All File Changes

v248_preview2 to v248_base (2011-03-01 to 2011-03-08) v248

• python/ucscgenomics/rafile/.read.py.swp
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    removed junk files from ucscgenomics/rafile/
• python/ucscgenomics/rafile/orderedDict.py
  • lines changed 87, context: html, text, full: html, text
    new versions of raFile.py and orderedDict.py, both more generalized and conforming to standards
• python/ucscgenomics/rafile/raEntry.py
  • lines changed 34, context: html, text, full: html, text
    new versions of raFile.py and orderedDict.py, both more generalized and conforming to standards
• python/ucscgenomics/rafile/raFile.py
  • lines changed 76, context: html, text, full: html, text
    new versions of raFile.py and orderedDict.py, both more generalized and conforming to standards
• python/ucscgenomics/rafile/radict.pyc
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    removed all junk files from ucscgenomics/rafile/
• python/ucscgenomics/rafile/read.py
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    removed junk files from ucscgenomics/rafile/
• python/ucscgenomics/rafile/testinput
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    removed junk files from ucscgenomics/rafile/
• python/ucscgenomics/rafile/write.py
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    removed junk files from ucscgenomics/rafile/
• src/hg/autoSql/tests/makefile
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    Feature #2820 ((tabix: add as optional linked library in kent/src):one last makefile target that wasn't using ${L}, caught by 'make test'.
• src/hg/encode/DAFs/2.0/caltechElements.daf
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    Added 2 more elements views
• src/hg/encode/DAFs/2.0/uncBsuProt.daf
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    Changed the capitalization of the composite suffix to be consistent with other ENCODE tracks
• src/hg/hgTables/bam.c
  • lines changed 6, context: html, text, full: html, text
    fix some problems with BAM support. Actually look at id's for filtering, and disable subtrack merge.
• src/hg/hgTables/mainPage.c
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    fix some problems with BAM support. Actually look at id's for filtering, and disable subtrack merge.
• src/hg/hgTracks/bigWarn.c
  • lines changed 7, context: html, text, full: html, text
    minor change to bigWarnNumLines() to use an existing lib function
• src/hg/hgTracks/hgTracks.c
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    Add NEW_JQUERY code for jQuery upgrade (currently a work in progress)
• src/hg/hgTracks/simpleTracks.c
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    track-handling code for ENCODE peptideMapping tracks
  • lines changed 62, context: html, text, full: html, text
    Enabling next/prev-exon arrows for DECIPHER track at b0b's request.Those arrows are implemented for linkedFeatures, so I convert the bed4 DECIPHER items into linkedFeatures during loading, and use lf->extra to store the phenotypes string used in draw and mapItems.
• src/hg/hgc/encodeClick.c
  • lines changed 55, context: html, text, full: html, text
    track-handling code for ENCODE peptideMapping tracks
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    Reordering the details a bit
• src/hg/hgc/hgc.c
  • lines changed 4, context: html, text, full: html, text
    track-handling code for ENCODE peptideMapping tracks
• src/hg/hgc/hgc.h
  • lines changed 3, context: html, text, full: html, text
    track-handling code for ENCODE peptideMapping tracks
• src/hg/htdocs/ENCODE/index.html
  • lines changed 2, context: html, text, full: html, text
    Fix year on latest news items
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 13, context: html, text, full: html, text
    Added some info from panTro3 release.
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 99, context: html, text, full: html, text
    Archived a few items, created a new 2011 section.
  • lines changed 94, context: html, text, full: html, text
    added announcement for color-scheme change in DGV and DECIPHER
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    modified a senetence for clarity
• src/hg/htdocs/images/Meleagris_gallopavo.jpg
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    Add picture of Turkey
• src/hg/htdocs/images/folderC.png
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    Thought this one was already checked in.
• src/hg/htdocs/indexNews.html
  • lines changed 106, context: html, text, full: html, text
    Added news item about panTro3, archived some other items.
  • lines changed 3, context: html, text, full: html, text
    Added italics.
  • lines changed 35, context: html, text, full: html, text
    added announcement for color-scheme change in DGV and DECIPHER
  • lines changed 2, context: html, text, full: html, text
    modified a senetence for clarity
  • lines changed 1, context: html, text, full: html, text
    correct typo found by Heather!
• src/hg/htdocs/style/jquery.ui.autocomplete.css
  • lines changed 58, context: html, text, full: html, text
    css file from jQuery UI 1.8.10
• src/hg/inc/mdb.h
  • lines changed 25, context: html, text, full: html, text
    Removed unused 'varType'. Changed longblob to varchar(2084). Changed the recreate load object to print to a temp file and use mysql 'LOAD DATA' command. Made secondary key non-unique and use disable/enable keys to speed up load.
• src/hg/inc/versionInfo.h
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    New version number v248
• src/hg/js/autocomplete.js
  • lines changed 5, context: html, text, full: html, text
    use built-in autocomplete if newJQuery is true
• src/hg/js/hgTracks.js
  • lines changed 63, context: html, text, full: html, text
    make right-click highlight found item in hgTracks (redmine 3062); also includes some code to handle transition to new jQuery libraries (currently dead code)
  • lines changed 5, context: html, text, full: html, text
    use built-in autocomplete if newJQuery is true
• src/hg/lib/mdb.c
  • lines changed 11, context: html, text, full: html, text
    Back out change to one function which introduced a bug
  • lines changed 196, context: html, text, full: html, text
    Removed unused 'varType'. Changed longblob to varchar(2084). Changed the recreate load object to print to a temp file and use mysql 'LOAD DATA' command. Made secondary key non-unique and use disable/enable keys to speed up load.
