CVS changes by file

branch to review (2010-04-06 to 2010-04-13) v229

• src/hg/bedItemOverlapCount/bedItemOverlapCount.c
  • 1.21 lines changed: 11, context: html, text, full: html, text
    fixup error in checking argc must be 3 and rework usage message
• src/hg/encode/encodeCharts/README
  • 1.3 lines changed: 7, context: html, text, full: html, text
    Updated to reflect that encodeTimeline.py is now a cgi-bin script
  • 1.2 lines changed: 14, context: html, text, full: html, text
    Updated file with instructions for new timeline script
• src/hg/encode/encodeCharts/encodeTimeline.py
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Updated path to important dates file
  • 1.2 lines changed: 15, context: html, text, full: html, text
    Script now specifies path to 2.6 version of Python. Added stuff to make it a cgi-bin script
  • 1.1 lines changed: 223, context: html, text, full: html, text
    Initial checking of python script to generate timeline html
• src/hg/encode/encodeCharts/gviz_api.py
  • 1.1 lines changed: 1054, context: html, text, full: html, text
    Google Visualization API python library initial checkin
• src/hg/encode/encodeMkChangeNotes/encodeMkChangeNotes
  • 1.12 lines changed: 1, context: html, text, full: html, text
    fixed double counting bug
  • 1.11 lines changed: 31, context: html, text, full: html, text
    now show full filename (not just extention) on warning
  • 1.10 lines changed: 21, context: html, text, full: html, text
    support for pairedTagAlign and better addtional files handeling
  • 1.9 lines changed: 98, context: html, text, full: html, text
    added support for .bb files
• src/hg/encode/encodeValidate/config/cv.ra
  • 1.226 lines changed: 81, context: html, text, full: html, text
    Added antibodies H3K4me3B, H3K27me3B, H3K36me3B, IRF3, TBP, and USF2
  • 1.225 lines changed: 2, context: html, text, full: html, text
    Changed the vendor ID and link for the PABP1 rip antibody, due to the vendor discontinuing the old product
  • 1.224 lines changed: 135, context: html, text, full: html, text
    Added a whole slew of RIP antibodies
• src/hg/encode/encodeValidate/config/fields.ra
  • 1.30 lines changed: 8, context: html, text, full: html, text
    comment out Melissa's recent change. Need to revisit this after some discussion
• src/hg/hgGene/hgGeneData/Human/links.ra
  • 1.38 lines changed: 8, context: html, text, full: html, text
    fixing Stanford SOURCE links
• src/hg/hgGene/hgGeneData/Mouse/links.ra
  • 1.19 lines changed: 7, context: html, text, full: html, text
    fixing Stanford SOURCE links
• src/hg/hgGene/hgGeneData/Rat/links.ra
  • 1.9 lines changed: 7, context: html, text, full: html, text
    fixing Stanford SOURCE links
• src/hg/hgGene/hgGeneData/links.ra
  • 1.39 lines changed: 7, context: html, text, full: html, text
    fixing Stanford SOURCE links
• src/hg/hgTables/bedList.c
  • 1.72 lines changed: 25, context: html, text, full: html, text
    Improving BED output for makeItems.
• src/hg/hgTables/custom.c
  • 1.46 lines changed: 12, context: html, text, full: html, text
    Improving BED output for makeItems.
  • 1.45 lines changed: 1, context: html, text, full: html, text
    Making filter work for makeItems. Hmm, what a complex piece of code!
  • 1.44 lines changed: 24, context: html, text, full: html, text
    Making all fields output work with makeItems.
• src/hg/hgTables/filterFields.c
  • 1.81 lines changed: 16, context: html, text, full: html, text
    Making filter work for makeItems. Hmm, what a complex piece of code!
  • 1.80 lines changed: 91, context: html, text, full: html, text
    Some more progress in making makeItems tracks work in table browser. Selected fields output now works. Filter puts up UI, but filter is still ignored.
• src/hg/hgTables/gffOut.c
  • 1.21 lines changed: 3, context: html, text, full: html, text
    Switch GTF output to being true GTF
• src/hg/hgTables/hgTables.c
  • 1.192 lines changed: 6, context: html, text, full: html, text
    Making filter work for makeItems. Hmm, what a complex piece of code!
  • 1.191 lines changed: 10, context: html, text, full: html, text
    Making all fields output work with makeItems.
  • 1.190 lines changed: 3, context: html, text, full: html, text
    Switch GTF output to being true GTF
• src/hg/hgTables/hgTables.h
  • 1.143 lines changed: 3, context: html, text, full: html, text
    Improving BED output for makeItems.
