CVS changes by file

review to branch (2009-03-17 to 2009-03-31) v203

• src/hg/archaeStuff/data/Genome-info-meta
  • 1.2 lines changed: 6, context: html, text, full: html, text
    change joseph's coat org name and multiz config
  • 1.1 lines changed: 75, context: html, text, full: html, text
    create genome info file for metagenomes
• src/hg/archaeStuff/data/Genome-info-mods
  • 1.62 lines changed: 9, context: html, text, full: html, text
    add geobLovl0 - retrievve from Todd's Genome-info-mods (32-bit src tree)
• src/hg/archaeStuff/scripts/archaeBrowser/Annotation.pm
  • 1.3 lines changed: 15, context: html, text, full: html, text
    comment out --wikibme; change --wiki for loading genome browser wiki track
• src/hg/archaeStuff/scripts/archaeBrowser/Constant.pm
  • 1.29 lines changed: 13, context: html, text, full: html, text
    add support for metagenomes
• src/hg/archaeStuff/scripts/archaeBrowser/GenomeInfo.pm
  • 1.14 lines changed: 1, context: html, text, full: html, text
    add support for metagenomes
• src/hg/archaeStuff/scripts/archaeBrowser/OrganismDb.pm
  • 1.29 lines changed: 166, context: html, text, full: html, text
    add support for metagenomes
• src/hg/archaeStuff/scripts/extract-genome-info
  • 1.4 lines changed: 14, context: html, text, full: html, text
    add altdb option for alternate centraldb
  • 1.3 lines changed: 179, context: html, text, full: html, text
    add options to retrieve data from centraldb
• src/hg/archaeStuff/scripts/make-browser-2.0
  • 1.37 lines changed: 5, context: html, text, full: html, text
    add support for metagenomes
  • 1.36 lines changed: 6, context: html, text, full: html, text
    comment out --wikibme; change --wiki for loading genome browser wiki track
• src/hg/autoSql/autoSql.c
  • 1.37 lines changed: 47, context: html, text, full: html, text
    Refactoring to move asColumnToSqlType to library.
• src/hg/autoSql/tests/expected/doc.sql
  • 1.2 lines changed: 0, context: html, text, full: html, text
    Updating test set to accommodate a harmless change in white space processing due to refactoring.
• src/hg/autoSql/tests/expected/symTest.sql
  • 1.2 lines changed: 0, context: html, text, full: html, text
    Updating test set to accommodate a harmless change in white space processing due to refactoring.
• src/hg/encode/encodeDownloadsPage/encodeDownloadsPage.pl
  • 1.6 lines changed: 45, context: html, text, full: html, text
    pull metadata out of README.txt (if any is available)
• src/hg/encode/encodeStatus/encodeStatus.pl
  • 1.5 lines changed: 1, context: html, text, full: html, text
    hgwbeta => hgobeta
• src/hg/encode/encodeValidate/config/cv.ra
  • 1.86 lines changed: 1, context: html, text, full: html, text
    Add longer ID string
  • 1.85 lines changed: 1, context: html, text, full: html, text
    Add source control identifier string
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • 1.170 lines changed: 7, context: html, text, full: html, text
    adding chrom/size checking against hg18
  • 1.169 lines changed: 24, context: html, text, full: html, text
    refactor openUtil into Encode.pm
• src/hg/encode/validateFiles/validateFiles.c
  • 1.13 lines changed: 73, context: html, text, full: html, text
    adding better error reporting on signed/unsigned ints and allow dots in sequence in tagAlign/pairedTagAlign
  • 1.12 lines changed: 12, context: html, text, full: html, text
    make library function to read all chromInfo, and add chromDb option to validateFiles to get chromInfo from DB
• src/hg/featureBits/featureBits.c
  • 1.54 lines changed: 2, context: html, text, full: html, text
    made this a library function, but need to make sure it is semantically identical and tested before removing from featureBits
• src/hg/hgSession/hgSession.c
  • 1.50 lines changed: 1, context: html, text, full: html, text
    boolshad hidden vars should default to '0' not '1'.
• src/hg/hgTables/asObj.c
  • 1.3 lines changed: 8, context: html, text, full: html, text
    Simplifying some logic where code was unnecessarily distinguishing between hPrintf and fprintf(stdout - which is an issue in the Genome Browser, but not here in the Table Browser. Also enabling select fields user interface.
• src/hg/hgTables/bedList.c
  • 1.64 lines changed: 5, context: html, text, full: html, text
    Making a lot more of the bigBed stuff work by implementing bigBedGetFilteredBedsOnRegions.
• src/hg/hgTables/bigBed.c
  • 1.8 lines changed: 51, context: html, text, full: html, text
    Making a lot more of the bigBed stuff work by implementing bigBedGetFilteredBedsOnRegions.
  • 1.7 lines changed: 303, context: html, text, full: html, text
    Getting filters to work on bigBed. Next up - intersections!
  • 1.6 lines changed: 28, context: html, text, full: html, text
    Starting to add filtering. Collects input now, but doesn't actually run filter.
  • 1.5 lines changed: 117, context: html, text, full: html, text
    Simplifying some logic where code was unnecessarily distinguishing between hPrintf and fprintf(stdout - which is an issue in the Genome Browser, but not here in the Table Browser. Also enabling select fields user interface.
• src/hg/hgTables/bigWig.c
  • 1.4 lines changed: 3, context: html, text, full: html, text
    Simplifying some logic where code was unnecessarily distinguishing between hPrintf and fprintf(stdout - which is an issue in the Genome Browser, but not here in the Table Browser. Also enabling select fields user interface.
• src/hg/hgTables/custom.c
  • 1.39 lines changed: 129, context: html, text, full: html, text
    Getting filters to work on bigBed. Next up - intersections!
  • 1.38 lines changed: 22, context: html, text, full: html, text
    Simplifying some logic where code was unnecessarily distinguishing between hPrintf and fprintf(stdout - which is an issue in the Genome Browser, but not here in the Table Browser. Also enabling select fields user interface.
• src/hg/hgTables/filterFields.c
  • 1.68 lines changed: 158, context: html, text, full: html, text
    Getting filters to work on bigBed. Next up - intersections!
  • 1.67 lines changed: 15, context: html, text, full: html, text
    Starting to add filtering. Collects input now, but doesn't actually run filter.
