CVS changes by file

branch to review (2010-04-19 to 2010-04-27) v230

• src/hg/archaeStuff/scripts/archaeBrowser/ncRNA.pm
  • 1.29 lines changed: 1, context: html, text, full: html, text
    change tRNA id for track
• src/hg/encode/DAFs/2.0/gisRnaPet.daf
  • 1.3 lines changed: 19, context: html, text, full: html, text
    add Clusters, make bam the alignment file type, only include fastq with read 1/2
• src/hg/encode/encodeDownloadsPage/encodeDownloadsPage.pl
  • 1.37 lines changed: 2, context: html, text, full: html, text
    Make mdb table queries go to the right db.
  • 1.36 lines changed: 1, context: html, text, full: html, text
    Changed the sort order once again to handle setType and inputType
  • 1.35 lines changed: 1, context: html, text, full: html, text
    added inputType into the sort order
• src/hg/encode/encodeLoad/doEncodeLoad.pl
  • 1.76 lines changed: 9, context: html, text, full: html, text
    add info about files.txt and md5sum to preamble
• src/hg/encode/encodeLoad/doEncodeUnload.pl
  • 1.8 lines changed: 1, context: html, text, full: html, text
    Unlink bigWig gbdb files as well.
  • 1.7 lines changed: 25, context: html, text, full: html, text
    Unloader can now handle bigWigs
• src/hg/encode/encodeValidate/config/cv.ra
  • 1.231 lines changed: 67, context: html, text, full: html, text
    Added some new antibodies
  • 1.230 lines changed: 8, context: html, text, full: html, text
    Demoted 'input' to 'control'
• src/hg/encode/encodeValidate/config/fields.ra
  • 1.31 lines changed: 10, context: html, text, full: html, text
    Added setType and inputType ddf fields
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • 1.222 lines changed: 9, context: html, text, full: html, text
    Fixed a couple of bugs from the last checkin
  • 1.221 lines changed: 41, context: html, text, full: html, text
    Added defaulting of setType and inputType which are needed for ChIPseq submissions.
  • 1.220 lines changed: 2, context: html, text, full: html, text
    Added setType and inputType to allowable ddf terms
• src/hg/encode/utils/elandExtToSAM/complex_eland_extended.txt
  • 1.1 lines changed: 8, context: html, text, full: html, text
    More complicated eland extended data file I found off the web at http://nextgenseq.blogspot.com/2008/10/file-formats.html
• src/hg/encode/utils/elandExtToSAM/elandExtToSAM.py
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Changed parser so that name doesn't have to start with chr
  • 1.1 lines changed: 133, context: html, text, full: html, text
    Initial checkin of eland extended to SAM format converter written for Stanford Lab
• src/hg/encode/utils/elandExtToSAM/sample_eland_extended.txt
  • 1.2 lines changed: 0, context: html, text, full: html, text
    File was flagged as have DOS carriage returns - filtered out via dos2unix
  • 1.1 lines changed: 10, context: html, text, full: html, text
    Sample eland extended file provided by pcayting@stanford.edu
• src/hg/hgGenome/import.c
  • 1.18 lines changed: 15, context: html, text, full: html, text
    handling wiggle density better for sparse variableStep wiggles
• src/hg/hgTables/bedList.c
  • 1.73 lines changed: 37, context: html, text, full: html, text
    Added support for integration between the table browser and GREAT.
• src/hg/hgTables/correlatePlot.c
  • 1.17 lines changed: 19, context: html, text, full: html, text
    Refactoring font-for-size code so that Table Browser can reuse it, and thus not make an error message in correlation page.
• src/hg/hgTables/great.c
  • 1.1 lines changed: 142, context: html, text, full: html, text
    Added support for integration between the table browser and GREAT.
• src/hg/hgTables/hgTables.c
  • 1.193 lines changed: 10, context: html, text, full: html, text
    Added support for integration between the table browser and GREAT.
• src/hg/hgTables/hgTables.h
  • 1.144 lines changed: 24, context: html, text, full: html, text
    Added support for integration between the table browser and GREAT.