  • 1.142 lines changed: 2, context: html, text, full: html, text
    Making filter work for makeItems. Hmm, what a complex piece of code!
  • 1.141 lines changed: 4, context: html, text, full: html, text
    Making all fields output work with makeItems.
  • 1.140 lines changed: 2, context: html, text, full: html, text
    Switch GTF output to being true GTF
• src/hg/hgTables/joining.c
  • 1.58 lines changed: 10, context: html, text, full: html, text
    Improving BED output for makeItems.
  • 1.57 lines changed: 14, context: html, text, full: html, text
    Making all fields output work with makeItems.
• src/hg/hgTables/maf.c
  • 1.19 lines changed: 10, context: html, text, full: html, text
    always check for mafFile in trackDb settings, and if present, use it.
• src/hg/hgTables/mainPage.c
  • 1.148 lines changed: 1, context: html, text, full: html, text
    Full support for the new metaTbl based metadata for ENCODE tracks. Uses sandbox table if one is found.
• src/hg/hgTables/schema.c
  • 1.63 lines changed: 2, context: html, text, full: html, text
    Some more progress in making makeItems tracks work in table browser. Selected fields output now works. Filter puts up UI, but filter is still ignored.
  • 1.62 lines changed: 28, context: html, text, full: html, text
    Starting to get makeItems custom tracks to work. Schema page is made now, though links in it don't work.
• src/hg/hgTrackUi/hgTrackUi.c
  • 1.519 lines changed: 5, context: html, text, full: html, text
    Got rid of old ifdefs
• src/hg/hgTracks/cds.h
  • 1.25 lines changed: 3, context: html, text, full: html, text
    Backing out Angie's change to r1.23 - dark blue not visible when zoomed in
• src/hg/hgTracks/hgTracks.c
  • 1.1641 lines changed: 36, context: html, text, full: html, text
    Taking a few more steps towards making the makeItems type custom track. It actually seems to be storing ranges in the customTrash database and displaying them now based on your javascript selections!
  • 1.1640 lines changed: 7, context: html, text, full: html, text
    Starting to get makeItems to work as a custom track type.
  • 1.1639 lines changed: 9, context: html, text, full: html, text
    Starting to implement more of the makeItems track javascript/C interface.
  • 1.1638 lines changed: 18, context: html, text, full: html, text
    Making it so that list of makeItems tracks to initialize is determined at run time. Making hgTracks.c generate a javascript function hgTrackInitTracks() that gets called during the javascript init.
  • 1.1637 lines changed: 23, context: html, text, full: html, text
    Fixing indentation and putting function comment in right place. Code standards people!
• src/hg/hgTracks/hgTracks.h
  • 1.207 lines changed: 6, context: html, text, full: html, text
    Taking a few more steps towards making the makeItems type custom track. It actually seems to be storing ranges in the customTrash database and displaying them now based on your javascript selections!
  • 1.206 lines changed: 15, context: html, text, full: html, text
    Starting to get makeItems to work as a custom track type.
  • 1.205 lines changed: 1, context: html, text, full: html, text
    Starting to implement more of the makeItems track javascript/C interface.
  • 1.204 lines changed: 3, context: html, text, full: html, text
    Starting to work on makeItems type tracks.
• src/hg/hgTracks/makeItemsTrack.c
  • 1.8 lines changed: 6, context: html, text, full: html, text
    A little cleanup.
  • 1.7 lines changed: 2, context: html, text, full: html, text
    Removing default values for name and description from makeItems.
  • 1.6 lines changed: 62, context: html, text, full: html, text
    Making it so can edit name and description of makeItems item.
  • 1.5 lines changed: 23, context: html, text, full: html, text
    Adding ID to makeItemsItem.
  • 1.4 lines changed: 40, context: html, text, full: html, text
    Replacing dummy first item with something better. Restoring click to details page, which is still sparse.
  • 1.3 lines changed: 67, context: html, text, full: html, text
    Taking a few more steps towards making the makeItems type custom track. It actually seems to be storing ranges in the customTrash database and displaying them now based on your javascript selections!
  • 1.2 lines changed: 6, context: html, text, full: html, text
    Starting to get makeItems to work as a custom track type.
  • 1.1 lines changed: 32, context: html, text, full: html, text
    Starting to work on makeItems type tracks.
• src/hg/hgTracks/makefile
  • 1.91 lines changed: 1, context: html, text, full: html, text
    Starting to work on makeItems type tracks.
