Commits for kent

v234_preview to v234_base (2010-06-15 to 2010-06-22) v234

• Adding -out=tab option and renaming old out=table to out=3col.
  • src/hg/utils/mdbQuery/mdbQuery.c - lines changed 49, context: html, text, full: html, text
• Implemented count(*)
  • src/hg/utils/mdbQuery/mdbQuery.c - lines changed 21, context: html, text, full: html, text
• First cut of mdbQuery utility.
  • src/hg/utils/mdbQuery/makefile - lines changed 18, context: html, text, full: html, text
  • src/hg/utils/mdbQuery/mdbQuery.c - lines changed 209, context: html, text, full: html, text
• Merge branch 'master' of kent@hgwdev.cse.ucsc.edu:/data/git/kent
• Making hgRenderTracks look up default track settings before layering on stuff passed in .
  • src/hg/hgTracks/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/hgTracks/renderMain.c - lines changed 50, context: html, text, full: html, text
• adding hTrackDbForTrackAndAncestors
  • src/hg/inc/hdb.h - lines changed 6, context: html, text, full: html, text
  • src/hg/lib/hdb.c - lines changed 38, context: html, text, full: html, text
• Propagating rename to makefile.
  • src/oneShot/testGitRename/makefile - lines changed 1, context: html, text, full: html, text
• MOved a function up a bit.
  • src/oneShot/testGitRename/justAnotherTest.c - lines changed 34, context: html, text, full: html, text
  • src/oneShot/testGitRename/makefile - lines changed 1, context: html, text, full: html, text
• Merged two files.
  • src/oneShot/testGitRename/justAnotherTest.c - lines changed 55, context: html, text, full: html, text
  • src/oneShot/testGitRename/testGitRename.c - lines changed 35, context: html, text, full: html, text
  • src/oneShot/testGitRename/upperFile.c - lines changed 20, context: html, text, full: html, text
• Renaming function and putting prototype for it in a shared header file. Again this is all part of testing renaming/splitting/merging functions.
  • src/oneShot/testGitRename/testGitRename.c - lines changed 4, context: html, text, full: html, text
  • src/oneShot/testGitRename/upperFile.c - lines changed 4, context: html, text, full: html, text
  • src/oneShot/testGitRename/upperFile.h - lines changed 4, context: html, text, full: html, text
• Split testGitRename into two modules.
  • src/oneShot/testGitRename/makefile - lines changed 5, context: html, text, full: html, text
  • src/oneShot/testGitRename/testGitRename.c - lines changed 13, context: html, text, full: html, text
• Split testGitRename into two modules.
  • src/oneShot/testGitRename/upperFile.c - lines changed 2, context: html, text, full: html, text
• Split testGitRename into two modules.
  • src/oneShot/testGitRename/testGitRename.c - lines changed 14, context: html, text, full: html, text
  • src/oneShot/testGitRename/upperFile.c - lines changed 19, context: html, text, full: html, text
• Checking in a little something just to work with renaming and merging in a safe place.
  • src/oneShot/testGitRename/makefile - lines changed 18, context: html, text, full: html, text
  • src/oneShot/testGitRename/test.expected - lines changed 2, context: html, text, full: html, text
  • src/oneShot/testGitRename/test.in - lines changed 2, context: html, text, full: html, text
  • src/oneShot/testGitRename/testGitRename.c - lines changed 38, context: html, text, full: html, text
• Renaming cartNewEmpty to cartFromCgiOnly.
  • src/hg/hgTracks/gbrowseTest.c - lines changed 1, context: html, text, full: html, text
• Adding a few functions to cart and trackDb to make it easier to buildcarts and trackDbs out of an existing string-valued hash.
  
  • src/hg/inc/cart.h - lines changed 9, context: html, text, full: html, text
  • src/hg/inc/trackDb.h - lines changed 10, context: html, text, full: html, text
  • src/hg/lib/cart.c - lines changed 25, context: html, text, full: html, text
  • src/hg/lib/trackDbCustom.c - lines changed 11, context: html, text, full: html, text
• Merge branch 'master' of kent@hgwdev.cse.ucsc.edu:/data/git/kent
• Rearranging things so that hgTracks.c module is not so severely changed by the web service stuff.
  • src/hg/hgTracks/hgTrackRender.c - lines changed 105, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.c - lines changed 5626, context: html, text, full: html, text
  • src/hg/hgTracks/mainMain.c - lines changed 78, context: html, text, full: html, text
  • src/hg/hgTracks/makefile - lines changed 12, context: html, text, full: html, text
  • src/hg/hgTracks/renderMain.c - lines changed 105, context: html, text, full: html, text
• Making hgTrackRender - a program that renders one track quickly - currently from the command line in postscript only.
  • src/hg/hgTracks/hgTrackRender.c - lines changed 105, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.c - lines changed 5605, context: html, text, full: html, text
  • src/hg/hgTracks/hgTracks.h - lines changed 18, context: html, text, full: html, text
  • src/hg/hgTracks/makefile - lines changed 7, context: html, text, full: html, text
• Renaming cartNewEmpty to cartFromCgiOnly.
  • src/hg/hgTracks/gbrowseTest.c - lines changed 1, context: html, text, full: html, text
• Adding a few functions to cart and trackDb to make it easier to buildcarts and trackDbs out of an existing string-valued hash.
  
