text, full: html, text
    New submissions added
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.ra
  • lines changed 1, context: html, text, full: html, text
    Pulled new html from public
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra
  • lines changed 116, context: html, text, full: html, text
    This was a test of the renamer. There was a list of files to rename in issue 3011. Venkat should be asked to double check this check in.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.html
  • lines changed 4, context: html, text, full: html, text
    changing link to Duke DNaseI HS from preview because Vanessa released the track; also fixing wording for FAIRE link which I forogt to change when I changed the link for that track when it was released
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.new.ra
  • lines changed 1046, context: html, text, full: html, text
    Four composites which are released but need fileSortOrder update for dccAccession
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.new.ra
  • lines changed 1225, context: html, text, full: html, text
    Four composites which are released but need fileSortOrder update for dccAccession
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.html
  • lines changed 1, context: html, text, full: html, text
    made the link relative per Katrinas code review
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.new.ra
  • lines changed 695, context: html, text, full: html, text
    Four composites which are released but need fileSortOrder update for dccAccession
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.html
  • lines changed 16, context: html, text, full: html, text
    Added a validation level filter and changed coloring and wording to clarify the difference between OC code and validation level.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.ra
  • lines changed 8, context: html, text, full: html, text
    staging Open Chrom Synth on beta, redmine #2881
  • lines changed 24, context: html, text, full: html, text
    Added a validation level filter and changed coloring and wording to clarify the difference between OC code and validation level.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra
  • lines changed 11, context: html, text, full: html, text
    Taking configuration off of the short labels. Making table and track names match for the normalized tracks, since part of ENCODE metadata system depends on table being a track in some track.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.html
  • lines changed 6, context: html, text, full: html, text
    Issue 37, Note 48, Items: 8,9,10 and 17, as well as the addition of md5sums and the changing of dataType to GeneST, these changes are all being reviewed by Katrina
  • lines changed 57, context: html, text, full: html, text
    To be reviewed by Katrina. This is a major rewrite of the track description. It is in process
  • lines changed 4, context: html, text, full: html, text
    minor edits to new Methods section
  • lines changed 39, context: html, text, full: html, text
    Issue 37, removing dccaccession and expId from mdb, adding clarifications in .html about the signal value and score, fixing ripInput to RIP-Input
  • lines changed 5, context: html, text, full: html, text
    minor edits
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.ra
  • lines changed 6, context: html, text, full: html, text
    Issue 37, Note 48, Items: 8,9,10 and 17, as well as the addition of md5sums and the changing of dataType to GeneST, these changes are all being reviewed by Katrina
  • lines changed 1, context: html, text, full: html, text
    Issue 37, removing dccaccession and expId from mdb, adding clarifications in .html about the signal value and score, fixing ripInput to RIP-Input
  • lines changed 3, context: html, text, full: html, text
    Issue 37 note 58 and 59, changed the dataType, updated the md5sums, fixed the greyValue by adding a min
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyTiling.new.ra
  • lines changed 3, context: html, text, full: html, text
    Starting a Release 2 for Tiling
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhNsome.html
  • lines changed 49, context: html, text, full: html, text
    Added Display Conventions section. Updated contacts to be more inline with labs initial track description. Updated References to be link.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra
  • lines changed 76, context: html, text, full: html, text
    This was a test of the renamer. There was a list of files to rename in issue 3011. Venkat should be asked to double check this check in.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUchicagoTfbs.ra
  • lines changed 13, context: html, text, full: html, text
    Input Control Replicate 1 was used as control for all Replicate 1's for each experiment. To correctly assign experiment Id's and groupings renamed the wgEncodeUchicagoTfbsK562InputControl*Rep1 files as wgEncodeUchicagoTfbsK562InputControlfos*Rep1. Then made symbolic links for all other experiments to wgEncodeUchicagoTfbsK562InputControlfos*Rep1 files following naming convention of inputs for replicate 2's. Added meta-data for this Rep1 input controls for each experiment. Also updated meta-data of control names for peaks and signals to explicitly state the control pairing used. Removed control as a sortable field in trackDb.
• src/hg/makeDb/trackDb/human/iscaRetrospective.html
  • lines changed 2, context: html, text, full: html, text
    removed specific lab names at request of isca
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 6, context: html, text, full: html, text
    Track #34 (dbVar): Added search spec for iscaRetrospective. Its termRegex can be used for any dbVar tracks.