  • 1.66 lines changed: 10, context: html, text, full: html, text
    Simplifying some logic where code was unnecessarily distinguishing between hPrintf and fprintf(stdout - which is an issue in the Genome Browser, but not here in the Table Browser. Also enabling select fields user interface.
• src/hg/hgTables/hgTables.c
  • 1.180 lines changed: 1, context: html, text, full: html, text
    Getting filters to work on bigBed. Next up - intersections!
  • 1.179 lines changed: 56, context: html, text, full: html, text
    Starting to add filtering. Collects input now, but doesn't actually run filter.
  • 1.178 lines changed: 4, context: html, text, full: html, text
    Added GSID servers to exclude for general Table Browser functions.
  • 1.177 lines changed: 12, context: html, text, full: html, text
    Simplifying some logic where code was unnecessarily distinguishing between hPrintf and fprintf(stdout - which is an issue in the Genome Browser, but not here in the Table Browser. Also enabling select fields user interface.
• src/hg/hgTables/hgTables.h
  • 1.133 lines changed: 5, context: html, text, full: html, text
    Making a lot more of the bigBed stuff work by implementing bigBedGetFilteredBedsOnRegions.
  • 1.132 lines changed: 30, context: html, text, full: html, text
    Getting filters to work on bigBed. Next up - intersections!
  • 1.131 lines changed: 24, context: html, text, full: html, text
    Starting to add filtering. Collects input now, but doesn't actually run filter.
  • 1.130 lines changed: 9, context: html, text, full: html, text
    Simplifying some logic where code was unnecessarily distinguishing between hPrintf and fprintf(stdout - which is an issue in the Genome Browser, but not here in the Table Browser. Also enabling select fields user interface.
• src/hg/hgTables/joining.c
  • 1.53 lines changed: 15, context: html, text, full: html, text
    Simplifying some logic where code was unnecessarily distinguishing between hPrintf and fprintf(stdout - which is an issue in the Genome Browser, but not here in the Table Browser. Also enabling select fields user interface.
• src/hg/hgTables/schema.c
  • 1.55 lines changed: 2, context: html, text, full: html, text
    Updated to support logicalDb.
• src/hg/hgTrackUi/hgTrackUi.c
  • 1.484 lines changed: 2, context: html, text, full: html, text
    Support for setting variable then posting (allows reset to default without ajax and potential reace condition)
  • 1.483 lines changed: 26, context: html, text, full: html, text
    Add 'Reset to defaults' to hgTrackUi. Currently only applied to multi-view, because it relies on cart var naming convention {tableName}.{varName}...
  • 1.482 lines changed: 10, context: html, text, full: html, text
    Now using the chainCfg business over in ../lib/hui.c
  • 1.481 lines changed: 7, context: html, text, full: html, text
    updated usage of chainFetchColorOption call
• src/hg/hgTracks/cds.c
  • 1.90 lines changed: 41, context: html, text, full: html, text
    Refactoring for performance issue raised by David: moved all baseColor work that was done at load-time to draw-time, and removed the freeing-by-default of original genePred and psl structs converted to lf. Now, when there are so many items in the window that limitVisibility kicks it down to dense mode, we don't waste time on baseColor stuff that won't be used. Also some refactoring for tidiness in cds.c: got rid of a couple unused function args.
• src/hg/hgTracks/cds.h
  • 1.20 lines changed: 5, context: html, text, full: html, text
    Refactoring for performance issue raised by David: moved all baseColor work that was done at load-time to draw-time, and removed the freeing-by-default of original genePred and psl structs converted to lf. Now, when there are so many items in the window that limitVisibility kicks it down to dense mode, we don't waste time on baseColor stuff that won't be used. Also some refactoring for tidiness in cds.c: got rid of a couple unused function args.
• src/hg/hgTracks/chainTrack.c
  • 1.33 lines changed: 1, context: html, text, full: html, text
    adding netCart settings and cleaning up chainCart settings
• src/hg/hgTracks/hgTracks.c
  • 1.1562 lines changed: 15, context: html, text, full: html, text
    Refactoring for performance issue raised by David: moved all baseColor work that was done at load-time to draw-time, and removed the freeing-by-default of original genePred and psl structs converted to lf. Now, when there are so many items in the window that limitVisibility kicks it down to dense mode, we don't waste time on baseColor stuff that won't be used. Also some refactoring for tidiness in cds.c: got rid of a couple unused function args.
• src/hg/hgTracks/hgTracks.h
  • 1.182 lines changed: 4, context: html, text, full: html, text
    Refactoring for performance issue raised by David: moved all baseColor work that was done at load-time to draw-time, and removed the freeing-by-default of original genePred and psl structs converted to lf. Now, when there are so many items in the window that limitVisibility kicks it down to dense mode, we don't waste time on baseColor stuff that won't be used. Also some refactoring for tidiness in cds.c: got rid of a couple unused function args.
• src/hg/hgTracks/netTrack.c
  • 1.25 lines changed: 9, context: html, text, full: html, text
    adding netCart settings and cleaning up chainCart settings
• src/hg/hgTracks/pslTrack.c
  • 1.30 lines changed: 94, context: html, text, full: html, text
    Refactoring for performance issue raised by David: moved all baseColor work that was done at load-time to draw-time, and removed the freeing-by-default of original genePred and psl structs converted to lf. Now, when there are so many items in the window that limitVisibility kicks it down to dense mode, we don't waste time on baseColor stuff that won't be used. Also some refactoring for tidiness in cds.c: got rid of a couple unused function args.
• src/hg/hgTracks/simpleTracks.c
  • 1.73 lines changed: 34, context: html, text, full: html, text
    Refactoring for performance issue raised by David: moved all baseColor work that was done at load-time to draw-time, and removed the freeing-by-default of original genePred and psl structs converted to lf. Now, when there are so many items in the window that limitVisibility kicks it down to dense mode, we don't waste time on baseColor stuff that won't be used. Also some refactoring for tidiness in cds.c: got rid of a couple unused function args.
  • 1.72 lines changed: 5, context: html, text, full: html, text
    Multi-view composites toggle dense/full
• src/hg/hgc/bigBedClick.c
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Adding parameter to bigBedIntervalQuery.