  • src/hg/inc/cart.h - lines changed 9, context: html, text, full: html, text
  • src/hg/inc/trackDb.h - lines changed 10, context: html, text, full: html, text
  • src/hg/lib/cart.c - lines changed 25, context: html, text, full: html, text
  • src/hg/lib/trackDbCustom.c - lines changed 11, context: html, text, full: html, text
• Merge branch 'master' of kent@hgwdev.cse.ucsc.edu:/data/git/kent
• Merge branch 'master' of kent@hgwdev.cse.ucsc.edu:/data/git/kent
• Changing score column from 7 to 6 and #defining it as a constant.
  • src/hg/regulate/regClusterBedExpCfg/regClusterBedExpCfg.c - lines changed 6, context: html, text, full: html, text
• Starting to work on integrating Hudsonalpha ChIP data. Describing how to call encodeMergeReplicates and convert from broad to narrow peak.
  • src/hg/makeDb/doc/hg18.txt - lines changed 32, context: html, text, full: html, text
• Improving usage statement.
  • src/hg/makeDb/hgBedsToBedExps/hgBedsToBedExps.c - lines changed 1, context: html, text, full: html, text
• Improving comment.
  • src/lib/peakCluster.c - lines changed 2, context: html, text, full: html, text
• Merge branch 'master' of kent@hgwdev.cse.ucsc.edu:/data/git/kent
• Improving some comments.
  • src/hg/encode/encodeMergeReplicates/encodeMergeReplicates.c - lines changed 2, context: html, text, full: html, text
• Merge branch 'master' of kent@hgwdev.cse.ucsc.edu:/data/git/kent
• Adding uniqueName option.
  • src/hg/encode/encodeMergeReplicates/encodeMergeReplicates.c - lines changed 49, context: html, text, full: html, text
• Adding another test case
  • src/hg/encode/encodeMergeReplicates/expRep1Rep2AddAddMin.narrowPeak - lines changed 30, context: html, text, full: html, text
  • src/hg/encode/encodeMergeReplicates/makefile - lines changed 5, context: html, text, full: html, text
• Adding threshold, maxMin, and addMin options.
  • src/hg/encode/encodeMergeReplicates/encodeMergeReplicates.c - lines changed 78, context: html, text, full: html, text
  • src/hg/encode/encodeMergeReplicates/expRep1Rep2Threshold10.narrowPeak - lines changed 28, context: html, text, full: html, text
  • src/hg/encode/encodeMergeReplicates/makefile - lines changed 4, context: html, text, full: html, text
• Adding -add option to add signal column rather than average within a cluster.
  • src/hg/encode/encodeMergeReplicates/encodeMergeReplicates.c - lines changed 36, context: html, text, full: html, text
  • src/hg/encode/encodeMergeReplicates/expRep1Rep2Add.narrowPeak - lines changed 36, context: html, text, full: html, text
  • src/hg/encode/encodeMergeReplicates/makefile - lines changed 6, context: html, text, full: html, text
• Merge branch 'master' of kent@hgwdev.cse.ucsc.edu:/data/git/kent
• Adding peakCluster to library.
  • src/lib/makefile - lines changed 2, context: html, text, full: html, text
• Making item variable a bit more local.
  • src/hg/regulate/regCluster/regCluster.c - lines changed 2, context: html, text, full: html, text
• Polishing names and labels for enhancer subtracks of wgEncodeReg.
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra - lines changed 36, context: html, text, full: html, text
• Adding some test cases
  • src/hg/encode/encodeMergeReplicates/makefile - lines changed 29, context: html, text, full: html, text
• Starting work on replicate merger. Works on narrowPeak files so far witha few options.
  
  • src/hg/encode/encodeMergeReplicates/encodeMergeReplicates.c - lines changed 168, context: html, text, full: html, text
  • src/hg/encode/encodeMergeReplicates/expRep1Rep2Agree.narrowPeak - lines changed 18, context: html, text, full: html, text
  • src/hg/encode/encodeMergeReplicates/expRep1Rep2Default.narrowPeak - lines changed 36, context: html, text, full: html, text
  • src/hg/encode/encodeMergeReplicates/rep1.narrowPeak - lines changed 32, context: html, text, full: html, text
  • src/hg/encode/encodeMergeReplicates/rep2.narrowPeak - lines changed 25, context: html, text, full: html, text
• Moving clustering to library.
  • src/hg/regulate/regCluster/makefile - lines changed 0, context: html, text, full: html, text
  • src/hg/regulate/regCluster/regCluster.c - lines changed 256, context: html, text, full: html, text
  • src/inc/peakCluster.h - lines changed 98, context: html, text, full: html, text
  • src/lib/peakCluster.c - lines changed 243, context: html, text, full: html, text