• src/hg/hgTracks/simpleTracks.c
  • 1.133 lines changed: 4, context: html, text, full: html, text
    Taking a few more steps towards making the makeItems type custom track. It actually seems to be storing ranges in the customTrash database and displaying them now based on your javascript selections!
  • 1.132 lines changed: 4, context: html, text, full: html, text
    Starting to work on makeItems type tracks.
  • 1.131 lines changed: 4, context: html, text, full: html, text
    Better handling of rounding when capping width of label area to 1/2 of width of size of image
• src/hg/hgTracks/wigTrack.c
  • 1.103 lines changed: 3, context: html, text, full: html, text
    fix a drawing bug in whiskers plot when graphRange is very near zero
• src/hg/hgc/hgc.c
  • 1.1611 lines changed: 7, context: html, text, full: html, text
    Full support for the new metaTbl based metadata for ENCODE tracks. Uses sandbox table if one is found.
  • 1.1610 lines changed: 2, context: html, text, full: html, text
    Adding some details page handling to makeItems.
  • 1.1609 lines changed: 1, context: html, text, full: html, text
    fixing Stanford SOURCE links
• src/hg/hgc/hgc.h
  • 1.51 lines changed: 3, context: html, text, full: html, text
    Adding some details page handling to makeItems.
• src/hg/hgc/makeItemsClick.c
  • 1.2 lines changed: 53, context: html, text, full: html, text
    Making it so can edit name and description of makeItems item.
  • 1.1 lines changed: 38, context: html, text, full: html, text
    Adding some details page handling to makeItems.
• src/hg/hgc/makefile
  • 1.66 lines changed: 1, context: html, text, full: html, text
    Adding some details page handling to makeItems.
• src/hg/inc/hui.h
  • 1.148 lines changed: 2, context: html, text, full: html, text
    Full support for the new metaTbl based metadata for ENCODE tracks. Uses sandbox table if one is found.
• src/hg/inc/makeItemsItem.h
  • 1.5 lines changed: 2, context: html, text, full: html, text
    Adding makeItemsItemAutoSqlString.
  • 1.4 lines changed: 2, context: html, text, full: html, text
    Adding id column
  • 1.3 lines changed: 6, context: html, text, full: html, text
    Taking a few more steps towards making the makeItems type custom track. It actually seems to be storing ranges in the customTrash database and displaying them now based on your javascript selections!
  • 1.2 lines changed: 44, context: html, text, full: html, text
    Updating comment and name.
  • 1.1 lines changed: 95, context: html, text, full: html, text
    Adding makeItemsItem autoSql object.
• src/hg/instinct/hgDetails/hgDetails.c
  • 1.4 lines changed: 1, context: html, text, full: html, text
    updated
  • 1.3 lines changed: 2, context: html, text, full: html, text
    updated
  • 1.2 lines changed: 27, context: html, text, full: html, text
    updated
  • 1.1 lines changed: 240, context: html, text, full: html, text
    initial commit
• src/hg/instinct/hgDetails/makefile
  • 1.1 lines changed: 17, context: html, text, full: html, text
    initial commit
• src/hg/instinct/hgHeatmap2/hgHeatmap2.c
  • 1.87 lines changed: 115, context: html, text, full: html, text
    added raDb functionality
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_intgenOVBio.ra
  • 1.15 lines changed: 701, context: html, text, full: html, text
    adding changes to columnDb
• src/hg/instinct/hgHeatmap2/hgHeatmapFrontend/js/hgHeatmap.js
  • 1.83 lines changed: 11, context: html, text, full: html, text
    added raDb functionality
  • 1.82 lines changed: 2, context: html, text, full: html, text
    Tukey -> Box plot label
• src/hg/instinct/inc/hgHeatmapLib.h
  • 1.42 lines changed: 10, context: html, text, full: html, text
    added raDb functionality
• src/hg/instinct/inc/raDb.h
  • 1.1 lines changed: 121, context: html, text, full: html, text
    added raDb functionality
• src/hg/instinct/lib/featuresLib.c
  • 1.31 lines changed: 4, context: html, text, full: html, text
    added raDb functionality
• src/hg/instinct/lib/hgHeatmapLib.c
  • 1.68 lines changed: 75, context: html, text, full: html, text
    added raDb functionality
• src/hg/instinct/lib/makefile
  • 1.16 lines changed: 1, context: html, text, full: html, text
    added raDb functionality
• src/hg/instinct/lib/raDb.c
  • 1.1 lines changed: 784, context: html, text, full: html, text
    added raDb functionality
• src/hg/instinct/makefile
  • 1.16 lines changed: 23, context: html, text, full: html, text
    added raDb functionality
• src/hg/instinct/raToDb/makefile
  • 1.4 lines changed: 1, context: html, text, full: html, text