• src/hg/hgc/hgc.c
  • 1.1524 lines changed: 2, context: html, text, full: html, text
    Moved a "<BR>" printf statement.
  • 1.1523 lines changed: 37, context: html, text, full: html, text
    Updated details page logic for omimGene.
  • 1.1522 lines changed: 47, context: html, text, full: html, text
    Updated omimGene section, to go after knownCanonical KG and get description from gbCdnaInfo instead of refLink for RefSeq entries.
  • 1.1521 lines changed: 2, context: html, text, full: html, text
    minor speed up of rendering of mRNA/ESTs by checking gbSeq table before seq table, avoiding two sql requests. Also simplified code.
  • 1.1520 lines changed: 1, context: html, text, full: html, text
    Added some padding to table on pgSnp page
  • 1.1519 lines changed: 1, context: html, text, full: html, text
    Added border to table
• src/hg/hgc/hgcData/hgdpGeoMap.eps
  • 1.4 lines changed: 53, context: html, text, full: html, text
    Added title for attribution to HGDP.
• src/hg/hgc/hgdpClick.c
  • 1.6 lines changed: 4, context: html, text, full: html, text
    Added links to population key images.
• src/hg/inc/bed.h
  • 1.53 lines changed: 19, context: html, text, full: html, text
    Adding bedFilter family of functions.
• src/hg/inc/cart.h
  • 1.45 lines changed: 7, context: html, text, full: html, text
    New routines to help reset cart for single table or composite.
• src/hg/inc/chainCart.h
  • 1.5 lines changed: 5, context: html, text, full: html, text
    More constants brought in here from the code
  • 1.4 lines changed: 4, context: html, text, full: html, text
    adding netCart settings and cleaning up chainCart settings
• src/hg/inc/chromInfo.h
  • 1.4 lines changed: 5, context: html, text, full: html, text
    make library function to read all chromInfo, and add chromDb option to validateFiles to get chromInfo from DB
• src/hg/inc/hdb.h
  • 1.166 lines changed: 7, context: html, text, full: html, text
    minor speed up of rendering of mRNA/ESTs by checking gbSeq table before seq table, avoiding two sql requests. Also simplified code.
• src/hg/inc/hui.h
  • 1.122 lines changed: 19, context: html, text, full: html, text
    adding netCart settings and cleaning up chainCart settings
• src/hg/inc/netCart.h
  • 1.1 lines changed: 34, context: html, text, full: html, text
    adding netCart settings and cleaning up chainCart settings
• src/hg/inc/versionInfo.h
  • 1.143 lines changed: 1, context: html, text, full: html, text
    "New version number v203"
• src/hg/instinct/bioInt2/bioController.c
  • 1.7 lines changed: 37, context: html, text, full: html, text
    updated
  • 1.6 lines changed: 255, context: html, text, full: html, text
    updated
  • 1.5 lines changed: 21, context: html, text, full: html, text
    updated
  • 1.4 lines changed: 306, context: html, text, full: html, text
    updated
  • 1.3 lines changed: 412, context: html, text, full: html, text
    moved stuff around
  • 1.2 lines changed: 64, context: html, text, full: html, text
    added routine to set cohorts
  • 1.1 lines changed: 425, context: html, text, full: html, text
    initial commit
• src/hg/instinct/bioInt2/bioController.h
  • 1.4 lines changed: 20, context: html, text, full: html, text
    updated
  • 1.3 lines changed: 27, context: html, text, full: html, text
    updated
  • 1.2 lines changed: 3, context: html, text, full: html, text
    moved stuff around
  • 1.1 lines changed: 34, context: html, text, full: html, text
    initial commit
• src/hg/instinct/bioInt2/bioGeneLevel.c
  • 1.3 lines changed: 165, context: html, text, full: html, text
    updated
  • 1.2 lines changed: 33, context: html, text, full: html, text
    updated
  • 1.1 lines changed: 77, context: html, text, full: html, text
    initial commit
• src/hg/instinct/bioInt2/bioIntDb.as
  • 1.4 lines changed: 15, context: html, text, full: html, text
    added to UI code
  • 1.3 lines changed: 12, context: html, text, full: html, text
    updated
  • 1.2 lines changed: 33, context: html, text, full: html, text
    added routine to set cohorts
  • 1.1 lines changed: 135, context: html, text, full: html, text
    initial commit
• src/hg/instinct/bioInt2/bioIntDb.c
  • 1.5 lines changed: 943, context: html, text, full: html, text
    added to UI code
  • 1.4 lines changed: 643, context: html, text, full: html, text
    updated code and added UI stubs
  • 1.3 lines changed: 235, context: html, text, full: html, text
    updated
  • 1.2 lines changed: 684, context: html, text, full: html, text
    added routine to set cohorts
  • 1.1 lines changed: 2828, context: html, text, full: html, text
    initial commit
• src/hg/instinct/bioInt2/bioIntDb.h
  • 1.5 lines changed: 212, context: html, text, full: html, text
    added to UI code
  • 1.4 lines changed: 63, context: html, text, full: html, text
    updated code and added UI stubs
  • 1.3 lines changed: 82, context: html, text, full: html, text
    updated
  • 1.2 lines changed: 309, context: html, text, full: html, text
    added routine to set cohorts
  • 1.1 lines changed: 1248, context: html, text, full: html, text
    initial commit
• src/hg/instinct/bioInt2/bioIntDb.sql
  • 1.4 lines changed: 17, context: html, text, full: html, text
    added to UI code
  • 1.3 lines changed: 13, context: html, text, full: html, text
    updated
  • 1.2 lines changed: 38, context: html, text, full: html, text
    added routine to set cohorts
  • 1.1 lines changed: 156, context: html, text, full: html, text
    initial commit
• src/hg/instinct/bioInt2/bioIntDriver.c
  • 1.2 lines changed: 42, context: html, text, full: html, text
    updated
  • 1.1 lines changed: 1706, context: html, text, full: html, text
    initial commit
• src/hg/instinct/bioInt2/bioIntDriver.h
  • 1.4 lines changed: 2, context: html, text, full: html, text
    added description field
  • 1.3 lines changed: 1, context: html, text, full: html, text
    added to UI code
  • 1.2 lines changed: 17, context: html, text, full: html, text
    updated