  • lines changed 22, context: html, text, full: html, text
    Temporarily adding varType back into table definition. This should smoothe the transition of the CGIs, etc. until the non-varType APIs are fully out on the RR.
• src/hg/lib/omimAv.sql
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    Created omimAv.sql.
• src/hg/lib/trackDbCustom.c
  • lines changed 1, context: html, text, full: html, text
    track-handling code for ENCODE peptideMapping tracks
• src/hg/makeDb/doc/encodeDccMm9/wgEncodePsuHistone.release1.notes
  • lines changed 92, context: html, text, full: html, text
    Added release notes for PSU mm9 tracks.
• src/hg/makeDb/doc/encodeDccMm9/wgEncodePsuTfbs.release1.notes
  • lines changed 121, context: html, text, full: html, text
    Added release notes for PSU mm9 tracks.
• src/hg/makeDb/doc/hg18.txt
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    Track #1656 (GWAS Catalog): monthly data update on hgwdev.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 12, context: html, text, full: html, text
    Additions to coverage track lift.
  • lines changed 3, context: html, text, full: html, text
    Track #1656 (GWAS Catalog): monthly data update on hgwdev.
  • lines changed 31, context: html, text, full: html, text
    add TFBS track from matt. Yay Matt!!!
• src/hg/makeDb/doc/mm9.txt
  • lines changed 4, context: html, text, full: html, text
    Working on some mm9 ucscGenes issues from Pauline, related to redmine issue 2682. Commented out some Robert Baertsch retroGene stuff from all.joiner that was never made public, and had fallen out of date. Regenerating some tables with time stamps that are off.
  • lines changed 2, context: html, text, full: html, text
    Fixing typo that caused an old version of the ucsc gene alignment table to be loaded.
• src/hg/makeDb/doc/panTro3.txt
  • lines changed 11, context: html, text, full: html, text
    danRer7 lastz done
  • lines changed 169, context: html, text, full: html, text
    failed Human Proteins track. Just can't chain for closely related organisms.
• src/hg/makeDb/doc/ucscGenes/mm9.ucscGenes12.csh
  • lines changed 22, context: html, text, full: html, text
    Fixed taxon human/mouse mixup. Have to rerun the whole thing now though! Also fixed missing knownToSnpCds table.
• src/hg/makeDb/genbank/common.mk
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    add hash table stats dump
  • lines changed 3, context: html, text, full: html, text
    Revert "add hash table stats dump" This reverts commit 58672666e0eb7000c5bf20dd34c86728e3e243d3. didn't want this just yet
  • lines changed 3, context: html, text, full: html, text
    improve performance of genbank alignments by adjusting size of some hash tables and making some of them more specialized. Generally trading off initializing a large hash table for a short lived program with has collisions
• src/hg/makeDb/genbank/etc/rr.dbs
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    added panTro3 to the list to start daily genbank updates
• src/hg/makeDb/genbank/src/align/gbAlignSetup
  • lines changed 1, context: html, text, full: html, text
    add hash table stats dump
  • lines changed 1, context: html, text, full: html, text
    Revert "add hash table stats dump" This reverts commit 58672666e0eb7000c5bf20dd34c86728e3e243d3. didn't want this just yet
  • lines changed 1, context: html, text, full: html, text
    improve performance of genbank alignments by adjusting size of some hash tables and making some of them more specialized. Generally trading off initializing a large hash table for a short lived program with has collisions
• src/hg/makeDb/genbank/src/dbload/gbBuildState.c
  • lines changed 6, context: html, text, full: html, text
    add hash table stats dump
  • lines changed 6, context: html, text, full: html, text
    Revert "add hash table stats dump" This reverts commit 58672666e0eb7000c5bf20dd34c86728e3e243d3. didn't want this just yet
  • lines changed 6, context: html, text, full: html, text
    improve performance of genbank alignments by adjusting size of some hash tables and making some of them more specialized. Generally trading off initializing a large hash table for a short lived program with has collisions
• src/hg/makeDb/genbank/src/dbload/gbIgnoreDelete.c
  • lines changed 1, context: html, text, full: html, text
    improve performance of genbank alignments by adjusting size of some hash tables and making some of them more specialized. Generally trading off initializing a large hash table for a short lived program with has collisions
• src/hg/makeDb/genbank/src/dbload/gbMDParse.c
  • lines changed 6, context: html, text, full: html, text
    add hash table stats dump
  • lines changed 6, context: html, text, full: html, text
    Revert "add hash table stats dump" This reverts commit 58672666e0eb7000c5bf20dd34c86728e3e243d3. didn't want this just yet
  • lines changed 6, context: html, text, full: html, text
    improve performance of genbank alignments by adjusting size of some hash tables and making some of them more specialized. Generally trading off initializing a large hash table for a short lived program with has collisions
• src/hg/makeDb/genbank/src/extFileUpdate/raInfoTbl.c
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    add hash table stats dump
  • lines changed 3, context: html, text, full: html, text
    Revert "add hash table stats dump" This reverts commit 58672666e0eb7000c5bf20dd34c86728e3e243d3. didn't want this just yet
  • lines changed 3, context: html, text, full: html, text
    improve performance of genbank alignments by adjusting size of some hash tables and making some of them more specialized. Generally trading off initializing a large hash table for a short lived program with has collisions
• src/hg/makeDb/genbank/src/gbConf/gbConf.c
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    add hash table stats dump
  • lines changed 3, context: html, text, full: html, text
    Revert "add hash table stats dump" This reverts commit 58672666e0eb7000c5bf20dd34c86728e3e243d3. didn't want this just yet
  • lines changed 3, context: html, text, full: html, text
    improve performance of genbank alignments by adjusting size of some hash tables and making some of them more specialized. Generally trading off initializing a large hash table for a short lived program with has collisions
• src/hg/makeDb/genbank/src/inc/gbIgnore.h
  • lines changed 8, context: html, text, full: html, text
    improve performance of genbank alignments by adjusting size of some hash tables and making some of them more specialized. Generally trading off initializing a large hash table for a short lived program with has collisions
• src/hg/makeDb/genbank/src/inc/gbRelease.h
  • lines changed 14, context: html, text, full: html, text
    improve performance of genbank alignments by adjusting size of some hash tables and making some of them more specialized. Generally trading off initializing a large hash table for a short lived program with has collisions