• src/hg/hgTables/mainPage.c
  • 1.149 lines changed: 26, context: html, text, full: html, text
    Added support for integration between the table browser and GREAT.
• src/hg/hgTables/makefile
  • 1.55 lines changed: 2, context: html, text, full: html, text
    Added support for integration between the table browser and GREAT.
• src/hg/hgTables/wiggle.c
  • 1.77 lines changed: 4, context: html, text, full: html, text
    Added support for integration between the table browser and GREAT.
• src/hg/hgTracks/cds.h
  • 1.26 lines changed: 4, context: html, text, full: html, text
    Make blue for query-insertion-at-end purple, so it is more easy to distinguish from green for polyA, essentially reverting back to r1.24 for hgTracks/cds.h
• src/hg/hgTracks/simpleTracks.c
  • 1.136 lines changed: 10, context: html, text, full: html, text
    removed hack put in because panTro2 treated human as native
  • 1.135 lines changed: 4, context: html, text, full: html, text
    removed accidental committed change to label width. (who forgot to keep me honest)
• src/hg/hgc/hgc.c
  • 1.1616 lines changed: 9, context: html, text, full: html, text
    removed hack put in because panTro2 treated human as native
  • 1.1615 lines changed: 41, context: html, text, full: html, text
    Don't put xeno refseq link up to aligned organism browser if it doesn't have refseq enabled.
  • 1.1614 lines changed: 4, context: html, text, full: html, text
    avoid URL refereces to NCBI for gold and ctgPos2 names they mean nothing there
• src/hg/inc/hdb.h
  • 1.169 lines changed: 3, context: html, text, full: html, text
    removed hack put in because panTro2 treated human as native
• src/hg/inc/hui.h
  • 1.149 lines changed: 1, context: html, text, full: html, text
    Link to hgBaseLabel.html for coloring help for tracks with sequence but no CDS info.
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_intgenMinOVBio.ra
  • 1.6 lines changed: 32, context: html, text, full: html, text
    Fixed db lookup.
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Bittner_Breast.ra
  • 1.1 lines changed: 576, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Bittner_Multi-cancer.ra
  • 1.1 lines changed: 760, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Bittner_Multi_cancer.ra
  • 1.1 lines changed: 855, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Chang_Breast.ra
  • 1.1 lines changed: 117, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Chowdary_Multi-cancer.ra
  • 1.1 lines changed: 112, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Chowdary_Multi_cancer.ra
  • 1.1 lines changed: 126, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Dairkee_Breast.ra
  • 1.1 lines changed: 18, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Farmer_Breast.ra
  • 1.1 lines changed: 45, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Finak_Breast.ra
  • 1.1 lines changed: 216, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Folgueira_Breast_2.ra
  • 1.1 lines changed: 27, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Frasor_Breast.ra
  • 1.1 lines changed: 36, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Gruvberger_Breast.ra
  • 1.1 lines changed: 18, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Hedenfalk_Breast.ra
  • 1.1 lines changed: 18, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Hedenfalk_Breast_2.ra
  • 1.1 lines changed: 27, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Hess_Breast.ra
  • 1.1 lines changed: 513, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Huang_Breast.ra
  • 1.1 lines changed: 72, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Iorio_Breast_2.ra
  • 1.1 lines changed: 16, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Kreike_Breast.ra
  • 1.1 lines changed: 153, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Ma_Breast.ra
  • 1.1 lines changed: 216, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Ma_Breast_2.ra
  • 1.1 lines changed: 162, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Ma_Breast_3.ra
  • 1.1 lines changed: 189, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Matt_Breast_2.ra
  • 1.1 lines changed: 162, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Matt_Breast_4.ra
  • 1.1 lines changed: 162, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Matt_Breast_8.ra
  • 1.1 lines changed: 162, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Miller_Breast.ra
  • 1.1 lines changed: 162, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Oh_Breast_4.ra
  • 1.1 lines changed: 45, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Pawitan_Breast.ra
  • 1.1 lines changed: 81, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Perou_Breast.ra
  • 1.1 lines changed: 63, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Perou_Breast_2.ra
  • 1.1 lines changed: 27, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Perreard_Breast.ra