  • 1.1 lines changed: 152, context: html, text, full: html, text
    initial commit
• src/hg/instinct/bioInt2/bioIntFrontend/bioIntStyle.css
  • 1.8 lines changed: 5, context: html, text, full: html, text
    Added info link and description handler
  • 1.7 lines changed: 1, context: html, text, full: html, text
    Changed the way correlated is handled
  • 1.6 lines changed: 11, context: html, text, full: html, text
    Added click select, removed old complex mode
  • 1.5 lines changed: 7, context: html, text, full: html, text
    Changed color to standard scale
  • 1.4 lines changed: 39, context: html, text, full: html, text
    Styled the UI, added the dialog
  • 1.3 lines changed: 2, context: html, text, full: html, text
    Added clinical features
  • 1.2 lines changed: 108, context: html, text, full: html, text
    First functional version
  • 1.1 lines changed: 17, context: html, text, full: html, text
    Adding a bunch of stuff for new bioint frontend to repo
• src/hg/instinct/bioInt2/bioIntFrontend/bioIntUI.js
  • 1.13 lines changed: 6, context: html, text, full: html, text
    Hacked in a info link fix when it's missing
  • 1.12 lines changed: 10, context: html, text, full: html, text
    Added info link and description handler
  • 1.11 lines changed: 27, context: html, text, full: html, text
    Changed to 3 color gradiant
  • 1.10 lines changed: 46, context: html, text, full: html, text
    Added generic input error handling
  • 1.9 lines changed: 91, context: html, text, full: html, text
    Changed the way correlated is handled
  • 1.8 lines changed: 58, context: html, text, full: html, text
    Added click select, removed old complex mode
  • 1.7 lines changed: 7, context: html, text, full: html, text
    Changed color to standard scale
  • 1.6 lines changed: 18, context: html, text, full: html, text
    Styled the UI, added the dialog
  • 1.5 lines changed: 26, context: html, text, full: html, text
    Added 'lite' mode
  • 1.4 lines changed: 38, context: html, text, full: html, text
    Got flot histograms working
  • 1.3 lines changed: 54, context: html, text, full: html, text
    Added clinical features
  • 1.2 lines changed: 214, context: html, text, full: html, text
    First functional version
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Adding a bunch of stuff for new bioint frontend to repo
• src/hg/instinct/bioInt2/bioIntFrontend/excanvas.pack.js
  • 1.1 lines changed: 1, context: html, text, full: html, text
    Adding a bunch of stuff for new bioint frontend to repo
• src/hg/instinct/bioInt2/bioIntFrontend/images/ui-bg_dots-small_75_2636d1_2x2.png
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Styled the UI, added the dialog
• src/hg/instinct/bioInt2/bioIntFrontend/images/ui-bg_fine-grain_25_aaaaaa_60x60.png
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Styled the UI, added the dialog
• src/hg/instinct/bioInt2/bioIntFrontend/images/ui-bg_flat_0_aaaaaa_40x100.png
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Styled the UI, added the dialog
• src/hg/instinct/bioInt2/bioIntFrontend/images/ui-bg_flat_75_ffffff_40x100.png
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Styled the UI, added the dialog
• src/hg/instinct/bioInt2/bioIntFrontend/images/ui-bg_glass_55_fbf9ee_1x400.png
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Styled the UI, added the dialog
• src/hg/instinct/bioInt2/bioIntFrontend/images/ui-bg_glass_65_ffffff_1x400.png
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Styled the UI, added the dialog
• src/hg/instinct/bioInt2/bioIntFrontend/images/ui-bg_glass_75_d9e4f8_1x400.png
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Styled the UI, added the dialog
• src/hg/instinct/bioInt2/bioIntFrontend/images/ui-bg_glass_75_dadada_1x400.png
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Styled the UI, added the dialog
• src/hg/instinct/bioInt2/bioIntFrontend/images/ui-bg_inset-soft_95_fef1ec_1x100.png
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Styled the UI, added the dialog
• src/hg/instinct/bioInt2/bioIntFrontend/images/ui-icons_222222_256x240.png
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Styled the UI, added the dialog
• src/hg/instinct/bioInt2/bioIntFrontend/images/ui-icons_2e83ff_256x240.png
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Styled the UI, added the dialog
• src/hg/instinct/bioInt2/bioIntFrontend/images/ui-icons_3d3d3d_256x240.png
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Styled the UI, added the dialog
• src/hg/instinct/bioInt2/bioIntFrontend/images/ui-icons_454545_256x240.png
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Styled the UI, added the dialog
• src/hg/instinct/bioInt2/bioIntFrontend/images/ui-icons_cd0a0a_256x240.png
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Styled the UI, added the dialog
• src/hg/instinct/bioInt2/bioIntFrontend/images/ui-icons_ffffff_256x240.png
  • 1.1 lines changed: 0, context: html, text, full: html, text
    Styled the UI, added the dialog
• src/hg/instinct/bioInt2/bioIntFrontend/index.html
  • 1.12 lines changed: 1, context: html, text, full: html, text
    Changed to 3 color gradiant
  • 1.11 lines changed: 11, context: html, text, full: html, text
    Added generic input error handling
  • 1.10 lines changed: 8, context: html, text, full: html, text
    Changed the way correlated is handled
  • 1.9 lines changed: 1, context: html, text, full: html, text
    Fixed blank feature submit
  • 1.8 lines changed: 6, context: html, text, full: html, text
    Added click select, removed old complex mode
  • 1.7 lines changed: 2, context: html, text, full: html, text
    Changed color to standard scale
  • 1.6 lines changed: 22, context: html, text, full: html, text
    Styled the UI, added the dialog
  • 1.5 lines changed: 2, context: html, text, full: html, text
    Added 'lite' mode
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Added clinical features
  • 1.3 lines changed: 44, context: html, text, full: html, text
    First functional version