• src/hg/makeDb/genbank/src/inc/gbUpdate.h
  • lines changed 3, context: html, text, full: html, text
    improve performance of genbank alignments by adjusting size of some hash tables and making some of them more specialized. Generally trading off initializing a large hash table for a short lived program with has collisions
• src/hg/makeDb/genbank/src/lib/extFileTbl.c
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    add hash table stats dump
  • lines changed 4, context: html, text, full: html, text
    Revert "add hash table stats dump" This reverts commit 58672666e0eb7000c5bf20dd34c86728e3e243d3. didn't want this just yet
  • lines changed 4, context: html, text, full: html, text
    improve performance of genbank alignments by adjusting size of some hash tables and making some of them more specialized. Generally trading off initializing a large hash table for a short lived program with has collisions
• src/hg/makeDb/genbank/src/lib/gbConf.c
  • lines changed 3, context: html, text, full: html, text
    add hash table stats dump
  • lines changed 3, context: html, text, full: html, text
    Revert "add hash table stats dump" This reverts commit 58672666e0eb7000c5bf20dd34c86728e3e243d3. didn't want this just yet
  • lines changed 3, context: html, text, full: html, text
    improve performance of genbank alignments by adjusting size of some hash tables and making some of them more specialized. Generally trading off initializing a large hash table for a short lived program with has collisions
• src/hg/makeDb/genbank/src/lib/gbIgnore.c
  • lines changed 4, context: html, text, full: html, text
    add hash table stats dump
  • lines changed 4, context: html, text, full: html, text
    Revert "add hash table stats dump" This reverts commit 58672666e0eb7000c5bf20dd34c86728e3e243d3. didn't want this just yet
  • lines changed 42, context: html, text, full: html, text
    improve performance of genbank alignments by adjusting size of some hash tables and making some of them more specialized. Generally trading off initializing a large hash table for a short lived program with has collisions
• src/hg/makeDb/genbank/src/lib/gbLoadedTbl.c
  • lines changed 4, context: html, text, full: html, text
    add hash table stats dump
  • lines changed 4, context: html, text, full: html, text
    Revert "add hash table stats dump" This reverts commit 58672666e0eb7000c5bf20dd34c86728e3e243d3. didn't want this just yet
  • lines changed 4, context: html, text, full: html, text
    improve performance of genbank alignments by adjusting size of some hash tables and making some of them more specialized. Generally trading off initializing a large hash table for a short lived program with has collisions
• src/hg/makeDb/genbank/src/lib/gbProcessed.c
  • lines changed 1, context: html, text, full: html, text
    improve performance of genbank alignments by adjusting size of some hash tables and making some of them more specialized. Generally trading off initializing a large hash table for a short lived program with has collisions
• src/hg/makeDb/genbank/src/lib/gbRelease.c
  • lines changed 18, context: html, text, full: html, text
    add hash table stats dump
  • lines changed 18, context: html, text, full: html, text
    Revert "add hash table stats dump" This reverts commit 58672666e0eb7000c5bf20dd34c86728e3e243d3. didn't want this just yet
  • lines changed 37, context: html, text, full: html, text
    improve performance of genbank alignments by adjusting size of some hash tables and making some of them more specialized. Generally trading off initializing a large hash table for a short lived program with has collisions
• src/hg/makeDb/genbank/src/lib/gbStatusTbl.c
  • lines changed 4, context: html, text, full: html, text
    add hash table stats dump
  • lines changed 4, context: html, text, full: html, text
    Revert "add hash table stats dump" This reverts commit 58672666e0eb7000c5bf20dd34c86728e3e243d3. didn't want this just yet
  • lines changed 4, context: html, text, full: html, text
    improve performance of genbank alignments by adjusting size of some hash tables and making some of them more specialized. Generally trading off initializing a large hash table for a short lived program with has collisions
• src/hg/makeDb/genbank/src/lib/gbUpdate.c
  • lines changed 16, context: html, text, full: html, text
    improve performance of genbank alignments by adjusting size of some hash tables and making some of them more specialized. Generally trading off initializing a large hash table for a short lived program with has collisions
• src/hg/makeDb/genbank/src/lib/uniqueStrTbl.c
  • lines changed 3, context: html, text, full: html, text
    add hash table stats dump
  • lines changed 3, context: html, text, full: html, text
    Revert "add hash table stats dump" This reverts commit 58672666e0eb7000c5bf20dd34c86728e3e243d3. didn't want this just yet
  • lines changed 3, context: html, text, full: html, text
    improve performance of genbank alignments by adjusting size of some hash tables and making some of them more specialized. Generally trading off initializing a large hash table for a short lived program with has collisions
• src/hg/makeDb/genbank/src/orfeome/orfeomeDbLoad.c
  • lines changed 3, context: html, text, full: html, text
    add hash table stats dump
  • lines changed 3, context: html, text, full: html, text
    Revert "add hash table stats dump" This reverts commit 58672666e0eb7000c5bf20dd34c86728e3e243d3. didn't want this just yet
  • lines changed 3, context: html, text, full: html, text
    improve performance of genbank alignments by adjusting size of some hash tables and making some of them more specialized. Generally trading off initializing a large hash table for a short lived program with has collisions
• src/hg/makeDb/genbank/src/repair/refPepRepair.c
  • lines changed 4, context: html, text, full: html, text
    add hash table stats dump
  • lines changed 4, context: html, text, full: html, text
    Revert "add hash table stats dump" This reverts commit 58672666e0eb7000c5bf20dd34c86728e3e243d3. didn't want this just yet
  • lines changed 4, context: html, text, full: html, text
    improve performance of genbank alignments by adjusting size of some hash tables and making some of them more specialized. Generally trading off initializing a large hash table for a short lived program with has collisions
• src/hg/makeDb/hgTrackDb/hgTrackDb.c
  • lines changed 47, context: html, text, full: html, text
    hgTrackDb now supports an SSI-like syntax for track .html files toinsert the contents of other files, so multiple tracks' html files can share text: <!-- #insert file="relativePathToSharedText.html" --> And the snp132* tracks (#1684) now use this: the shared description text is in snp132.shared.html, and the four track .htmls all use the new syntax to insert the shared text.