  • 1.1 lines changed: 108, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Perreard_Breast_2.ra
  • 1.1 lines changed: 144, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Perreard_Breast_3.ra
  • 1.1 lines changed: 117, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Pollack_Breast.ra
  • 1.1 lines changed: 126, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Pollack_Breast_2.ra
  • 1.1 lines changed: 126, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Poola_Breast.ra
  • 1.1 lines changed: 72, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Ramaswamy_Multi-cancer.ra
  • 1.1 lines changed: 40, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Ramaswamy_Multi_cancer.ra
  • 1.1 lines changed: 45, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Richardson_Breast_2.ra
  • 1.1 lines changed: 216, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Schlingemann_Breast.ra
  • 1.1 lines changed: 54, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Schuetz_Breast.ra
  • 1.1 lines changed: 81, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Schuetz_Breast_2.ra
  • 1.1 lines changed: 117, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Sorlie_Breast.ra
  • 1.1 lines changed: 180, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Sorlie_Breast_2.ra
  • 1.1 lines changed: 180, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Sotiriou_Breast_2.ra
  • 1.1 lines changed: 306, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Sotiriou_Breast_3.ra
  • 1.1 lines changed: 216, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Teschendorff_Breast.ra
  • 1.1 lines changed: 27, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Teschendorff_Breast_2.ra
  • 1.1 lines changed: 27, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Teschendorff_Breast_3.ra
  • 1.1 lines changed: 27, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Thuerigen_Breast.ra
  • 1.1 lines changed: 90, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Uhlen_Multi-Tissue_5.ra
  • 1.1 lines changed: 24, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Uhlen_Multi_Tissue_5.ra
  • 1.1 lines changed: 27, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Usary_Breast.ra
  • 1.1 lines changed: 54, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Wang_Breast.ra
  • 1.1 lines changed: 126, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Weigelt_Breast.ra
  • 1.1 lines changed: 90, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_Weigelt_Breast_2.ra
  • 1.1 lines changed: 189, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_West_Breast.ra
  • 1.1 lines changed: 36, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_vandeVijver_Breast.ra
  • 1.1 lines changed: 234, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb_su2c_vantVeer_Breast.ra
  • 1.1 lines changed: 117, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.su2c_processed.ra
  • 1.1 lines changed: 1166, context: html, text, full: html, text
    Adding to repo
• src/hg/instinct/hgHeatmap2/hgHeatmapFrontend/js/hgHeatmap.js
  • 1.87 lines changed: 30, context: html, text, full: html, text
    Added buttons to jump to hgMicroscope
• src/hg/instinct/hgHeatmap2/hgToolTip.c
  • 1.11 lines changed: 1, context: html, text, full: html, text
    fixed buffer overflow
• src/hg/instinct/hgMicroscope/microscope/microscopeSearch.c
  • 1.6 lines changed: 2, context: html, text, full: html, text
    Search bug fix.
• src/hg/instinct/lib/json.c
  • 1.7 lines changed: 11, context: html, text, full: html, text
    Fixed string representation in keys, need to be double quoted strings according to strict spec
• src/hg/instinct/raToDb/raToDb.c
  • 1.11 lines changed: 37, context: html, text, full: html, text
    added series of checks for mistakes in microarrayGroups.ra
  • 1.10 lines changed: 8, context: html, text, full: html, text
    added helpful check for clinical info
• src/hg/instinct/webUserAdmin/batchLet1.txt
  • 1.2 lines changed: 0, context: html, text, full: html, text
    Made the default passwords a bit simpler (0-9A-Za-z) and removed the space from the letter that made it seem like you had the wrong pass
• src/hg/instinct/webUserAdmin/makefile
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Added batchLetter copy to makefile
• src/hg/instinct/webUserAdmin/webUserAdmin.c
  • 1.16 lines changed: 16, context: html, text, full: html, text
    Made the default passwords a bit simpler (0-9A-Za-z) and removed the space from the letter that made it seem like you had the wrong pass
  • 1.15 lines changed: 2, context: html, text, full: html, text
    Added code to prevent blank emails in batch file from working
  • 1.14 lines changed: 101, context: html, text, full: html, text
    Lots of changes, including header which needs to be customized per server
• src/hg/js/hui.js
  • 1.51 lines changed: 8, context: html, text, full: html, text
    Added tooltip for each matrix cell, so moved 3rd state matrix CB hint to CB only.