    updated
  • 1.3 lines changed: 1, context: html, text, full: html, text
    updated
  • 1.2 lines changed: 2, context: html, text, full: html, text
    renamed files
  • 1.1 lines changed: 18, context: html, text, full: html, text
    initial commit
• src/hg/instinct/raToDb/raDb.as
  • 1.3 lines changed: 1, context: html, text, full: html, text
    updated
  • 1.2 lines changed: 4, context: html, text, full: html, text
    updated
  • 1.1 lines changed: 33, context: html, text, full: html, text
    renamed files
• src/hg/instinct/raToDb/raDb.sql
  • 1.3 lines changed: 1, context: html, text, full: html, text
    updated
  • 1.2 lines changed: 6, context: html, text, full: html, text
    updated
  • 1.1 lines changed: 39, context: html, text, full: html, text
    renamed files
• src/hg/instinct/raToDb/raToDb.c
  • 1.9 lines changed: 10, context: html, text, full: html, text
    fixed
  • 1.8 lines changed: 17, context: html, text, full: html, text
    fixed sorting by priority
  • 1.7 lines changed: 14, context: html, text, full: html, text
    updated
  • 1.6 lines changed: 86, context: html, text, full: html, text
    updated
  • 1.5 lines changed: 81, context: html, text, full: html, text
    updated
  • 1.4 lines changed: 41, context: html, text, full: html, text
    updated
  • 1.3 lines changed: 434, context: html, text, full: html, text
    updated
  • 1.2 lines changed: 19, context: html, text, full: html, text
    renamed files
  • 1.1 lines changed: 40, context: html, text, full: html, text
    initial commit
• src/hg/js/hgGateway.js
  • 1.4 lines changed: 1, context: html, text, full: html, text
    change minchars to 2
• src/hg/js/hgTracks.js
  • 1.66 lines changed: 69, context: html, text, full: html, text
    Refactoring so that ruler and makeItems share code to convert from pixel to chromosome coordinates.
  • 1.65 lines changed: 44, context: html, text, full: html, text
    The makeItems drag now returns a proper track name, chrom, start, end.
  • 1.64 lines changed: 2, context: html, text, full: html, text
    Making it so that list of makeItems tracks to initialize is determined at run time. Making hgTracks.c generate a javascript function hgTrackInitTracks() that gets called during the javascript init.
  • 1.63 lines changed: 20, context: html, text, full: html, text
    Starting to work on makeItems type tracks.
• src/hg/lib/cart.c
  • 1.117 lines changed: 4, context: html, text, full: html, text
    Better cart cleanup for tdb and children
• src/hg/lib/customFactory.c
  • 1.122 lines changed: 1, context: html, text, full: html, text
    Removing default values for name and description from makeItems.
  • 1.121 lines changed: 2, context: html, text, full: html, text
    Adding id field to makeItemsItem.
  • 1.120 lines changed: 19, context: html, text, full: html, text
    Taking a few more steps towards making the makeItems type custom track. It actually seems to be storing ranges in the customTrash database and displaying them now based on your javascript selections!
  • 1.119 lines changed: 133, context: html, text, full: html, text
    Starting to get makeItems to work as a custom track type.
• src/hg/lib/hCytoBand.c
  • 1.7 lines changed: 1, context: html, text, full: html, text
    Continued tuning of new font system.
• src/hg/lib/hgMaf.c
  • 1.14 lines changed: 2, context: html, text, full: html, text
    check for an error case that used to core dump
• src/hg/lib/hui.c
  • 1.274 lines changed: 2, context: html, text, full: html, text
    Fixed a bug from cut and pasting
  • 1.273 lines changed: 156, context: html, text, full: html, text
    Full support for the new metaTbl based metadata for ENCODE tracks. Uses sandbox table if one is found.
• src/hg/lib/makeItemsItem.as
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Adding id column
  • 1.3 lines changed: 5, context: html, text, full: html, text
    Taking a few more steps towards making the makeItems type custom track. It actually seems to be storing ranges in the customTrash database and displaying them now based on your javascript selections!
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Updating comment and name.
  • 1.1 lines changed: 13, context: html, text, full: html, text
    Adding makeItemsItem autoSql object.
• src/hg/lib/makeItemsItem.c
  • 1.6 lines changed: 19, context: html, text, full: html, text
    Adding makeItemsItemAutoSqlString.
  • 1.5 lines changed: 11, context: html, text, full: html, text
    Adding id column
  • 1.4 lines changed: 2, context: html, text, full: html, text
    Adding id field to makeItemsItem.