  • 1.2 lines changed: 242, context: html, text, full: html, text
    Adding a bunch of stuff for new bioint frontend to repo
  • 1.1 lines changed: 254, context: html, text, full: html, text
    updated code and added UI stubs
• src/hg/instinct/bioInt2/bioIntFrontend/jquery-1.3.2.js
  • 1.1 lines changed: 4376, context: html, text, full: html, text
    Adding a bunch of stuff for new bioint frontend to repo
• src/hg/instinct/bioInt2/bioIntFrontend/jquery-ui-1.7.1.css
  • 1.1 lines changed: 404, context: html, text, full: html, text
    Styled the UI, added the dialog
• src/hg/instinct/bioInt2/bioIntFrontend/jquery-ui-1.7.1.min.js
  • 1.1 lines changed: 298, context: html, text, full: html, text
    Adding a bunch of stuff for new bioint frontend to repo
• src/hg/instinct/bioInt2/bioIntFrontend/jquery.flot.js
  • 1.1 lines changed: 2136, context: html, text, full: html, text
    Adding a bunch of stuff for new bioint frontend to repo
• src/hg/instinct/bioInt2/bioIntFrontend/json2.js
  • 1.1 lines changed: 475, context: html, text, full: html, text
    Adding a bunch of stuff for new bioint frontend to repo
• src/hg/instinct/bioInt2/bioIntUI.c
  • 1.7 lines changed: 6, context: html, text, full: html, text
    add description to clinical info
  • 1.6 lines changed: 208, context: html, text, full: html, text
    added search
  • 1.5 lines changed: 28, context: html, text, full: html, text
    added description field
  • 1.4 lines changed: 2, context: html, text, full: html, text
    fixed bug with correlated response
  • 1.3 lines changed: 250, context: html, text, full: html, text
    added to UI code
  • 1.2 lines changed: 213, context: html, text, full: html, text
    updated
  • 1.1 lines changed: 112, context: html, text, full: html, text
    updated code and added UI stubs
• src/hg/instinct/bioInt2/bioIntUI.h
  • 1.4 lines changed: 1, context: html, text, full: html, text
    added search
  • 1.3 lines changed: 1, context: html, text, full: html, text
    added to UI code
  • 1.2 lines changed: 5, context: html, text, full: html, text
    updated
  • 1.1 lines changed: 38, context: html, text, full: html, text
    updated code and added UI stubs
• src/hg/instinct/bioInt2/bioIntegrator.c
  • 1.1 lines changed: 413, context: html, text, full: html, text
    initial commit
• src/hg/instinct/bioInt2/bioLevelI.c
  • 1.4 lines changed: 9, context: html, text, full: html, text
    updated
  • 1.3 lines changed: 201, context: html, text, full: html, text
    updated
  • 1.2 lines changed: 3, context: html, text, full: html, text
    updated
  • 1.1 lines changed: 430, context: html, text, full: html, text
    moved stuff around
• src/hg/instinct/bioInt2/bioMeta.c
  • 1.1 lines changed: 572, context: html, text, full: html, text
    initial commit
• src/hg/instinct/bioInt2/cohortCorrelations.c
  • 1.1 lines changed: 359, context: html, text, full: html, text
    added correlation code
• src/hg/instinct/bioInt2/makefile
  • 1.6 lines changed: 8, context: html, text, full: html, text
    added to UI code
  • 1.5 lines changed: 24, context: html, text, full: html, text
    updated code and added UI stubs
  • 1.4 lines changed: 1, context: html, text, full: html, text
    updated
  • 1.3 lines changed: 1, context: html, text, full: html, text
    moved stuff around
  • 1.2 lines changed: 8, context: html, text, full: html, text
    added routine to set cohorts
  • 1.1 lines changed: 36, context: html, text, full: html, text
    initial commit
• src/hg/instinct/bioInt2/populateDb.c
  • 1.5 lines changed: 2, context: html, text, full: html, text
    updated
  • 1.4 lines changed: 71, context: html, text, full: html, text
    updated
  • 1.3 lines changed: 0, context: html, text, full: html, text
    updated
  • 1.2 lines changed: 1, context: html, text, full: html, text
    moved stuff around
  • 1.1 lines changed: 1274, context: html, text, full: html, text
    initial commit
• src/hg/instinct/bioInt2/setCohorts.c
  • 1.4 lines changed: 31, context: html, text, full: html, text
    added to UI code
  • 1.3 lines changed: 15, context: html, text, full: html, text
    updated
  • 1.2 lines changed: 4, context: html, text, full: html, text
    updated
  • 1.1 lines changed: 280, context: html, text, full: html, text
    added routine to set cohorts
• src/hg/instinct/hgHeatmap2/hgHeatmapData/columnDb.ra
  • 1.4 lines changed: 4, context: html, text, full: html, text
    change RCB color setting
• src/hg/instinct/hgHeatmap2/hgHeatmapData/datasets.instinct.ra
  • 1.3 lines changed: 22, context: html, text, full: html, text
    add ispyAgiExpNov08_median_T1 track
• src/hg/instinct/hgHeatmap2/hgHeatmapFrontend/index.html
  • 1.32 lines changed: 1, context: html, text, full: html, text
    Removed dev warning
• src/hg/instinct/inc/hgStatsLib.h
  • 1.5 lines changed: 3, context: html, text, full: html, text
    added signed fishers
• src/hg/instinct/lib/hgStatsLib.c
  • 1.12 lines changed: 35, context: html, text, full: html, text
    added signed fishers
• src/hg/instinct/lib/json.c
  • 1.3 lines changed: 4, context: html, text, full: html, text
    fixed another bug
  • 1.2 lines changed: 1, context: html, text, full: html, text
    fixed bug with container printing
• src/hg/js/ajax.js
  • 1.4 lines changed: 15, context: html, text, full: html, text
    Support for setting reset to defaults variable and submitting self.
• src/hg/js/utils.js
  • 1.14 lines changed: 62, context: html, text, full: html, text
    Support for setting a variable then posting (allows reset to default)
• src/hg/lib/baseMaskCommon.c
  • 1.8 lines changed: 45, context: html, text, full: html, text
    make library function to read all chromInfo, and add chromDb option to validateFiles to get chromInfo from DB
• src/hg/lib/bed.c
  • 1.63 lines changed: 101, context: html, text, full: html, text
    Adding bedFilter family of functions.
• src/hg/lib/cart.c
  • 1.105 lines changed: 21, context: html, text, full: html, text
    New routines to help reset cart for single table or composite.
