hiram: changes by commit

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

• Add in the all_mrna and all_est entries since the tables are unsplit
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra 1.8 - lines changed: 30, context: html, text, full: html, text
• adding netCart settings and cleaning up chainCart settings
  • src/hg/hgTracks/chainTrack.c 1.33 - lines changed: 1, context: html, text, full: html, text
  • src/hg/hgTracks/netTrack.c 1.25 - lines changed: 9, context: html, text, full: html, text
  • src/hg/inc/chainCart.h 1.4 - lines changed: 4, context: html, text, full: html, text
  • src/hg/inc/hui.h 1.122 - lines changed: 19, context: html, text, full: html, text
  • src/hg/inc/netCart.h 1.1 - lines changed: 34, context: html, text, full: html, text
  • src/hg/lib/chainCart.c 1.3 - lines changed: 42, context: html, text, full: html, text
  • src/hg/lib/hui.c 1.177 - lines changed: 69, context: html, text, full: html, text
  • src/hg/lib/netCart.c 1.1 - lines changed: 68, context: html, text, full: html, text
• updated usage of chainFetchColorOption call
  • src/hg/hgTrackUi/hgTrackUi.c 1.481 - lines changed: 7, context: html, text, full: html, text
• Adding netCart to the build
  • src/hg/lib/makefile 1.388 - lines changed: 1, context: html, text, full: html, text
• Fixup the broken chain options
  • src/hg/lib/hui.c 1.179 - lines changed: 4, context: html, text, full: html, text
• Now using the chainCfg business over in ../lib/hui.c
  • src/hg/hgTrackUi/hgTrackUi.c 1.482 - lines changed: 10, context: html, text, full: html, text
• More constants brought in here from the code
  • src/hg/inc/chainCart.h 1.5 - lines changed: 5, context: html, text, full: html, text
• It is not necessary to have specialized value constants for trackDb entries, they can have spaces
  • src/hg/lib/chainCart.c 1.4 - lines changed: 4, context: html, text, full: html, text
• files to place in IP/extensions/ to turn this on
  • src/hg/wikiMods/configuration.SpecialUserloginUCSC.php 1.1 - lines changed: 9, context: html, text, full: html, text
  • src/hg/wikiMods/configuration.SpecialUserlogoutUCSC.php 1.1 - lines changed: 9, context: html, text, full: html, text
• Add information about the configuration IP/extensions/ files
  • src/hg/wikiMods/README 1.2 - lines changed: 11, context: html, text, full: html, text
• Fixup known issues as this went into the archae browser
  • src/hg/wikiMods/README 1.3 - lines changed: 19, context: html, text, full: html, text
• Do not show the level limit option yet on netAlign tracks
  • src/hg/lib/hui.c 1.180 - lines changed: 2, 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/makeDownloads.pl 1.20 - lines changed: 17, 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/doBlastzChainNet.pl 1.28 - lines changed: 5, context: html, text, full: html, text
  • src/hg/utils/automation/doRepeatMasker.pl 1.14 - lines changed: 5, context: html, text, full: html, text
• Add synNets for chr6 haps
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra 1.9 - lines changed: 50, context: html, text, full: html, text
• Have determined the location of the PAR regions on X and Y
  • src/hg/makeDb/trackDb/human/hg19/description.html 1.4 - lines changed: 3, context: html, text, full: html, text
• Adding multizMHC track and fixing up sortOrder error
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra 1.10 - lines changed: 24, context: html, text, full: html, text
• Turn on iRows for multizMHC
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra 1.11 - lines changed: 1, context: html, text, full: html, text
• creating userApps target to deliver user programs
  • src/makefile 1.55 - lines changed: 10, context: html, text, full: html, text
• Proper depend target for userApps build
  • src/makefile 1.56 - lines changed: 2, context: html, text, full: html, text
• Initial contents for a script to fetch chrom.sizes from UCSC
  • src/utils/userApps/fetchChromSizes 1.1 - lines changed: 94, context: html, text, full: html, text
• Properly sort by size DESC, and eliminate useless stdout messages from ftp
  • src/utils/userApps/fetchChromSizes 1.2 - lines changed: 4, context: html, text, full: html, text
• Initial contents, honoring DESTDIR and BINDIR arguments
  • src/utils/userApps/makefile 1.1 - lines changed: 11, context: html, text, full: html, text
• updated to use DESTDIR and BINDIR
  • src/utils/bedToBigBed/makefile 1.3 - lines changed: 7, context: html, text, full: html, text
  • src/utils/bigBedSummary/makefile 1.3 - lines changed: 8, context: html, text, full: html, text
  • src/utils/bigBedToBed/makefile 1.3 - lines changed: 8, context: html, text, full: html, text