  • 1.3 lines changed: 33, context: html, text, full: html, text
    Taking a few more steps towards making the makeItems type custom track. It actually seems to be storing ranges in the customTrash database and displaying them now based on your javascript selections!
  • 1.2 lines changed: 40, context: html, text, full: html, text
    Updating comment and name.
  • 1.1 lines changed: 233, context: html, text, full: html, text
    Adding makeItemsItem autoSql object.
• src/hg/lib/makeItemsItem.sql
  • 1.4 lines changed: 2, context: html, text, full: html, text
    Adding id field to makeItemsItem.
  • 1.3 lines changed: 5, context: html, text, full: html, text
    Taking a few more steps towards making the makeItems type custom track. It actually seems to be storing ranges in the customTrash database and displaying them now based on your javascript selections!
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Updating comment and name.
  • 1.1 lines changed: 19, context: html, text, full: html, text
    Adding makeItemsItem autoSql object.
• src/hg/lib/makefile
  • 1.406 lines changed: 2, context: html, text, full: html, text
    Adding makeItemsItem autoSql object.
• src/hg/lib/metaTbl.c
  • 1.11 lines changed: 13, context: html, text, full: html, text
    Extended special case for ENCODE metadata lines
• src/hg/lib/trackDb.c
  • 1.10 lines changed: 1, context: html, text, full: html, text
    Clean up extras hash
• src/hg/makeDb/doc/ailMel1.txt
  • 1.9 lines changed: 4, context: html, text, full: html, text
    rerun genbank for panda
  • 1.8 lines changed: 1, context: html, text, full: html, text
    add time from gap finding
  • 1.7 lines changed: 45, context: html, text, full: html, text
    done with all.joiner featureBits downloads and in the pushQ
• src/hg/makeDb/doc/encodeDccHg18/wgEncodeGisDnaPet.release1.notes.txt
  • 1.2 lines changed: 10, context: html, text, full: html, text
    changed some file names so they're consistent with the others
  • 1.1 lines changed: 78, context: html, text, full: html, text
    release1 of wgEncodeGisDnaPet
• src/hg/makeDb/doc/encodeDccHg18/wgEncodeGisRnaSeq.release1.notes.txt
  • 1.2 lines changed: 33, context: html, text, full: html, text
    better notes from Krish
• src/hg/makeDb/doc/encodeHg18.txt
  • 1.33 lines changed: 12, context: html, text, full: html, text
    reload encodeGencodeGeneKnownMar07
• src/hg/makeDb/doc/equCab2.txt
  • 1.30 lines changed: 51, context: html, text, full: html, text
    Adding oviAri1 lastz support
• src/hg/makeDb/doc/felCatV17e.txt
  • 1.8 lines changed: 47, context: html, text, full: html, text
    put into pushQ
• src/hg/makeDb/doc/hg19.txt
  • 1.99 lines changed: 50, context: html, text, full: html, text
    Adding oviAri1 lastz support
  • 1.98 lines changed: 69, context: html, text, full: html, text
    working on H-Inv 7.0 and new Ensembl name mapping table
  • 1.97 lines changed: 18, context: html, text, full: html, text
    Rerun blastz with felCatV17e
  • 1.96 lines changed: 28, context: html, text, full: html, text
    vegaGene update to 37 for mouse to 38 for human
• src/hg/makeDb/doc/makeEnsembl.txt
  • 1.16 lines changed: 244, context: html, text, full: html, text
    finished with v57 ensGene update
• src/hg/makeDb/doc/mm9.txt
  • 1.134 lines changed: 49, context: html, text, full: html, text
    Adding oviAri1 lastz support
  • 1.133 lines changed: 28, context: html, text, full: html, text
    vegaGene update to 37 for mouse to 38 for human
• src/hg/makeDb/doc/monDom5.txt
  • 1.22 lines changed: 49, context: html, text, full: html, text
    Adding oviAri1 lastz support
• src/hg/makeDb/doc/oviAri1.txt
  • 1.2 lines changed: 151, context: html, text, full: html, text
    Adding oviAri1 lastz swap support
• src/hg/makeDb/doc/panTro1.txt
  • 1.9 lines changed: 15, context: html, text, full: html, text
    redo chimp genbank to not special case huamn
• src/hg/makeDb/doc/panTro2.txt
  • 1.19 lines changed: 12, context: html, text, full: html, text
    redo chimp genbank to not special case huamn
• src/hg/makeDb/doc/susScr2.txt
  • 1.5 lines changed: 14, context: html, text, full: html, text
    finished with v57 ensGene update
• src/hg/makeDb/doc/ucscGenes/mm9.ucscGenes12.csh
  • 1.5 lines changed: 42, context: html, text, full: html, text
    Committing changes made a while back for last bits of mm9 known gene rebuild.