• src/hg/makeDb/trackDb/lizard/anoCar2/description.html
  • lines changed 16, context: html, text, full: html, text
    update assembly details
  • lines changed 2, context: html, text, full: html, text
    add comment about microchromosomes
• src/hg/makeDb/trackDb/marmoset/calJac3/cons13way.html
  • lines changed 1, context: html, text, full: html, text
    gorGor is using Syntenic Net
• src/hg/makeDb/trackDb/mouse/mm9/allMm9RS_BW.html
  • lines changed 71, context: html, text, full: html, text
    Created allMm9RS_BW.html.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra
  • lines changed 194, context: html, text, full: html, text
    Added submissoin 3920 and 3921. Sub 3921 replaced 3275.
  • lines changed 261, context: html, text, full: html, text
    Added missing input signals for Heart and Kidney.
  • lines changed 287, context: html, text, full: html, text
    Added Lung experiments.
  • lines changed 287, context: html, text, full: html, text
    Added CTCF and input experiments for Liver.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhHistone.ra
  • lines changed 4, context: html, text, full: html, text
    Removed fileIndex reference from meta-data.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 293, context: html, text, full: html, text
    More renamer work. The list is in Bug3011 in the MM9 file. Venkat should check off on this change
  • lines changed 24, context: html, text, full: html, text
    Removed fileIndex reference from meta-data.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra
  • lines changed 2, context: html, text, full: html, text
    Fixed term error: 0 adult-8wks to be age adult-8wks.
  • lines changed 12, context: html, text, full: html, text
    Removed fileIndex, as this metaData var is being phased out.
  • lines changed 1322, context: html, text, full: html, text
    Add 12 submissions. Some were attic that I currently handheld into the proper metadata and handling in trackDb.
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
  • lines changed 9, context: html, text, full: html, text
    Fine tuned GERP track.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.ra
  • lines changed 10, context: html, text, full: html, text
    Added submissoin 3920 and 3921. Sub 3921 replaced 3275.
  • lines changed 18, context: html, text, full: html, text
    Added missing input signals for Heart and Kidney.
  • lines changed 27, context: html, text, full: html, text
    Added Lung experiments forgot the trackDb.ra
  • lines changed 27, context: html, text, full: html, text
    Added CTCF and input experiments for Liver.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.newR2.ra
  • lines changed 20, context: html, text, full: html, text
    More renamer work. The list is in Bug3011 in the MM9 file. Venkat should check off on this change
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.ra
  • lines changed 342, context: html, text, full: html, text
    Add 12 submissions. Some were attic that I currently handheld into the proper metadata and handling in trackDb.
  • lines changed 1, context: html, text, full: html, text
    Added fileSortOrder in trackDb to display new downlaods page.
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Turning off snp131 by default. For real this time.
• src/hg/makeDb/trackDb/zebrafish/danRer5/UMassChIP-SeqSuper.html
  • lines changed 1, context: html, text, full: html, text
    "Trying git commit to get rid of symbolic links."
• src/hg/makeDb/trackDb/zebrafish/danRer5/UMassInput.html
  • lines changed 1, context: html, text, full: html, text
    "Trying git commit to get rid of symbolic links."
• src/hg/makeDb/trackDb/zebrafish/danRer5/UMassME1.html
  • lines changed 1, context: html, text, full: html, text
    "Trying git commit to get rid of symbolic links."
• src/hg/makeDb/trackDb/zebrafish/danRer5/UMassME1Hotspot.html
  • lines changed 1, context: html, text, full: html, text
    "Trying git commit to get rid of symbolic links."
• src/hg/makeDb/trackDb/zebrafish/danRer5/UMassME1Peak.html
  • lines changed 1, context: html, text, full: html, text
    "Trying git commit to get rid of symbolic links."
• src/hg/makeDb/trackDb/zebrafish/danRer5/UMassME3.html
  • lines changed 1, context: html, text, full: html, text
    "Trying git commit to get rid of symbolic links."
• src/hg/makeDb/trackDb/zebrafish/danRer5/UMassME3Hotspot.html
  • lines changed 1, context: html, text, full: html, text
    "Trying git commit to get rid of symbolic links."
• src/hg/makeDb/trackDb/zebrafish/danRer5/UMassME3Peak.html
  • lines changed 1, context: html, text, full: html, text
    "Trying git commit to get rid of symbolic links."
• src/hg/makeDb/trackDb/zebrafish/danRer7/UMassChIP-Seq.html
  • lines changed 31, context: html, text, full: html, text
    Created UMassChIP-Seq.html.
• src/hg/makeDb/trackDb/zebrafish/danRer7/trackDb.ra
  • lines changed 91, context: html, text, full: html, text
    Added U Mass ChIP-Seq tracks.