• src/hg/lib/customFactory.c
  • 1.123 lines changed: 2, context: html, text, full: html, text
    needed to keep setBbiViewLimits() inside the error-trapped block, otherwise get SIGSEGV now if bigDataUrl invalid
• src/hg/lib/hdb.c
  • 1.424 lines changed: 7, context: html, text, full: html, text
    removed hack put in because panTro2 treated human as native
• src/hg/lib/hgFind.c
  • 1.227 lines changed: 41, context: html, text, full: html, text
    removed hack put in because panTro2 treated human as native
• src/hg/lib/hui.c
  • 1.279 lines changed: 166, context: html, text, full: html, text
    Removed not ready for prime time 'slant titles', 'hint cols and rows' and 'scrolling table'. Added tooltip for each matrix cell.
  • 1.278 lines changed: 1, context: html, text, full: html, text
    Make blue for query-insertion-at-end purple, so it is more easy to distinguish from green for polyA, essentially reverting back to r1.24 for hgTracks/cds.h
  • 1.277 lines changed: 1, context: html, text, full: html, text
    Link to hgBaseLabel.html for coloring help for tracks with sequence but no CDS info.
  • 1.276 lines changed: 144, context: html, text, full: html, text
    Change ENCODCE metdata sort order. Initial check in of both Slant cols and hint cols and rows (both ifdefed out for now).
• src/hg/lib/mdb.c
  • 1.4 lines changed: 42, context: html, text, full: html, text
    Handle '#' comments more gracefully and include quotes in non-RA style printing
• src/hg/lib/trackLayout.c
  • 1.5 lines changed: 91, context: html, text, full: html, text
    Refactoring font-for-size code so that Table Browser can reuse it, and thus not make an error message in correlation page.
• src/hg/makeDb/doc/calJac3.txt
  • 1.7 lines changed: 24, context: html, text, full: html, text
    added N-SCAN
• src/hg/makeDb/doc/cavPor3.txt
  • 1.22 lines changed: 19, context: html, text, full: html, text
    adding lastz oryCun2 to monDom5 and cavPor3 and mm9 swap to oryCun2
• src/hg/makeDb/doc/encodeDccHg18/wgEncodeBuOrchid.release1.notes.txt
  • 1.2 lines changed: 10, context: html, text, full: html, text
    fix up some problems
  • 1.1 lines changed: 54, context: html, text, full: html, text
    release1 notes
• src/hg/makeDb/doc/encodeDccHg18/wgEncodeGisPet.release1.notes.txt
  • 1.1 lines changed: 220, context: html, text, full: html, text
    notes for relase1
• src/hg/makeDb/doc/encodeDccHg18/wgEncodeHudsonalphaRnaSeq.release1.notes.txt
  • 1.1 lines changed: 74, context: html, text, full: html, text
    notes for release1
• src/hg/makeDb/doc/equCab2.txt
  • 1.31 lines changed: 8, context: html, text, full: html, text
    Finished lastz with Sheep oviAri1
• src/hg/makeDb/doc/hg19.txt
  • 1.103 lines changed: 89, context: html, text, full: html, text
    Add sno/,iRNA track
  • 1.102 lines changed: 7, context: html, text, full: html, text
    Finished lastz with Sheep oviAri1
• src/hg/makeDb/doc/mm9.txt
  • 1.135 lines changed: 8, context: html, text, full: html, text
    Finished lastz with Sheep oviAri1
• src/hg/makeDb/doc/monDom5.txt
  • 1.24 lines changed: 18, context: html, text, full: html, text
    adding lastz oryCun2 to monDom5 and cavPor3 and mm9 swap to oryCun2
  • 1.23 lines changed: 9, context: html, text, full: html, text
    Finished lastz with Sheep oviAri1
• src/hg/makeDb/doc/oryCun2.txt
  • 1.8 lines changed: 19, context: html, text, full: html, text
    adding lastz oryCun2 to monDom5 and cavPor3 and mm9 swap to oryCun2
• src/hg/makeDb/doc/oviAri1.txt
  • 1.4 lines changed: 84, context: html, text, full: html, text
    Finished lastz with Sheep oviAri1
• src/hg/makeDb/doc/susScr2.txt
  • 1.9 lines changed: 2, context: html, text, full: html, text
    removed stray junk
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh
  • 1.3 lines changed: 6, context: html, text, full: html, text
    removed hg19 from vgTextDbs, for consistency with the comment
  • 1.2 lines changed: 16, context: html, text, full: html, text