• src/hg/makeDb/genbank/common.mk
  • 1.27 lines changed: 4, context: html, text, full: html, text
    fixed library dependency problems
• src/hg/makeDb/genbank/etc/align.dbs
  • 1.117 lines changed: 1, context: html, text, full: html, text
    reenable panda ailMel1
  • 1.116 lines changed: 2, context: html, text, full: html, text
    disable chimp
  • 1.115 lines changed: 1, context: html, text, full: html, text
    restart ailMel1 panda to fix up xeno Ref Seqs
• src/hg/makeDb/genbank/etc/genbank.conf
  • 1.369 lines changed: 1, context: html, text, full: html, text
    disable native panda refgene, since there are none
  • 1.368 lines changed: 7, context: html, text, full: html, text
    remove hacks to align human as native on chimp
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • 1.109 lines changed: 1, context: html, text, full: html, text
    turning panda back on
  • 1.108 lines changed: 2, context: html, text, full: html, text
    disable chimp
  • 1.107 lines changed: 1, context: html, text, full: html, text
    restart ailMel1 panda to fix up xeno Ref Seqs
• src/hg/makeDb/genbank/etc/hgwdev.dbs
  • 1.121 lines changed: 1, context: html, text, full: html, text
    reenable panda ailMel1
  • 1.120 lines changed: 2, context: html, text, full: html, text
    disable chimp
  • 1.119 lines changed: 1, context: html, text, full: html, text
    restart ailMel1 panda to fix up xeno Ref Seqs
• src/hg/makeDb/genbank/etc/rr.dbs
  • 1.89 lines changed: 2, context: html, text, full: html, text
    disable chimp
• src/hg/makeDb/genbank/makefile
  • 1.17 lines changed: 1, context: html, text, full: html, text
    fixed library dependency problems
• src/hg/makeDb/genbank/src/align/gbAlignCommon.c
  • 1.6 lines changed: 9, context: html, text, full: html, text
    remove hacks to align human as native on chimp
• src/hg/makeDb/genbank/src/align/gbAlignRun
  • 1.11 lines changed: 1, context: html, text, full: html, text
    don't include /cluster/bin in PATH when not running on build server to avoid annoy our kind admins by fill up the log with autofs errors
• src/hg/makeDb/genbank/src/align/gbAlignStep
  • 1.25 lines changed: 1, context: html, text, full: html, text
    don't include /cluster/bin in PATH when not running on build server to avoid annoy our kind admins by fill up the log with autofs errors
• src/hg/makeDb/genbank/src/align/gbBlat
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    remove hacks to align human as native on chimp
• src/hg/makeDb/genbank/src/copy/gbMakeDownload
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    need /cluster/bin/ for making downloads
• src/hg/makeDb/genbank/src/download/gbDownloadStep
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    don't include /cluster/bin in PATH when not running on build server to avoid annoy our kind admins by fill up the log with autofs errors
• src/hg/makeDb/genbank/src/lib/gbCommon.pm
  • 1.49 lines changed: 19, context: html, text, full: html, text
    don't include /cluster/bin in PATH when not running on build server to avoid annoy our kind admins by fill up the log with autofs errors
• src/hg/makeDb/genbank/src/lib/gbGenome.c
  • 1.79 lines changed: 6, context: html, text, full: html, text
    remove hacks to align human as native on chimp
  • 1.78 lines changed: 3, context: html, text, full: html, text
    limit panda to just panda
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    Add oviAr1Names entry
• src/hg/makeDb/genbank/src/process/gbProcessStep
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    don't include /cluster/bin in PATH when not running on build server to avoid annoy our kind admins by fill up the log with autofs errors
• src/hg/makeDb/schema/all.joiner
  • 1.786 lines changed: 3, context: html, text, full: html, text
    add HINV-7.0 tables to ignore list for hg19
  • 1.785 lines changed: 19, context: html, text, full: html, text
    fixup hg19 references so it is clean on beta
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    Add ctgPos2 for felCatV17e
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    adding tablesIgnored clause for aplCal1
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    Added line to list of hg tables ignored so that all Burge RNA-seq tables are ignored.
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    SusScr2 leaked into chainDest twice
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    adding susScr2 to Whole Genome Shotgun and chain/net variables
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    panda update
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    adding calJac3
• src/hg/makeDb/trackDb/README
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    Expanding bigWig type docs a little.