• src/hg/makeDb/mdbUpdate/mdbUpdate.c
  • lines changed 15, context: html, text, full: html, text
    Removed unused 'varType'. Changed longblob to varchar(2084). Changed the recreate load object to print to a temp file and use mysql 'LOAD DATA' command. Made secondary key non-unique and use disable/enable keys to speed up load.
• src/hg/makeDb/schema/all.joiner
  • lines changed 14, context: html, text, full: html, text
    Working on some mm9 ucscGenes issues from Pauline, related to redmine issue 2682. Commented out some Robert Baertsch retroGene stuff from all.joiner that was never made public, and had fallen out of date. Regenerating some tables with time stamps that are off.
  • lines changed 7, context: html, text, full: html, text
    Moved ccds item in ensembl rule into its own stanza see redmine 2682, note 17
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    Made the transMapGeneUcscGenesId identifier fuzzy, since the transMap table covers known genes for all assemblies, and you can't really express this in all.joiner precisely, but it is still worthwhile to join on that column.
  • lines changed 4, context: html, text, full: html, text
    Making all.joiner tolerate empty UniProt fields in some UCSC genes related tables.
• src/hg/makeDb/schema/joinTwoInfo/joinTwoInfo.c
  • lines changed 105, context: html, text, full: html, text
    Added new utility to check if two columns look joinable in a database.
  • lines changed 24, context: html, text, full: html, text
    Adding count of unique overlapping fields.
• src/hg/makeDb/schema/joinTwoInfo/makefile
  • lines changed 18, context: html, text, full: html, text
    Added new utility to check if two columns look joinable in a database.
• src/hg/makeDb/trackDb/README
  • lines changed 14, context: html, text, full: html, text
    Added description of hgTrackDb's new support for #insert'ing a file'scontents (git show b9b57796) into track .html files to trackDb/README.
• src/hg/makeDb/trackDb/chimp/panTro3/description.html
  • lines changed 80, context: html, text, full: html, text
    Edited and updated this file.
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 17, context: html, text, full: html, text
    Removed duplication of MAX and MAX_(C-17). Sunseted MAX_(C-17) as no lab has used this distinction.
  • lines changed 10, context: html, text, full: html, text
    Added 5 cell growth protocols provided by UW (Stam lab).
  • lines changed 15, context: html, text, full: html, text
    Updated a host of Myers lab antibody validation documents
  • lines changed 9, context: html, text, full: html, text
    Changed remining searchable 'select's to 'multiSelect's as per Katrina's QA request for regularity
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    Changing things so that replicates 3 and 4 are labeled 1 and 2 and the generation 0 data that has no replicate will now be labeled 1. Added a ddcRep field to the CV so that we can track where our replicates vary from the lab, this could have been done with labRep
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    Changed the last bits of metaData to have now two replicates, the lab replicate and the dccRep, changed the cv.ra to prioritize this dccRep the same as replicate, introduced a bug in that the replicate numbers now click through to tier numbers, will talk to Tim
  • lines changed 2, context: html, text, full: html, text
    G1E-E4+E2 Should be G1E-ER4+E2 . Fixed redmine issue 3508.
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    dccRep is not CV defined and needed to be noted in both files
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    Changed the labels for dccRep to UCSC Rep and UCSC replicate number
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    Fixed missing commit for 27f5162ffb937de52f5b234a24d9b6cc4e42cc2b. Updated unit spacing to be consistent with rest of browswer. Issue 59, note 30.
  • lines changed 24, context: html, text, full: html, text
    Added one new cell line and several links to the White lab antibody validation document (which includes validation for several different antibodies
  • lines changed 1, context: html, text, full: html, text
    Updated description of the H3K79me2 description.