    - incremented curVer and lastVer - replaced proteins09(something) with proteins100331 - added hg19 to vgTextDbs - moved the brackets to start executing the first step
  • 1.1 lines changed: 1272, context: html, text, full: html, text
    First stab at setting up the script to build version 13 of human ucscGenes (on hg19)
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • 1.112 lines changed: 2, context: html, text, full: html, text
    turning on genbank updates on hgwbeta for panTro1:2
• src/hg/makeDb/genbank/etc/rr.dbs
  • 1.91 lines changed: 1, context: html, text, full: html, text
    adding rabbit to genbank update
• src/hg/makeDb/hgCgiData/Human/microarrayGroups.ra
  • 1.104 lines changed: 588, context: html, text, full: html, text
    Added su2c generated data to end
• src/hg/makeDb/mdbUpdate/mdbPrint.c
  • 1.4 lines changed: 3, context: html, text, full: html, text
    Show plurals properly
  • 1.3 lines changed: 3, context: html, text, full: html, text
    Making -ra the default resulted in erroneous usage message
  • 1.2 lines changed: 17, context: html, text, full: html, text
    Made RA style the default output
• src/hg/makeDb/trackDb/chimp/panTro1/trackDb.ra
  • 1.43 lines changed: 1, context: html, text, full: html, text
    removing release beta for old genbank tables so that can stage new genbank tracks on beta
• src/hg/makeDb/trackDb/chimp/panTro2/trackDb.ra
  • 1.57 lines changed: 6, context: html, text, full: html, text
    removing release beta for old version of genbank tables so that can stage new genbank tables on beta
• src/hg/makeDb/trackDb/human/hg18/mdbBroad.ra
  • 1.3 lines changed: 1099, context: html, text, full: html, text
    Extended setType and inputType to Broad
• src/hg/makeDb/trackDb/human/hg18/mdbHaibTfbs.ra
  • 1.5 lines changed: 1383, context: html, text, full: html, text
    Chaged input:yes/no to setType:input/exp
  • 1.4 lines changed: 1383, context: html, text, full: html, text
    Fixed Haib Inputs further by adding inputType variable allowing pairing of exp.inputType = inp.inputType
  • 1.3 lines changed: 5592, context: html, text, full: html, text
    Fixed Haib Inputs (I hope)
• src/hg/makeDb/trackDb/human/hg18/mdbOpenChrom.ra
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Fixed labVersions with leading blank that were screwing up MAGIC
  • 1.3 lines changed: 866, context: html, text, full: html, text
    Extended setType and inputType to Open Chromatin
• src/hg/makeDb/trackDb/human/hg18/mdbUwDgf.ra
  • 1.1 lines changed: 469, context: html, text, full: html, text
    Adding Uw DGF metadata into mdb
• src/hg/makeDb/trackDb/human/hg18/mdbUwDnase.ra
  • 1.1 lines changed: 7608, context: html, text, full: html, text
    Adding Uw DNase metadata into mdb
• src/hg/makeDb/trackDb/human/hg18/mdbUwHist.ra
  • 1.2 lines changed: 1123, context: html, text, full: html, text
    Extended setType and inputType to UW Histones
  • 1.1 lines changed: 11674, context: html, text, full: html, text
    Adding Uw Histone metadata into mdb
• src/hg/makeDb/trackDb/human/hg18/mdbYaleTfbs.ra
  • 1.7 lines changed: 19, context: html, text, full: html, text
    Straightened out Yale K562/None/SETDB1/MNase at last
  • 1.6 lines changed: 1074, context: html, text, full: html, text
    Added control term for Yale because it's experiments must be defined by 4 terms
  • 1.5 lines changed: 2147, context: html, text, full: html, text
    Chaged input:yes/no to setType:input/exp
  • 1.4 lines changed: 2951, context: html, text, full: html, text
    Fixed Yale Inputs to match the HAIB model allowing pairing of exp.inputType = inp.inputType
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.958 lines changed: 6, context: html, text, full: html, text
    added minGrayLevel 3 to the WU DGF track so everything isn't white
  • 1.957 lines changed: 2, context: html, text, full: html, text
    Added cellType=cell to wgEncodeUwDGF and wgEncodeUmasshaTfbsValid tracks to get the cell links on hgTrackUi to work.