• src/hg/lib/chainCart.c
  • 1.4 lines changed: 4, context: html, text, full: html, text
    It is not necessary to have specialized value constants for trackDb entries, they can have spaces
  • 1.3 lines changed: 42, context: html, text, full: html, text
    adding netCart settings and cleaning up chainCart settings
• src/hg/lib/chromInfo.c
  • 1.7 lines changed: 47, context: html, text, full: html, text
    make library function to read all chromInfo, and add chromDb option to validateFiles to get chromInfo from DB
• src/hg/lib/hdb.c
  • 1.399 lines changed: 84, context: html, text, full: html, text
    minor speed up of rendering of mRNA/ESTs by checking gbSeq table before seq table, avoiding two sql requests. Also simplified code.
• src/hg/lib/hui.c
  • 1.181 lines changed: 2, context: html, text, full: html, text
    No longer need to call jquery from here. Calling in hgTrackUi
  • 1.180 lines changed: 2, context: html, text, full: html, text
    Do not show the level limit option yet on netAlign tracks
  • 1.179 lines changed: 4, context: html, text, full: html, text
    Fixup the broken chain options
  • 1.178 lines changed: 19, context: html, text, full: html, text
    Altered Z-dimension to use table columns
  • 1.177 lines changed: 69, context: html, text, full: html, text
    adding netCart settings and cleaning up chainCart settings
• src/hg/lib/jsHelper.c
  • 1.25 lines changed: 1, context: html, text, full: html, text
    Fix to another make Checkbox routing for the hidden var being 0
• src/hg/lib/makefile
  • 1.388 lines changed: 1, context: html, text, full: html, text
    Adding netCart to the build
• src/hg/lib/netCart.c
  • 1.1 lines changed: 68, context: html, text, full: html, text
    adding netCart settings and cleaning up chainCart settings
• src/hg/lib/omimToKnownCanonical.as
  • 1.1 lines changed: 6, context: html, text, full: html, text
    Created omimToKnownCanonical.as.
• src/hg/liftOver/makefile
  • 1.12 lines changed: 17, context: html, text, full: html, text
    Improved for userApps use
• src/hg/makeDb/doc/hg18.txt
  • 1.359 lines changed: 2, context: html, text, full: html, text
    Manually updated 1 record in omimToKnownCanonical table.
• src/hg/makeDb/doc/hgdpGeo.txt
  • 1.2 lines changed: 7, context: html, text, full: html, text
    Made a population key image (thanks b0b for suggestion).
• src/hg/makeDb/hgCgiData/Human/microarrayGroups.ra
  • 1.66 lines changed: 11, context: html, text, full: html, text
    add ispyAgiExpNov08_median_T1 info
• src/hg/makeDb/trackDb/human/hg18/ensembl31wayGerp.html
  • 1.1 lines changed: 142, context: html, text, full: html, text
    First cut at track description for GERP conservation
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.385 lines changed: 106, context: html, text, full: html, text
    Update population variants and MKAR tracks
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.225 lines changed: 2, context: html, text, full: html, text
    change sort order to interleave view
  • 1.224 lines changed: 20, context: html, text, full: html, text
    removed release alpha for select Raw Signal tracks for Broad Histone
  • 1.223 lines changed: 92, context: html, text, full: html, text
    adding back in 'release alpha' to Raw Signal subtracks of Broad Histone (not releasing now -- not enough room!)
  • 1.222 lines changed: 187, context: html, text, full: html, text
    removed release alpha from SUNY and Broad tracks
  • 1.221 lines changed: 2, context: html, text, full: html, text
    Changed sort order on Broad
  • 1.220 lines changed: 228, context: html, text, full: html, text
    Polish Broad Histone settings: add colors, tweak labels & defaults for consistency
  • 1.219 lines changed: 1, context: html, text, full: html, text
    Tweak short label (no sites here)
  • 1.218 lines changed: 28, context: html, text, full: html, text
    Usability improvements, based on input from SUNY. Ready for QA.
  • 1.217 lines changed: 19, context: html, text, full: html, text
    removing a broken track while it is regnerated
  • 1.216 lines changed: 19, context: html, text, full: html, text
    removing a broken track while it is regnerated
  • 1.215 lines changed: 208, context: html, text, full: html, text
    fixing conflicts
  • 1.214 lines changed: 28, context: html, text, full: html, text
    Added Yale RNAseq PolyA (temporarily?) to their TFBS composite. First bedGrah.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadChIPseq.html
  • 1.2 lines changed: 123, context: html, text, full: html, text
    Remove obsolete version
• src/hg/makeDb/trackDb/human/hg18/wgEncodeBroadChipSeq.html
  • 1.11 lines changed: 24, context: html, text, full: html, text
    shortened Methods section (thanks Pauline!) and put the details in a new txt doc: /browser/ENCODE/protocols/general/wgEncodeBroadChipSeq.txt
  • 1.10 lines changed: 10, context: html, text, full: html, text
    fixing citations
  • 1.9 lines changed: 10, context: html, text, full: html, text
    alpha order for citations
  • 1.8 lines changed: 9, context: html, text, full: html, text
    Added data release policy to the end
  • 1.7 lines changed: 4, context: html, text, full: html, text
    cutting lines to 80 chars where possible
  • 1.6 lines changed: 4, context: html, text, full: html, text
    Added a contact.
  • 1.5 lines changed: 4, context: html, text, full: html, text
    Add some explanation of histone code
  • 1.4 lines changed: 18, context: html, text, full: html, text
    Minor changes for consistency
  • 1.3 lines changed: 52, context: html, text, full: html, text
    Pre-pushQ cleanup
• src/hg/makeDb/trackDb/human/hg18/wgEncodeHudsonalphaChipSeq.html
  • 1.13 lines changed: 4, context: html, text, full: html, text
    add more details about RawSignal
• src/hg/makeDb/trackDb/human/hg18/wgEncodeSunyalbanyRnaGeneChip.html
  • 1.11 lines changed: 81, context: html, text, full: html, text
    Shortened methods and moved details to protocols doc.