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    This addresses many things in Issue#1664 Note #14, including adding the view capability back into the track
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    Renamed the G1E-E4+E2 mouse cell line to G1E-ER4+E2, at request of Venkat for the Hardison lab
• src/hg/makeDb/trackDb/cv/public/cv.ra
  • lines changed 91, context: html, text, full: html, text
    releasing approved cv.ra changes to public
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    backing out multiSelect from public because CGIs to support it aren't out yet. Not changing beta, once CGIs released, I will copy beta over public and release again
• src/hg/makeDb/trackDb/human/decipher.html
  • lines changed 2, context: html, text, full: html, text
    added comment about when color scheme changed
• src/hg/makeDb/trackDb/human/dgv.html
  • lines changed 1, context: html, text, full: html, text
    added comment about when color scheme changed
• src/hg/makeDb/trackDb/human/dgvOldColors.html
  • lines changed 77, context: html, text, full: html, text
    Bug #2917 (DGV colors need changing): oops, I let the new descriptionsneak out to the RR before the track! Adding the old description back for beta,public versions. It should be removed again when we push v10.
• src/hg/makeDb/trackDb/human/encodeBu_ORChID1.html
  • lines changed 5, context: html, text, full: html, text
    Fixed link and updated description as requested by Tom Tullius
• src/hg/makeDb/trackDb/human/encodeEgaspSuper.html
  • lines changed 1, context: html, text, full: html, text
    Fixed broken link for Nineteen additional unpredicted transcripts article
• src/hg/makeDb/trackDb/human/encodeStanfordChip.html
  • lines changed 3, context: html, text, full: html, text
    Fixed link for Meyer Lab website
• src/hg/makeDb/trackDb/human/encodeStanfordChipSmoothed.html
  • lines changed 3, context: html, text, full: html, text
    Fixed link to Myer Lab
• src/hg/makeDb/trackDb/human/encodeStanfordChipSuper.html
  • lines changed 2, context: html, text, full: html, text
    Fixed link for Meyer Lab
• src/hg/makeDb/trackDb/human/encodeStanfordPromoters.html
  • lines changed 4, context: html, text, full: html, text
    Fixed link to Myer Lab
  • lines changed 1, context: html, text, full: html, text
    Removed extra period after HudsonAlpha link
• src/hg/makeDb/trackDb/human/encodeStanfordRtPcr.html
  • lines changed 3, context: html, text, full: html, text
    Fixed link for Meyer Lab
• src/hg/makeDb/trackDb/human/hg18/encodeBUORChID.html
  • lines changed 6, context: html, text, full: html, text
    Fixed link and updated description as requested by Tom Tullius
• src/hg/makeDb/trackDb/human/hg18/encodeNhgriDukeDnaseHs.html
  • lines changed 1, context: html, text, full: html, text
    Fixed broken link for McArthur article
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • lines changed 12, context: html, text, full: html, text
    make al 4 NumtS trables searchable using regex HSA_NumtS_
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadHmm.html
  • lines changed 2, context: html, text, full: html, text
    Removing max-width=900 by Katrina's request.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 8457, context: html, text, full: html, text
    Updated and printed mdb, removed post from freeze
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisChiaPet.ra
  • lines changed 193, context: html, text, full: html, text
    This addresses many things in Issue#1664 Note #14, including adding the view capability back into the track
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra
  • lines changed 206, context: html, text, full: html, text
    Added accession numbers
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 3395, context: html, text, full: html, text
    First pass removal of 143 files (9 files are suspect due to meta-data inconsistenties, waiting on lab for proper procedure)
  • lines changed 49, context: html, text, full: html, text
    Removed reference to 7 files in metaDb and trackDb. Restored 2 files fully in browser.
  • lines changed 3259, context: html, text, full: html, text
    Moved 137 files that had meta-data problems that will be replaced.
  • lines changed 23, context: html, text, full: html, text
    Added meta-data for missing fastq in submission 3108.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRikenCage.ra
  • lines changed 112, context: html, text, full: html, text
    Added missing bioRep info
  • lines changed 250, context: html, text, full: html, text
    Changing things so that replicates 3 and 4 are labeled 1 and 2 and the generation 0 data that has no replicate will now be labeled 1. Added a ddcRep field to the CV so that we can track where our replicates vary from the lab, this could have been done with labRep
  • lines changed 79, context: html, text, full: html, text
    Changed the last bits of metaData to have now two replicates, the lab replicate and the dccRep, changed the cv.ra to prioritize this dccRep the same as replicate, introduced a bug in that the replicate numbers now click through to tier numbers, will talk to Tim
  • lines changed 862, context: html, text, full: html, text
    undo the mistake of committing a mdb file over trackDb file
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhHistone.ra
  • lines changed 353, context: html, text, full: html, text
    Changed H3K4me3 -> H3K4me3B antibody variant.
  • lines changed 353, context: html, text, full: html, text
    Fixed object and table names that had H3K4me3b instead of H3k4me3b.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra
  • lines changed 22, context: html, text, full: html, text
    Removed extra meta-data for obj wgEncodeSydhTfbsHuvecInputUcdAln in metaDb.ra file.
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeRikenCage.ra
  • lines changed 664, context: html, text, full: html, text
    restaging updated metadata, redmine #41, note# 60
  • lines changed 250, context: html, text, full: html, text
    updating the metaDb on hgwbeta, redmine issue #41, note #64
• src/hg/makeDb/trackDb/human/hg19/omimAvSnp.html
  • lines changed 14, context: html, text, full: html, text
    polished up the text a bit
• src/hg/makeDb/trackDb/human/hg19/omimGeneClass3.html
  • lines changed 19, context: html, text, full: html, text
    wordsmithing
  • lines changed 3, context: html, text, full: html, text
    small wordsmithing
  • lines changed 11, context: html, text, full: html, text
    clarified the method a bit, and moved some method-y text from description to Methods
• src/hg/makeDb/trackDb/human/hg19/omimLocation.html
  • lines changed 1, context: html, text, full: html, text
    tiny tweak
  • lines changed 1, context: html, text, full: html, text
    added a bit more explanation of gray color
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 3, context: html, text, full: html, text
    Changed labels, release notes, and release tags, removed replicates 3 and4 to the attic
  • lines changed 26, context: html, text, full: html, text
    reorganized all of the tracks into one super track for the Open Chromatin by DNaseI HS and FAIRE Tracks
  • lines changed 4, context: html, text, full: html, text
    removed an extra ( and also added an alpha tag to wgEncodeOpenChromFaire.ra so that I can remove them from the .ra file.