  • src/utils/bigWigSummary/makefile 1.3 - lines changed: 8, context: html, text, full: html, text
  • src/utils/bigWigToBedGraph/makefile 1.3 - lines changed: 8, context: html, text, full: html, text
  • src/utils/faFrag/makefile 1.6 - lines changed: 10, context: html, text, full: html, text
  • src/utils/faOneRecord/makefile 1.7 - lines changed: 9, context: html, text, full: html, text
  • src/utils/faRandomize/makefile 1.3 - lines changed: 10, context: html, text, full: html, text
  • src/utils/faSize/makefile 1.6 - lines changed: 10, context: html, text, full: html, text
  • src/utils/faSomeRecords/makefile 1.7 - lines changed: 10, context: html, text, full: html, text
  • src/utils/faToNib/makefile 1.11 - lines changed: 11, context: html, text, full: html, text
  • src/utils/faToTwoBit/makefile 1.12 - lines changed: 8, context: html, text, full: html, text
  • src/utils/gtfToGenePred/makefile 1.4 - lines changed: 9, context: html, text, full: html, text
  • src/utils/htmlCheck/makefile 1.7 - lines changed: 8, context: html, text, full: html, text
  • src/utils/nibFrag/makefile 1.9 - lines changed: 9, context: html, text, full: html, text
  • src/utils/textHistogram/makefile 1.13 - lines changed: 8, context: html, text, full: html, text
  • src/utils/twoBitInfo/makefile 1.7 - lines changed: 8, context: html, text, full: html, text
  • src/utils/twoBitToFa/makefile 1.12 - lines changed: 8, context: html, text, full: html, text
  • src/utils/userApps/makefile 1.2 - lines changed: 7, context: html, text, full: html, text
  • src/utils/wigToBigWig/makefile 1.4 - lines changed: 8, context: html, text, full: html, text
• Adding userApps directory to the UTILS_APPLIST directory list
  • src/makefile 1.57 - lines changed: 4, context: html, text, full: html, text
• Separate lists for executables and documentation
  • src/utils/userApps/makefile 1.3 - lines changed: 8, context: html, text, full: html, text
• fixup use of -lm on lib dependency
  • src/utils/bedToBigBed/makefile 1.4 - lines changed: 2, context: html, text, full: html, text
  • src/utils/bigBedSummary/makefile 1.4 - lines changed: 2, context: html, text, full: html, text
  • src/utils/bigBedToBed/makefile 1.4 - lines changed: 2, context: html, text, full: html, text
  • src/utils/bigWigSummary/makefile 1.4 - lines changed: 2, context: html, text, full: html, text
  • src/utils/bigWigToBedGraph/makefile 1.4 - lines changed: 2, context: html, text, full: html, text
  • src/utils/faFrag/makefile 1.7 - lines changed: 2, context: html, text, full: html, text
  • src/utils/faSize/makefile 1.7 - lines changed: 2, context: html, text, full: html, text
  • src/utils/faSomeRecords/makefile 1.8 - lines changed: 2, context: html, text, full: html, text
  • src/utils/faToNib/makefile 1.12 - lines changed: 2, context: html, text, full: html, text
  • src/utils/faToTwoBit/makefile 1.13 - lines changed: 2, context: html, text, full: html, text
  • src/utils/gtfToGenePred/makefile 1.5 - lines changed: 2, context: html, text, full: html, text
  • src/utils/htmlCheck/makefile 1.8 - lines changed: 2, context: html, text, full: html, text
  • src/utils/textHistogram/makefile 1.14 - lines changed: 2, context: html, text, full: html, text
  • src/utils/twoBitInfo/makefile 1.8 - lines changed: 2, context: html, text, full: html, text
  • src/utils/twoBitToFa/makefile 1.13 - lines changed: 3, context: html, text, full: html, text
  • src/utils/wigToBigWig/makefile 1.5 - lines changed: 2, context: html, text, full: html, text
• Improve the makefile created, add compile target, shorten compile command
  • src/utils/newProg/newProg.c 1.27 - lines changed: 11, context: html, text, full: html, text
• prepare the makefile for userApps make target, now with DESTDIR
  • src/utils/faCount/makefile 1.4 - lines changed: 11, context: html, text, full: html, text
• forgot dependency on the $O for the compile target
  • src/utils/faCount/makefile 1.5 - lines changed: 1, context: html, text, full: html, text
• Add faCount to the userApps list
  • src/makefile 1.58 - lines changed: 3, context: html, text, full: html, text
• Add note about removing track and browser lines
  • src/utils/userApps/bigBedWigs.txt 1.2 - lines changed: 12, context: html, text, full: html, text
• Initial contents
  • src/utils/userApps/bigBedWigs.txt 1.1 - lines changed: 71, context: html, text, full: html, text
  • src/utils/userApps/mkREADME.sh 1.1 - lines changed: 26, context: html, text, full: html, text
• Improved for userApps use
  • src/hg/liftOver/makefile 1.12 - lines changed: 17, context: html, text, full: html, text
• Adding liftOver to the userApps build list
  • src/makefile 1.59 - lines changed: 5, context: html, text, full: html, text