  • 1.956 lines changed: 4, context: html, text, full: html, text
    Changed labeling of Yale/K562b/MNase/SETDB1
  • 1.955 lines changed: 143, context: html, text, full: html, text
    make hudsonalphaRnaSeq a separate include file
• src/hg/makeDb/trackDb/human/hg18/wgEncodeCaltechRnaSeq.alpha.ra
  • 1.9 lines changed: 1, context: html, text, full: html, text
    take out "Map Algorithm"
  • 1.8 lines changed: 138, context: html, text, full: html, text
    use our standard RNA-seq
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisPet.alpha.ra
  • 1.13 lines changed: 80, context: html, text, full: html, text
    make long labels fit in 80 chars
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaRnaSeq.alpha.ra
  • 1.6 lines changed: 5, context: html, text, full: html, text
    changed long labels from "No Treatment" to w/None
  • 1.5 lines changed: 20, context: html, text, full: html, text
    fix long labels
  • 1.4 lines changed: 1, context: html, text, full: html, text
    small change
  • 1.3 lines changed: 12, context: html, text, full: html, text
    fix up long labels
  • 1.2 lines changed: 34, context: html, text, full: html, text
    some edits
  • 1.1 lines changed: 144, context: html, text, full: html, text
    separate it out
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaRnaSeq.html
  • 1.2 lines changed: 61, context: html, text, full: html, text
    make into HTML
  • 1.1 lines changed: 26, context: html, text, full: html, text
    first pass
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDGF.html
  • 1.6 lines changed: 8, context: html, text, full: html, text
    Fixed some minor wording and replaced an unknown with Percent Tags in Hotspots ~40pct
  • 1.5 lines changed: 40, context: html, text, full: html, text
    Several small wording changes, commented out footprint view, made references conform to PubMed citation format.
• src/hg/makeDb/trackDb/human/hg19/description.html
  • 1.15 lines changed: 1, context: html, text, full: html, text
    fixed typo (thanks Jen!)