• src/hg/makeDb/trackDb/human/hg19/description.html
  • 1.4 lines changed: 3, context: html, text, full: html, text
    Have determined the location of the PAR regions on X and Y
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • 1.11 lines changed: 1, context: html, text, full: html, text
    Turn on iRows for multizMHC
  • 1.10 lines changed: 24, context: html, text, full: html, text
    Adding multizMHC track and fixing up sortOrder error
  • 1.9 lines changed: 50, context: html, text, full: html, text
    Add synNets for chr6 haps
  • 1.8 lines changed: 30, context: html, text, full: html, text
    Add in the all_mrna and all_est entries since the tables are unsplit
• src/hg/makeDb/trackDb/human/omimGene.html
  • 1.14 lines changed: 12, context: html, text, full: html, text
    Changed some wording; added note about knownIsoforms.
  • 1.13 lines changed: 1, context: html, text, full: html, text
    single word change.
  • 1.12 lines changed: 20, context: html, text, full: html, text
    Added a display conventions and configuration section.
  • 1.11 lines changed: 9, context: html, text, full: html, text
    Reworded first paragraph, fixed reference.
• src/hg/makeDb/trackDb/human/trackDb.ra
  • 1.443 lines changed: 1, context: html, text, full: html, text
    Changed OMIM-Related to OMIM-Associated
• src/hg/makeDb/trackDb/lowelab/description-template.html
  • 1.9 lines changed: 3, context: html, text, full: html, text
    add LLT and scaffold lists
• src/hg/makeDb/trackDb/lowelab/trackDb.ra
  • 1.72 lines changed: 9, context: html, text, full: html, text
    add scaffolds track
  • 1.71 lines changed: 12, context: html, text, full: html, text
    add AlignFeatures
• src/hg/makeDb/trackDb/mgcFullMrna.html
  • 1.4 lines changed: 4, context: html, text, full: html, text
    Added more of a description of MGC, lifted from the MGC site.
• src/hg/makeDb/trackDb/mgcGenes.html
  • 1.15 lines changed: 5, context: html, text, full: html, text
    Added more of a description of MGC, lifted from the MGC site.
• src/hg/makeDb/trackDb/xenTro/mgcFullMrna.html
  • 1.2 lines changed: 4, context: html, text, full: html, text
    Added more of a description of MGC, lifted from the MGC site.
• src/hg/makeDb/trackDb/zebrafish/mgcFullMrna.html
  • 1.2 lines changed: 4, context: html, text, full: html, text
    Added more of a description of MGC, lifted from the MGC site.
• src/hg/mouseStuff/mafToClustalw/mafToClustalw.c
  • 1.1 lines changed: 61, context: html, text, full: html, text
    convert maf to clustalw-like format
• src/hg/mouseStuff/mafToClustalw/makefile
  • 1.1 lines changed: 14, context: html, text, full: html, text
    convert maf to clustalw-like format
• src/hg/mouseStuff/mafToFa/mafToFa.c
  • 1.2 lines changed: 13, context: html, text, full: html, text
    option to strip dots and dashes
  • 1.1 lines changed: 77, context: html, text, full: html, text
    utility to convert maf to fasta
• src/hg/mouseStuff/mafToFa/makefile
  • 1.1 lines changed: 14, context: html, text, full: html, text
    utility to convert maf to fasta
• src/hg/mouseStuff/netFilter/netFilter.c
  • 1.21 lines changed: 8, context: html, text, full: html, text
    Check -minSize{Q,T} only for fills, not for gaps -- discarding gaps makes the parent fill incorrectly appear gapless. I think it's odd that we discard all of a fill's gap's children when the fill is disqualified because it's possible for some lower-level nets to pass a filter that excludes a higher-level net, but will leave that as-is for now.
• src/hg/protein/kgBestMrna/kgPrepBestMrna.c
  • 1.4 lines changed: 2, context: html, text, full: html, text
    minor speed up of rendering of mRNA/ESTs by checking gbSeq table before seq table, avoiding two sql requests. Also simplified code.
• src/hg/protein/kgBestMrna/kgPrepBestMrna2.c
  • 1.3 lines changed: 2, context: html, text, full: html, text
    minor speed up of rendering of mRNA/ESTs by checking gbSeq table before seq table, avoiding two sql requests. Also simplified code.
• src/hg/protein/kgBestMrna/kgResultBestMrna.c
  • 1.4 lines changed: 2, context: html, text, full: html, text
    minor speed up of rendering of mRNA/ESTs by checking gbSeq table before seq table, avoiding two sql requests. Also simplified code.
• src/hg/protein/kgBestMrna2/kgPrepBestMrna2.c
  • 1.7 lines changed: 1, context: html, text, full: html, text
    removed unused variable
  • 1.6 lines changed: 2, context: html, text, full: html, text
    removed usless yank-n-put declaration
• src/hg/protein/kgBestRef2/kgPrepBestRef2.c
  • 1.7 lines changed: 1, context: html, text, full: html, text
    removed unused variable
  • 1.6 lines changed: 3, context: html, text, full: html, text
    minor speed up of rendering of mRNA/ESTs by checking gbSeq table before seq table, avoiding two sql requests. Also simplified code.
• src/hg/protein/spm6/spm6.c
  • 1.6 lines changed: 5, context: html, text, full: html, text
    minor speed up of rendering of mRNA/ESTs by checking gbSeq table before seq table, avoiding two sql requests. Also simplified code.
• src/hg/qa/apacheMonitor.c
  • 1.16 lines changed: 4, context: html, text, full: html, text
    Added date and time to output of error-500 details query.
• src/hg/qaPushQ/qaPushQ.c
  • 1.114 lines changed: 3, context: html, text, full: html, text
    dealing with move to hgofbeta
• src/hg/utils/automation/Encode.pm
  • 1.36 lines changed: 16, context: html, text, full: html, text
    refactor openUtil from doEncodeValidate.pl
• src/hg/utils/automation/doBlastzChainNet.pl
  • 1.28 lines changed: 5, context: html, text, full: html, text
    Allow non-split tables, and inclHap option to the blastz pipeline to include haplotypes in the chains
• src/hg/utils/automation/doRepeatMasker.pl
  • 1.14 lines changed: 5, context: html, text, full: html, text
    Allow non-split tables, and inclHap option to the blastz pipeline to include haplotypes in the chains
• src/hg/utils/automation/makeDownloads.pl
  • 1.20 lines changed: 17, context: html, text, full: html, text
    Allow some missing TRF files, option to avoid RepeatMasker, and special business to find haplotypes when they are in separate directories
• src/hg/utils/automation/makePushQSql.pl
  • 1.23 lines changed: 3, context: html, text, full: html, text
    Use hgofbeta instead of hgwbeta as the mysql server for qapushq.