  • lines changed 110, context: html, text, full: html, text
    Reordered the composites to Vanessa's request. Labeling not done
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.html
  • lines changed 2, context: html, text, full: html, text
    Removing max-width=900 by Katrina's request.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.new.ra
  • lines changed 6415, context: html, text, full: html, text
    Not a new release, new.ra moved to .ra
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.ra
  • lines changed 2294, context: html, text, full: html, text
    Added New Submissions And Views
  • lines changed 417, context: html, text, full: html, text
    Updated with new submissions
• src/hg/makeDb/trackDb/human/hg19/wgEncodeDukeAffyExon.html
  • lines changed 2, context: html, text, full: html, text
    Changed labels, release notes, and release tags, removed replicates 3 and4 to the attic
• src/hg/makeDb/trackDb/human/hg19/wgEncodeDukeAffyExon.ra
  • lines changed 311, context: html, text, full: html, text
    Changed labels, release notes, and release tags, removed replicates 3 and4 to the attic
  • lines changed 1, context: html, text, full: html, text
    Added fileSortOrder
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencode.html
  • lines changed 51, context: html, text, full: html, text
    updated GENCODE credits and references
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisChiaPet.html
  • lines changed 71, context: html, text, full: html, text
    Recieved the track description for GisChiaPet
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisChiaPet.ra
  • lines changed 69, context: html, text, full: html, text
    This addresses many things in Issue#1664 Note #14, including adding the view capability back into the track
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra
  • lines changed 551, context: html, text, full: html, text
    First pass removal of 143 files (9 files are suspect due to meta-data inconsistenties, waiting on lab for proper procedure)
  • lines changed 40, context: html, text, full: html, text
    Removed reference to 7 files in metaDb and trackDb. Restored 2 files fully in browser.
  • lines changed 657, context: html, text, full: html, text
    Moved 137 files that had meta-data problems that will be replaced.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.html
  • lines changed 4, context: html, text, full: html, text
    Removing max-width=900 by Katrina's request.
  • lines changed 7, context: html, text, full: html, text
    Corrected the methods as per Terry.
  • lines changed 4, context: html, text, full: html, text
    Changed reference to the Dulke exluded regions to refer to supplemental materials.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromChip.ra
  • lines changed 2, context: html, text, full: html, text
    Using mean+whiskers as default.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.html
  • lines changed 2, context: html, text, full: html, text
    Removing max-width=900 by Katrina's request.
  • lines changed 7, context: html, text, full: html, text
    Corrected the methods as per Terry.
  • lines changed 3, context: html, text, full: html, text
    Changed reference to the Dulke exluded regions to refer to supplemental materials.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromDnase.ra
  • lines changed 2, context: html, text, full: html, text
    Using mean+whiskers as default.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.html
  • lines changed 2, context: html, text, full: html, text
    Removing max-width=900 by Katrina's request.
  • lines changed 7, context: html, text, full: html, text
    Corrected the methods as per Terry.
  • lines changed 4, context: html, text, full: html, text
    Changed reference to the Dulke exluded regions to refer to supplemental materials.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromFaire.ra
  • lines changed 75, context: html, text, full: html, text
    removed release tags to follow the new release tag convention using trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    Using mean+whiskers as default.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeOpenChromSynth.html
  • lines changed 2, context: html, text, full: html, text
    Removing max-width=900 by Katrina's request.
  • lines changed 1, context: html, text, full: html, text
    Corrected the methods as per Terry.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRbpSuper.html
  • lines changed 32, context: html, text, full: html, text
    Added a note and a few more references and a commented out paragraph that were requests of the lab
  • lines changed 38, context: html, text, full: html, text
    changed one word, fixed spacing, and alphabetized credits, still need to fix links, redmine #460
  • lines changed 7, context: html, text, full: html, text
    Fixed broken links to pubmed
  • lines changed 40, context: html, text, full: html, text
    Fixed alphabetization
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.html
  • lines changed 2, context: html, text, full: html, text
    Made Changes to clarify the Generation 0 data. 1 - removed all cases of Gen 0 data where we had Generation 1 data to replace. 2 - Clarified in release notes. 3 - Added Gen 0 into labels. 4 - Added 0 into short label.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRikenCage.ra
  • lines changed 86, context: html, text, full: html, text
    Made Changes to clarify the Generation 0 data. 1 - removed all cases of Gen 0 data where we had Generation 1 data to replace. 2 - Clarified in release notes. 3 - Added Gen 0 into labels. 4 - Added 0 into short label.