• src/hg/makeDb/trackDb/human/hg19/mdbHaibTfbs.ra
  • 1.1 lines changed: 889, context: html, text, full: html, text
    Initial Check In of HudsonAlpha
• src/hg/makeDb/trackDb/human/hg19/trackDb.enc.ra
  • 1.9 lines changed: 294, context: html, text, full: html, text
    Initial HaibTfbs composite check in
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • 1.114 lines changed: 8, context: html, text, full: html, text
    changing which rabbit track is in composite
• src/hg/makeDb/trackDb/marmoset/calJac3/trackDb.ra
  • 1.4 lines changed: 4, context: html, text, full: html, text
    added N-SCAN
• src/hg/makeDb/trackDb/marmoset/trackDb.chainNet.ra
  • 1.10 lines changed: 2, context: html, text, full: html, text
    changed matrix for rheMac2
• src/hg/makeDb/trackDb/mouse/mm9/mdbSydhTfbs.txt
  • 1.1 lines changed: 1, context: html, text, full: html, text
    First mm9 ENCODE track added and metadata
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.enc.ra
  • 1.1 lines changed: 61, context: html, text, full: html, text
    First mm9 ENCODE track added
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
  • 1.90 lines changed: 1, context: html, text, full: html, text
    First mm9 ENCODE track added (included)
• src/hg/makeDb/trackDb/panda/ailMel1/description.html
  • 1.10 lines changed: 1, context: html, text, full: html, text
    fixing some spacing issues
  • 1.9 lines changed: 1, context: html, text, full: html, text
    small change to searches
  • 1.8 lines changed: 2, context: html, text, full: html, text
    small change to searches
• src/hg/makeDb/trackDb/rabbit/oryCun2/description.html
  • 1.4 lines changed: 11, context: html, text, full: html, text
    changing searches
• src/hg/makeDb/trackDb/tagTypes.tab
  • 1.12 lines changed: 1, context: html, text, full: html, text
    Added codingAnnoLabel_snp131CodingDbSnp (thanks Ann).
• src/hg/makeDb/trackDb/trackDb.ra
  • 1.626 lines changed: 1, context: html, text, full: html, text
    changing color of MGC Genes to work with new indel display options
• src/hg/regulate/enhancerTraining/k562.bed
  • 1.1 lines changed: 50, context: html, text, full: html, text
    First cut of training sets for k562 enhancer prepared with makeItem track by Jim.
• src/hg/regulate/enhancerTraining/k562Not.bed
  • 1.1 lines changed: 10, context: html, text, full: html, text
    First cut of training sets for k562 enhancer prepared with makeItem track by Jim.
• src/hg/tcga/pBamBam/asBamBam.c
  • 1.10 lines changed: 88, context: html, text, full: html, text
    added ref FASTA reading
• src/hg/tcga/pBamBam/bam_helper.c
  • 1.2 lines changed: 13, context: html, text, full: html, text
    added ref FASTA reading
• src/hg/tcga/pBamBam/bam_helper.h
  • 1.2 lines changed: 5, context: html, text, full: html, text
    added ref FASTA reading
• src/hg/utils/automation/Encode.pm
  • 1.64 lines changed: 1, context: html, text, full: html, text
    Back to the roundly hated, rudely arcane and vulgarly capitalized wgEncode prefix.
  • 1.63 lines changed: 1, context: html, text, full: html, text
    off by one error
  • 1.62 lines changed: 8, context: html, text, full: html, text
    changed expVar.ra read to get list for given track
  • 1.61 lines changed: 8, context: html, text, full: html, text
    added support for expVar.ra file
• src/inc/common.h
  • 1.171 lines changed: 2, context: html, text, full: html, text
    made parameter name C++ friendly
• src/inc/memgfx.h
  • 1.29 lines changed: 15, context: html, text, full: html, text
    Refactoring font-for-size code so that Table Browser can reuse it, and thus not make an error message in correlation page.
• src/lib/cheapcgi.c
  • 1.134 lines changed: 9, context: html, text, full: html, text
    Initial definition of .slantUp,.slantDn,.hintCol,.hintRow classes
• src/lib/common.c
  • 1.148 lines changed: 7, context: html, text, full: html, text
    made parameter name C++ friendly
• src/lib/memgfx.c
  • 1.53 lines changed: 106, context: html, text, full: html, text
    Refactoring font-for-size code so that Table Browser can reuse it, and thus not make an error message in correlation page.
• src/lib/portimpl.c
  • 1.16 lines changed: 1, context: html, text, full: html, text
    Tolerate double-slash in path
• src/utils/qa/chain.csh
  • 1.31 lines changed: 2, context: html, text, full: html, text
    changed what the tr command was looking for and added warning text alerting the user that the path could be wrong
  • 1.30 lines changed: 15, context: html, text, full: html, text
    updated instructions on matrices
• src/utils/qa/weeklybld/buildEnv.csh
  • 1.110 lines changed: 2, context: html, text, full: html, text
    v230 preview

• lines changed: 53240
• files changed: 159