• src/hg/utils/refreshNamedSessionCustomTracks/makeExclusionList.pl
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Tweaking name of output file to avoid clobbering the main one if there's a problem upstream or downstream.
• src/hg/utils/refreshNamedSessionCustomTracks/refreshNamedSessionCustomTracks.c
  • 1.8 lines changed: 2, context: html, text, full: html, text
    customFactoryTestExistence requires new arg (db).
• src/hg/wikiMods/README
  • 1.3 lines changed: 19, context: html, text, full: html, text
    Fixup known issues as this went into the archae browser
  • 1.2 lines changed: 11, context: html, text, full: html, text
    Add information about the configuration IP/extensions/ files
• src/hg/wikiMods/configuration.SpecialUserloginUCSC.php
  • 1.1 lines changed: 9, context: html, text, full: html, text
    files to place in IP/extensions/ to turn this on
• src/hg/wikiMods/configuration.SpecialUserlogoutUCSC.php
  • 1.1 lines changed: 9, context: html, text, full: html, text
    files to place in IP/extensions/ to turn this on
• src/inc/asParse.h
  • 1.4 lines changed: 3, context: html, text, full: html, text
    Adding asColumnToSqlType
• src/inc/bbiFile.h
  • 1.8 lines changed: 2, context: html, text, full: html, text
    Updating comment.
• src/lib/asParse.c
  • 1.7 lines changed: 31, context: html, text, full: html, text
    Adding asColumnToSqlType
• src/lib/cheapcgi.c
  • 1.113 lines changed: 1, context: html, text, full: html, text
    For consistency, multi-shad should be defaultingh to '0' not '1'
  • 1.112 lines changed: 1, context: html, text, full: html, text
    New boolShad logic requires shadow to be '0' even when checked.
• src/makefile
  • 1.59 lines changed: 5, context: html, text, full: html, text
    Adding liftOver to the userApps build list
  • 1.58 lines changed: 3, context: html, text, full: html, text
    Add faCount to the userApps list
  • 1.57 lines changed: 4, context: html, text, full: html, text
    Adding userApps directory to the UTILS_APPLIST directory list
  • 1.56 lines changed: 2, context: html, text, full: html, text
    Proper depend target for userApps build
  • 1.55 lines changed: 10, context: html, text, full: html, text
    creating userApps target to deliver user programs
• src/test/buildTableDescriptions.pl
  • 1.42 lines changed: 15, context: html, text, full: html, text
    Added support for db.host in hgConf, and properly set HGDB_CONF when -hgConf is given so hgsql uses it too.
  • 1.41 lines changed: 1, context: html, text, full: html, text
    Added another duplicate .as to %autoSqlIgnore.
• src/test/perllib/HgConf.pm
  • 1.2 lines changed: 5, context: html, text, full: html, text
    Use HGDB_CONF environment variable if defined.
• src/test/perllib/TrackDb.pm
  • 1.4 lines changed: 16, context: html, text, full: html, text
    Added proper HgConf usage including db.host, since we can no longer assume localhost etc.
• src/utils/bedToBigBed/makefile
  • 1.4 lines changed: 2, context: html, text, full: html, text
    fixup use of -lm on lib dependency
  • 1.3 lines changed: 7, context: html, text, full: html, text
    updated to use DESTDIR and BINDIR
• src/utils/bigBedSummary/makefile
  • 1.4 lines changed: 2, context: html, text, full: html, text
    fixup use of -lm on lib dependency
  • 1.3 lines changed: 8, context: html, text, full: html, text
    updated to use DESTDIR and BINDIR
• src/utils/bigBedToBed/makefile
  • 1.4 lines changed: 2, context: html, text, full: html, text
    fixup use of -lm on lib dependency
  • 1.3 lines changed: 8, context: html, text, full: html, text
    updated to use DESTDIR and BINDIR
• src/utils/bigWigSummary/makefile
  • 1.4 lines changed: 2, context: html, text, full: html, text
    fixup use of -lm on lib dependency
  • 1.3 lines changed: 8, context: html, text, full: html, text
    updated to use DESTDIR and BINDIR
• src/utils/bigWigToBedGraph/makefile
  • 1.4 lines changed: 2, context: html, text, full: html, text
    fixup use of -lm on lib dependency
  • 1.3 lines changed: 8, context: html, text, full: html, text
    updated to use DESTDIR and BINDIR
• src/utils/faCount/makefile
  • 1.5 lines changed: 1, context: html, text, full: html, text
    forgot dependency on the $O for the compile target
  • 1.4 lines changed: 11, context: html, text, full: html, text
    prepare the makefile for userApps make target, now with DESTDIR
• src/utils/faFrag/makefile
  • 1.7 lines changed: 2, context: html, text, full: html, text
    fixup use of -lm on lib dependency
  • 1.6 lines changed: 10, context: html, text, full: html, text
    updated to use DESTDIR and BINDIR
• src/utils/faOneRecord/makefile
  • 1.7 lines changed: 9, context: html, text, full: html, text
    updated to use DESTDIR and BINDIR
• src/utils/faRandomize/makefile
  • 1.3 lines changed: 10, context: html, text, full: html, text
    updated to use DESTDIR and BINDIR
• src/utils/faSize/makefile
  • 1.7 lines changed: 2, context: html, text, full: html, text
    fixup use of -lm on lib dependency
  • 1.6 lines changed: 10, context: html, text, full: html, text
    updated to use DESTDIR and BINDIR
• src/utils/faSomeRecords/makefile
  • 1.8 lines changed: 2, context: html, text, full: html, text
    fixup use of -lm on lib dependency
  • 1.7 lines changed: 10, context: html, text, full: html, text
    updated to use DESTDIR and BINDIR
• src/utils/faToNib/makefile
  • 1.12 lines changed: 2, context: html, text, full: html, text
    fixup use of -lm on lib dependency
  • 1.11 lines changed: 11, context: html, text, full: html, text
    updated to use DESTDIR and BINDIR
• src/utils/faToTwoBit/makefile
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• src/utils/userApps/makefile
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• src/utils/userApps/mkREADME.sh
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• src/utils/wigToBigWig/makefile
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