• src/hg/makeDb/trackDb/cat/felCatV17e/description.html
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    Yet more minor correction...
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    More minor corrections
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    Add photo credit
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    Mirroe correction
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    Add more description to html
• src/hg/makeDb/trackDb/cat/felCatV17e/gap.html
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    More minor corrections
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    Add more description to html
• src/hg/makeDb/trackDb/cat/felCatV17e/gold.html
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    More minor corrections
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    Add more description to html
• src/hg/makeDb/trackDb/chimp/panTro1/trackDb.ra
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    remove hack to treat human cDNAs and RefSeqs as native chimp
• src/hg/makeDb/trackDb/chimp/panTro1/xenoRefGene.html
  • 1.6 lines changed: 55, context: html, text, full: html, text
    remove hack to treat human cDNAs and RefSeqs as native chimp
• src/hg/makeDb/trackDb/chimp/panTro1/xenoRefGeneNoHs.html
  • 1.1 lines changed: 55, context: html, text, full: html, text
    remove hack to treat human cDNAs and RefSeqs as native chimp
• src/hg/makeDb/trackDb/chimp/panTro2/est.html
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    remove hack to treat human cDNAs and RefSeqs as native chimp
• src/hg/makeDb/trackDb/chimp/panTro2/estWithHs.html
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    remove hack to treat human cDNAs and RefSeqs as native chimp
• src/hg/makeDb/trackDb/chimp/panTro2/intronEst.html
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    remove hack to treat human cDNAs and RefSeqs as native chimp
• src/hg/makeDb/trackDb/chimp/panTro2/intronEstWithHs.html
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    remove hack to treat human cDNAs and RefSeqs as native chimp
• src/hg/makeDb/trackDb/chimp/panTro2/mrna.html
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    remove hack to treat human cDNAs and RefSeqs as native chimp
• src/hg/makeDb/trackDb/chimp/panTro2/mrnaWithHs.html
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    remove hack to treat human cDNAs and RefSeqs as native chimp
• src/hg/makeDb/trackDb/chimp/panTro2/refGene.html
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    remove hack to treat human cDNAs and RefSeqs as native chimp
• src/hg/makeDb/trackDb/chimp/panTro2/refGeneWithHs.html
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    remove hack to treat human cDNAs and RefSeqs as native chimp
• src/hg/makeDb/trackDb/chimp/panTro2/trackDb.ra
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    remove hack to treat human cDNAs and RefSeqs as native chimp
• src/hg/makeDb/trackDb/chimp/panTro2/xenoMrna.html
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    remove hack to treat human cDNAs and RefSeqs as native chimp
• src/hg/makeDb/trackDb/chimp/panTro2/xenoMrnaNoHs.html
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    remove hack to treat human cDNAs and RefSeqs as native chimp
• src/hg/makeDb/trackDb/chimp/panTro2/xenoRefGene.html
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    remove hack to treat human cDNAs and RefSeqs as native chimp
• src/hg/makeDb/trackDb/chimp/panTro2/xenoRefGeneNoHs.html
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    remove hack to treat human cDNAs and RefSeqs as native chimp
• src/hg/makeDb/trackDb/cow/trackDb.chainNet.ra
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    adding priority override for susScr2
• src/hg/makeDb/trackDb/human/hg18/metaBroad.ra
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    Initial check-in of metaTbl data from 3 ENCODE labs
• src/hg/makeDb/trackDb/human/hg18/metaOpenChrom.ra
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    Initial check-in of metaTbl data from 3 ENCODE labs
• src/hg/makeDb/trackDb/human/hg18/metaYaleTfbs.ra
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    Initial check-in of metaTbl data from 3 ENCODE labs
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
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    adding html override to vega
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
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    Adjusted short and long labels for Yale TFBS
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    take out color for GisDnaPet K562 20k track
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    some tiny changes to long labels in GIS RNA-seq track
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    Changed UW DNase DGF track from release alpha to release alpha,beta.