• src/hg/oneShot/freen/freen.c
  • lines changed 6, context: html, text, full: html, text
    Freen tests timing of opening files.
• src/hg/oneShot/wgEncodeRegGenRa/wgEncodeRegGenRa.c
  • lines changed 14, context: html, text, full: html, text
    Adding a few more histone marks and a scale.
• src/hg/regulate/companion/regCompanion5C/makefile
  • lines changed 18, context: html, text, full: html, text
    Starting on program to work with 5C data. Seems to read in matrix file ok now.
• src/hg/regulate/companion/regCompanion5C/regCompanion5C.c
  • lines changed 213, context: html, text, full: html, text
    Starting on program to work with 5C data. Seems to read in matrix file ok now.
  • lines changed 58, context: html, text, full: html, text
    Making it produce a bed file with all the same-chromosome pairs over threshold.
  • lines changed 2, context: html, text, full: html, text
    Very minor tweaks.
• src/hg/regulate/companion/regCompanionChia/regCompanionChia.c
  • lines changed 17, context: html, text, full: html, text
    Moving one of the hardcoded files to the command line.
• src/hg/regulate/companion/regCompanionPickEnhancers/regCompanionPickEnhancers.c
  • lines changed 116, context: html, text, full: html, text
    Adding a proper score field from enhancer pick rather than just passing on DNAse score.
• src/hg/regulate/regBeadPos/makefile
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    Starting to work on a HMM that positions DNAse relative to a histone
• src/hg/regulate/regBeadPos/regBeadPos.c
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    Starting to work on a HMM that positions DNAse relative to a histone
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    Manages to produce completely incorrect output without crashing.
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    Seems to emit something worth converting to bed at any rate.
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    Refactoring towards making bed output possible.
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    Did a bunch of testing. Seems to work.
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    Constant tweaking of parameters by hand. Probably best to call it good enough.
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    Added capability to output summaries along most likely path and use this to define emission probs. Simplified model just to allow low state, or DNAse flaked by histone.
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    Making HMM model simpler and adding some new output types.
• src/hg/regulate/regBeadPos/test.csh
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    Did a bunch of testing. Seems to work.
  • lines changed 2, context: html, text, full: html, text
    Added capability to output summaries along most likely path and use this to define emission probs. Simplified model just to allow low state, or DNAse flaked by histone.
  • lines changed 1, context: html, text, full: html, text
    Making HMM model simpler and adding some new output types.
• src/hg/regulate/regBeadPos/test.in
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    Did a bunch of testing. Seems to work.
• src/hg/txGraph/txWalk/txWalk.c
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    Added rfam and trna to the expected accessions
• src/hg/utils/automation/EnsGeneAutomate.pm
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    adding v62 definitions
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    fix incorrect name for ensGeneFtpMySqlFileNames_62
• src/hg/utils/automation/unigene.csh
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    Script to check for uniGene updates. Inherited from Angie. (redmine #2047)
• src/inc/genoFind.h
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    blat segfault fix for maxIntron <= 11 when tileSize <= 11
• src/jkOwnLib/ffAliHelp.c
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    blat segfault fix for maxIntron <= 11 when tileSize <= 11
• src/jkOwnLib/supStitch.c
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    blat segfault fix for maxIntron <= 11 when tileSize <= 11
• src/lib/common.c
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    make slPairListFromString handle "=" inside names(when quoted) and values
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    adding tolerance of leading spaces as required by a few naughty trackDb.ra files
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    startsWithWordByDelimit failed when the line only contained the word.
• src/lib/htmshell.c
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    Checking in CGI usage of DOCTYPE 4.01 Transitional (instead of 3.2). Also removed some minor FONT tags that should be replaced by CSS.
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    Need the 'f' param for fput.
• src/lib/ra.c
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    Changed a wrong comment that Angie pointed out.
• src/lib/seqOut.c
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    Insignificant change from FONT tags to CSS.
• src/lib/udc.c
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    Streamlining transparent case a little.
• src/utils/bedGeneParts/bedGeneParts.c
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    Adding missing quotes to usage statement.
• src/utils/bigWigMerge/bigWigMerge.c
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    Adding clipping options.
• src/utils/makefile
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    Adding test to makefile.
• src/utils/qa/weeklybld/buildEnv.csh
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    v251 preview1
• src/utils/wigCorrelate/wigCorrelate.c
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    Removing commented out line of code.

• lines changed: 31766
• files changed: 321