  • lines changed 62, context: html, text, full: html, text
    Changing rep 0 to Gen 0, removing 0 from the shortLabels
  • lines changed 116, context: html, text, full: html, text
    Changing things so that replicates 3 and 4 are labeled 1 and 2 and the generation 0 data that has no replicate will now be labeled 1. Added a ddcRep field to the CV so that we can track where our replicates vary from the lab, this could have been done with labRep
  • lines changed 1, context: html, text, full: html, text
    Changing the replicate labels to dccRep
  • lines changed 1, context: html, text, full: html, text
    dccRep is not CV defined and needed to be noted in both files
  • lines changed 8168, context: html, text, full: html, text
    Added downloads files for TSS
  • lines changed 8168, context: html, text, full: html, text
    undo the mistake of committing a mdb file over trackDb file
  • lines changed 1, context: html, text, full: html, text
    Changed the labels for dccRep to UCSC Rep and UCSC replicate number
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyRipSeq.html
  • lines changed 13, context: html, text, full: html, text
    Changed the methods section with lab update
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSuper.ra
  • lines changed 1, context: html, text, full: html, text
    Changed the shortlabel on the RNA binding protein supertrack
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.ra
  • lines changed 19, context: html, text, full: html, text
    Changed H3K4me3 -> H3K4me3B antibody variant.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.ra
  • lines changed 2, context: html, text, full: html, text
    track-handling code for ENCODE peptideMapping tracks
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.html
  • lines changed 1, context: html, text, full: html, text
    changed present tense to past as suggested by Katrina in code review. Redmine issues# 3014 & 59
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwAffyExonArray.ra
  • lines changed 136, context: html, text, full: html, text
    Changed long labels at Kate's request
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.ra
  • lines changed 258, context: html, text, full: html, text
    Updated composite long and short labels to new labels decided by Kate. Also updated view long labels: TFBS -> TFBS ChIP-seq. Redmine: 1604, note 22.
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    Bug #2917 (DGV colors need changing): oops, I let the new descriptionsneak out to the RR before the track! Adding the old description back for beta,public versions. It should be removed again when we push v10.
  • lines changed 11, context: html, text, full: html, text
    Adding back the regular omimGene stanza. See redmine #3053.
  • lines changed 18, context: html, text, full: html, text
    Updated trackDb in prep for DGV release see redmine #1702
  • lines changed 1, context: html, text, full: html, text
    removed beta,public tags from dgv track so they display on dev
  • lines changed 2, context: html, text, full: html, text
    Enabling next/prev-exon arrows for DECIPHER track at b0b's request.Those arrows are implemented for linkedFeatures, so I convert the bed4 DECIPHER items into linkedFeatures during loading, and use lf->extra to store the phenotypes string used in draw and mapItems.
• src/hg/makeDb/trackDb/marmoset/calJac3/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    Set multiz display default to on for human, gorilla and mouse
  • lines changed 6, context: html, text, full: html, text
    Change short lables for the subtracks
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuHistone.ra
  • lines changed 211, context: html, text, full: html, text
    G1E-E4+E2 Should be G1E-ER4+E2 . Fixed redmine issue 3508.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuTfbs.ra
  • lines changed 47, context: html, text, full: html, text
    G1E-E4+E2 Should be G1E-ER4+E2 . Fixed redmine issue 3508.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.html
  • lines changed 180, context: html, text, full: html, text
    Added track description for LICR TFBS and Histone Modificiation tracks.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.html
  • lines changed 180, context: html, text, full: html, text
    Added track description for LICR TFBS and Histone Modificiation tracks.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuHistone.ra
  • lines changed 1, context: html, text, full: html, text
    Fixed error with broken controlled vocabulary links on track configuration page.
  • lines changed 25, context: html, text, full: html, text
    G1E-E4+E2 Should be G1E-ER4+E2 . Fixed redmine issue 3508.
  • lines changed 1, context: html, text, full: html, text
    Added fileSortOrder information for updated downloads page.
  • lines changed 25, context: html, text, full: html, text
    Added notes for track configuration. Also updated windowingFunction to maximum according to lab.
  • lines changed 15, context: html, text, full: html, text
    Updated short and long labels to follow ENCODE labeling standards.
  • lines changed 8, context: html, text, full: html, text
    First pass at short label shortening. Will ask Kate for opnions.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.ra
  • lines changed 3, context: html, text, full: html, text
    Set Defaults to display all Cell-Antibody combinations, as there is very little data.
  • lines changed 1, context: html, text, full: html, text
    Fixed error with broken controlled vocabulary links on track configuration page.
  • lines changed 17, context: html, text, full: html, text
    G1E-E4+E2 Should be G1E-ER4+E2 . Fixed redmine issue 3508.
  • lines changed 1, context: html, text, full: html, text
    Added fileSortOrder information for updated downloads page.
  • lines changed 31, context: html, text, full: html, text
    Updated track comments with configuration. Removed Pol2-4H8 as a deafult track. Deafulted windowing function to maximum for Signal.
  • lines changed 1, context: html, text, full: html, text
    Updated note for track name.
  • lines changed 21, context: html, text, full: html, text
    Updated short and long labels to follow ENCODE labelling standards.
  • lines changed 11, context: html, text, full: html, text
    First pass at short label shortening. Will ask Kate for opnions.
• src/hg/makeDb/trackDb/snp132.html
  • lines changed 5, context: html, text, full: html, text
    Adding back the regular omimGene stanza. See redmine #3053.
  • lines changed 355, context: html, text, full: html, text
    hgTrackDb now supports an SSI-like syntax for track .html files toinsert the contents of other files, so multiple tracks' html files can share text: <!-- #insert file="relativePathToSharedText.html" --> And the snp132* tracks (#1684) now use this: the shared description text is in snp132.shared.html, and the four track .htmls all use the new syntax to insert the shared text.
• src/hg/makeDb/trackDb/snp132.shared.html
  • lines changed 355, context: html, text, full: html, text
    hgTrackDb now supports an SSI-like syntax for track .html files toinsert the contents of other files, so multiple tracks' html files can share text: <!-- #insert file="relativePathToSharedText.html" --> And the snp132* tracks (#1684) now use this: the shared description text is in snp132.shared.html, and the four track .htmls all use the new syntax to insert the shared text.