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    changed a table name to look like the others
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    add K562 with frag size 20k to GisDnaPet
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisPet.alpha.ra
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    change H1hesc cytosol to H1hesc cell
• src/hg/makeDb/trackDb/human/hg19/hinv70Composite.html
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    fixup URL links to HINV db resources
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    Adding HInv-7.0 gene prediction update
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
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    adding html override to vega
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    fixup URL links to HINV db resources
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    experimental gc5Base track as bigWig
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    Adding HInv-7.0 gene prediction update
• src/hg/makeDb/trackDb/human/trackDb.chainNet.ra
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    moving all shortLabel chainNet overrides for susScr1 to highest level
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    adding susScr1 chainNet overrides for human
• src/hg/makeDb/trackDb/mouse/mm9/mapability.html
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    Changing email adress
• src/hg/makeDb/trackDb/mouse/trackDb.chainNet.ra
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    moving all shortLabel chainNet overrides for susScr1 to highest level
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    adding shortLabel overrides for susScr1 and priority overrides for susScr2 for mouse
• src/hg/makeDb/trackDb/opossum/trackDb.chainNet.ra
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    moving all shortLabel chainNet overrides for susScr1 to highest level
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    adding shortLabel overrides for susScr1
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    adding priority override for susScr2
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    taking out unnecessary matrix override for susScr2
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    chainNet overrides for susScr2
• src/hg/makeDb/trackDb/panda/ailMel1/description.html
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    changing searches
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    changing searches
• src/hg/makeDb/trackDb/pig/susScr2/trackDb.ra
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    adding broken bigWig illustration
• src/hg/makeDb/trackDb/sheep/oviAri1/description.html
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    Remove / from end of URL
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    Minor correction
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    Add more descriptions to html
• src/hg/makeDb/trackDb/sheep/oviAri1/gold.html
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    Remove / from end of URL
• src/hg/makeDb/trackDb/trackDb.chainNet.ra
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    moving all shortLabel chainNet overrides for susScr1 to highest level
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    adding susScr2
• src/hg/utils/automation/doBlastzChainNet.pl
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    default big hub is swarm and workhorse is hgwdev
• src/hg/utils/automation/makeDownloads.pl
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    indicate sequence is masked in chromosomes/README and bigZips/README
• src/inc/bbiFile.h
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    Adding extra sig for detection of truncation at end of file.
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    Fixing max field in second and higher level zooms of bedGraphToBigWig and bedToBigBed.
• src/inc/memgfx.h
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    Adding mgTimes34Font()
• src/lib/bbiWrite.c
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    Fixing max field in second and higher level zooms of bedGraphToBigWig and bedToBigBed.
• src/lib/bwgCreate.c
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    Adding extra sig for detection of truncation at end of file.
• src/lib/font/mgCourier10.c
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    Continued tuning of new font system.
• src/lib/font/mgCourier12.c
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    Continued tuning of new font system.
• src/lib/font/mgCourier14.c
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    Continued tuning of new font system.
• src/lib/font/mgCourier8.c
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    Continued tuning of new font system.
• src/lib/font/mgHelvetica10.c
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    Continued tuning of new font system.
• src/lib/font/mgHelvetica12.c
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    Continued tuning of new font system.
• src/lib/font/mgHelvetica18.c
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    Continued tuning of new font system.
• src/lib/font/mgHelvetica24.c
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    Continued tuning of new font system.
• src/lib/font/mgHelvetica8.c
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    Continued tuning of new font system.
• src/lib/font/mgHelveticaBold10.c
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    Continued tuning of new font system.
• src/lib/font/mgHelveticaBold12.c
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    Continued tuning of new font system.
• src/lib/font/mgHelveticaBold24.c
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    Continued tuning of new font system.
• src/lib/font/mgHelveticaBold8.c
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    Continued tuning of new font system.
• src/lib/font/mgSixhi6.c
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    Continued tuning of new font system.
• src/lib/font/mgTimes10.c
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    Continued tuning of new font system.
• src/lib/font/mgTimes12.c
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    Continued tuning of new font system.
• src/lib/font/mgTimes8.c
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    Continued tuning of new font system.
• src/product/README.trackDb
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    missing the root designation on the hgTrackDb command
• src/utils/bedGraphToBigWig/bedGraphToBigWig.c
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    Adding extra sig for detection of truncation at end of file.
• src/utils/bedToBigBed/bedToBigBed.c
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    Adding extra sig for detection of truncation at end of file.
• src/utils/bigWigInfo/bigWigInfo.c
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    fixed typo in usage statement
• src/utils/qa/alertBqueue.csh
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    modified message
• src/utils/qa/makefile
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    spacing fix
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    adding qaThis.csh to makefile
• src/utils/qa/qaThis.csh
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    removing bad if
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    usage statement change
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    added cleanup functionality
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    added cleanup functionality
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    slight interface change
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    slight interface change
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    usage statement clean up
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    switching from checkOffend to checkTableCoords
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    adding this script
• src/utils/qa/weeklybld/buildEnv.csh
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    v229 preview
• src/utils/qa/weeklybld/doNewBranch.csh
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    adding some ppl to notification

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