hiram: changes by file

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

• 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/hg/hgTrackUi/hgTrackUi.c
  • 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/chainTrack.c
  • 1.33 lines changed: 1, context: html, text, full: html, text
    adding netCart settings and cleaning up chainCart settings
• 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/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/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/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/hui.c
  • 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
  • 1.177 lines changed: 69, context: html, text, full: html, text
    adding netCart settings and cleaning up chainCart settings
• 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/liftOver/makefile
  • 1.12 lines changed: 17, context: html, text, full: html, text
    Improved for userApps use
• 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/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/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/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
  • 1.13 lines changed: 2, context: html, text, full: html, text
    fixup use of -lm on lib dependency
  • 1.12 lines changed: 8, context: html, text, full: html, text
    updated to use DESTDIR and BINDIR
• src/utils/gtfToGenePred/makefile
  • 1.5 lines changed: 2, context: html, text, full: html, text
    fixup use of -lm on lib dependency
  • 1.4 lines changed: 9, context: html, text, full: html, text
    updated to use DESTDIR and BINDIR
• src/utils/htmlCheck/makefile
  • 1.8 lines changed: 2, context: html, text, full: html, text
    fixup use of -lm on lib dependency
  • 1.7 lines changed: 8, context: html, text, full: html, text
    updated to use DESTDIR and BINDIR
• src/utils/newProg/newProg.c
  • 1.27 lines changed: 11, context: html, text, full: html, text
    Improve the makefile created, add compile target, shorten compile command
• src/utils/nibFrag/makefile
  • 1.9 lines changed: 9, context: html, text, full: html, text
    updated to use DESTDIR and BINDIR
• src/utils/textHistogram/makefile
  • 1.14 lines changed: 2, context: html, text, full: html, text
    fixup use of -lm on lib dependency
  • 1.13 lines changed: 8, context: html, text, full: html, text
    updated to use DESTDIR and BINDIR
• src/utils/twoBitInfo/makefile
  • 1.8 lines changed: 2, context: html, text, full: html, text
    fixup use of -lm on lib dependency
  • 1.7 lines changed: 8, context: html, text, full: html, text
    updated to use DESTDIR and BINDIR
• src/utils/twoBitToFa/makefile
  • 1.13 lines changed: 3, context: html, text, full: html, text
    fixup use of -lm on lib dependency
  • 1.12 lines changed: 8, context: html, text, full: html, text
    updated to use DESTDIR and BINDIR
• src/utils/userApps/bigBedWigs.txt
  • 1.2 lines changed: 12, context: html, text, full: html, text
    Add note about removing track and browser lines
  • 1.1 lines changed: 71, context: html, text, full: html, text
    Initial contents
• src/utils/userApps/fetchChromSizes
  • 1.2 lines changed: 4, context: html, text, full: html, text
    Properly sort by size DESC, and eliminate useless stdout messages from ftp
  • 1.1 lines changed: 94, context: html, text, full: html, text
    Initial contents for a script to fetch chrom.sizes from UCSC
• src/utils/userApps/makefile
  • 1.3 lines changed: 8, context: html, text, full: html, text
    Separate lists for executables and documentation
  • 1.2 lines changed: 7, context: html, text, full: html, text
    updated to use DESTDIR and BINDIR
  • 1.1 lines changed: 11, context: html, text, full: html, text
    Initial contents, honoring DESTDIR and BINDIR arguments
• src/utils/userApps/mkREADME.sh
  • 1.1 lines changed: 26, context: html, text, full: html, text
    Initial contents
• src/utils/wigToBigWig/makefile
  • 1.5 lines changed: 2, context: html, text, full: html, text
    fixup use of -lm on lib dependency
  • 1.4 lines changed: 8, context: html, text, full: html, text
    updated to use DESTDIR and BINDIR