• src/hg/makeDb/trackDb/snp132Common.html
  • lines changed 351, context: html, text, full: html, text
    hgTrackDb now supports an SSI-like syntax for track .html files toinsert the contents of other files, so multiple tracks' html files can share text: <!-- #insert file="relativePathToSharedText.html" --> And the snp132* tracks (#1684) now use this: the shared description text is in snp132.shared.html, and the four track .htmls all use the new syntax to insert the shared text.
• src/hg/makeDb/trackDb/snp132NonUnique.html
  • lines changed 351, context: html, text, full: html, text
    hgTrackDb now supports an SSI-like syntax for track .html files toinsert the contents of other files, so multiple tracks' html files can share text: <!-- #insert file="relativePathToSharedText.html" --> And the snp132* tracks (#1684) now use this: the shared description text is in snp132.shared.html, and the four track .htmls all use the new syntax to insert the shared text.
• src/hg/makeDb/trackDb/snp132Patient.html
  • lines changed 351, context: html, text, full: html, text
    hgTrackDb now supports an SSI-like syntax for track .html files toinsert the contents of other files, so multiple tracks' html files can share text: <!-- #insert file="relativePathToSharedText.html" --> And the snp132* tracks (#1684) now use this: the shared description text is in snp132.shared.html, and the four track .htmls all use the new syntax to insert the shared text.
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 5, context: html, text, full: html, text
    Adding back the regular omimGene stanza. See redmine #3053.
  • lines changed 0, context: html, text, full: html, text
    Fixes to snp132 track. See redmine #1684. Accidentally checked in the bulk of these changes with git commit 270da1a76c129.
• src/hg/oneShot/doOmimAv/doOmimAv.c
  • lines changed 202, context: html, text, full: html, text
    Added oneShot/doOmimAv as part of the OMIM AV SNP track build pipeline.
• src/hg/oneShot/doOmimAv/makefile
  • lines changed 38, context: html, text, full: html, text
    Added oneShot/doOmimAv as part of the OMIM AV SNP track build pipeline.
• src/hg/protein/kgBioCyc0/kgBioCyc0.c
  • lines changed 2, context: html, text, full: html, text
    Adding hAllocConn parameter.
• src/hg/snp/snpLoad/snpNcbiToUcsc.c
  • lines changed 114, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): Brooke noticed that all PAR SNPs werecounted as multiply-mapped -- I added an exception to snpNcbiToUcsc's logic that detects multiply-mapped SNPs to take a bed4 file specifying PAR regions, and allow a SNP to map once to the same PAR on both X and Y without counting it as multiply mapped. Still need to update doDbSnp.pl to dump $db.par if it exists and apply the new option to snpNcbiToUcsc.
• src/hg/utils/bedToPsl/bedToPsl.c
  • lines changed 125, context: html, text, full: html, text
    added utility to convert BEDs to pseudo-psls
• src/hg/utils/bedToPsl/makefile
  • lines changed 28, context: html, text, full: html, text
    added utility to convert BEDs to pseudo-psls
  • lines changed 1, context: html, text, full: html, text
    fixed library path issues
• src/hg/utils/bedToPsl/tests/expected/basicTest.psl
  • lines changed 5, context: html, text, full: html, text
    added utility to convert BEDs to pseudo-psls
• src/hg/utils/bedToPsl/tests/input/basic.bed
  • lines changed 5, context: html, text, full: html, text
    added utility to convert BEDs to pseudo-psls
• src/hg/utils/bedToPsl/tests/input/chrom.sizes
  • lines changed 2, context: html, text, full: html, text
    added utility to convert BEDs to pseudo-psls
• src/hg/utils/bedToPsl/tests/makefile
  • lines changed 17, context: html, text, full: html, text
    added utility to convert BEDs to pseudo-psls
• src/hg/utils/makefile
  • lines changed 1, context: html, text, full: html, text
    added utility to convert BEDs to pseudo-psls
• src/hg/utils/mdbQuery/mdbQuery.c
  • lines changed 5, context: html, text, full: html, text
    Removed varType from mdb
• src/inc/common.h
  • lines changed 4, context: html, text, full: html, text
    used inline function and memset for zeroing memory to give optimizer a chance
• src/inc/dnautil.h
  • lines changed 6, context: html, text, full: html, text
    Added 'X' to aminoAcidTable and to functions to get AA abbrev and letter.
• src/inc/hash.h
  • lines changed 4, context: html, text, full: html, text
    added method to print out stats for hash usage
• src/lib/common.c
  • lines changed 8, context: html, text, full: html, text
    used inline function and memset for zeroing memory to give optimizer a chance
• src/lib/dnautil.c
  • lines changed 15, context: html, text, full: html, text
    Added 'X' to aminoAcidTable and to functions to get AA abbrev and letter.
• src/lib/hash.c
  • lines changed 23, context: html, text, full: html, text
    added method to print out stats for hash usage
• src/lib/maf.c
  • lines changed 0, context: html, text, full: html, text
    fixed indent
• src/makefile
  • lines changed 1, context: html, text, full: html, text
    add paraFetch to userApps
• src/utils/git-reports/git-reports.c
  • lines changed 2, context: html, text, full: html, text
    adding a comment when linesChanged==0 to explain to users about white-space only change creates empty diff
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 3, context: html, text, full: html, text
    v248 final build

• lines changed: 52792
• files changed: 279