File Changes for kent

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

• src/hg/encode/encodeMergeReplicates/encodeMergeReplicates.c
  • lines changed 2, context: html, text, full: html, text
    Improving some comments.
  • lines changed 49, context: html, text, full: html, text
    Adding uniqueName option.
  • lines changed 78, context: html, text, full: html, text
    Adding threshold, maxMin, and addMin options.
  • lines changed 36, context: html, text, full: html, text
    Adding -add option to add signal column rather than average within a cluster.
  • lines changed 168, context: html, text, full: html, text
    Starting work on replicate merger. Works on narrowPeak files so far witha few options.
    
• src/hg/encode/encodeMergeReplicates/expRep1Rep2Add.narrowPeak
  • lines changed 36, context: html, text, full: html, text
    Adding -add option to add signal column rather than average within a cluster.
• src/hg/encode/encodeMergeReplicates/expRep1Rep2AddAddMin.narrowPeak
  • lines changed 30, context: html, text, full: html, text
    Adding another test case
• src/hg/encode/encodeMergeReplicates/expRep1Rep2Agree.narrowPeak
  • lines changed 18, context: html, text, full: html, text
    Starting work on replicate merger. Works on narrowPeak files so far witha few options.
    
• src/hg/encode/encodeMergeReplicates/expRep1Rep2Default.narrowPeak
  • lines changed 36, context: html, text, full: html, text
    Starting work on replicate merger. Works on narrowPeak files so far witha few options.
    
• src/hg/encode/encodeMergeReplicates/expRep1Rep2Threshold10.narrowPeak
  • lines changed 28, context: html, text, full: html, text
    Adding threshold, maxMin, and addMin options.
• src/hg/encode/encodeMergeReplicates/makefile
  • lines changed 5, context: html, text, full: html, text
    Adding another test case
  • lines changed 4, context: html, text, full: html, text
    Adding threshold, maxMin, and addMin options.
  • lines changed 6, context: html, text, full: html, text
    Adding -add option to add signal column rather than average within a cluster.
  • lines changed 29, context: html, text, full: html, text
    Adding some test cases
• src/hg/encode/encodeMergeReplicates/rep1.narrowPeak
  • lines changed 32, context: html, text, full: html, text
    Starting work on replicate merger. Works on narrowPeak files so far witha few options.
    
• src/hg/encode/encodeMergeReplicates/rep2.narrowPeak
  • lines changed 25, context: html, text, full: html, text
    Starting work on replicate merger. Works on narrowPeak files so far witha few options.
    
• src/hg/hgTracks/gbrowseTest.c
  • lines changed 1, context: html, text, full: html, text
    Renaming cartNewEmpty to cartFromCgiOnly.
  • lines changed 1, context: html, text, full: html, text
    Renaming cartNewEmpty to cartFromCgiOnly.
• src/hg/hgTracks/hgTrackRender.c
  • lines changed 105, context: html, text, full: html, text
    Rearranging things so that hgTracks.c module is not so severely changed by the web service stuff.
  • 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/hgTracks.c
  • lines changed 5626, context: html, text, full: html, text
    Rearranging things so that hgTracks.c module is not so severely changed by the web service stuff.
  • lines changed 5605, 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/hgTracks.h
  • lines changed 18, 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/mainMain.c
  • lines changed 78, context: html, text, full: html, text
    Rearranging things so that hgTracks.c module is not so severely changed by the web service stuff.
• src/hg/hgTracks/makefile
  • lines changed 1, context: html, text, full: html, text
    Making hgRenderTracks look up default track settings before layering on stuff passed in .
  • lines changed 12, context: html, text, full: html, text
    Rearranging things so that hgTracks.c module is not so severely changed by the web service stuff.
  • lines changed 7, 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/renderMain.c
  • lines changed 50, context: html, text, full: html, text
    Making hgRenderTracks look up default track settings before layering on stuff passed in .
  • lines changed 105, context: html, text, full: html, text
    Rearranging things so that hgTracks.c module is not so severely changed by the web service stuff.
• src/hg/inc/cart.h
  • lines changed 9, 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.
    
  • lines changed 9, 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/hdb.h
  • lines changed 6, context: html, text, full: html, text
    adding hTrackDbForTrackAndAncestors
• src/hg/inc/trackDb.h
  • lines changed 10, 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.
    
  • lines changed 10, 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/lib/cart.c
  • lines changed 25, 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.
    
  • lines changed 25, 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/lib/hdb.c
  • lines changed 38, context: html, text, full: html, text
    adding hTrackDbForTrackAndAncestors
• src/hg/lib/trackDbCustom.c
  • lines changed 11, 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.
    
  • lines changed 11, 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/makeDb/doc/hg18.txt
  • lines changed 32, 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/hgBedsToBedExps/hgBedsToBedExps.c
  • lines changed 1, context: html, text, full: html, text
    Improving usage statement.
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • lines changed 36, context: html, text, full: html, text
    Polishing names and labels for enhancer subtracks of wgEncodeReg.
• src/hg/regulate/regCluster/makefile
  • lines changed 0, context: html, text, full: html, text
    Moving clustering to library.
• src/hg/regulate/regCluster/regCluster.c
  • lines changed 2, context: html, text, full: html, text
    Making item variable a bit more local.
  • lines changed 256, context: html, text, full: html, text
    Moving clustering to library.
• src/hg/regulate/regClusterBedExpCfg/regClusterBedExpCfg.c
  • lines changed 6, context: html, text, full: html, text
    Changing score column from 7 to 6 and #defining it as a constant.
• src/hg/utils/mdbQuery/makefile
  • lines changed 18, context: html, text, full: html, text
    First cut of mdbQuery utility.
• src/hg/utils/mdbQuery/mdbQuery.c
  • lines changed 49, context: html, text, full: html, text
    Adding -out=tab option and renaming old out=table to out=3col.
  • lines changed 21, context: html, text, full: html, text
    Implemented count(*)
  • lines changed 209, context: html, text, full: html, text
    First cut of mdbQuery utility.
• src/inc/peakCluster.h
  • lines changed 98, context: html, text, full: html, text
    Moving clustering to library.
• src/lib/makefile
  • lines changed 2, context: html, text, full: html, text
    Adding peakCluster to library.
• src/lib/peakCluster.c
  • lines changed 2, context: html, text, full: html, text
    Improving comment.
  • lines changed 243, context: html, text, full: html, text
    Moving clustering to library.
• src/oneShot/testGitRename/justAnotherTest.c
  • lines changed 34, context: html, text, full: html, text
    MOved a function up a bit.
  • lines changed 55, context: html, text, full: html, text
    Merged two files.
• src/oneShot/testGitRename/makefile
  • lines changed 1, context: html, text, full: html, text
    Propagating rename to makefile.
  • lines changed 1, context: html, text, full: html, text
    MOved a function up a bit.
  • lines changed 5, context: html, text, full: html, text
    Split testGitRename into two modules.
  • lines changed 18, 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/test.expected
  • lines changed 2, 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/test.in
  • lines changed 2, 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/testGitRename.c
  • lines changed 35, context: html, text, full: html, text
    Merged two files.
  • lines changed 4, 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.
  • lines changed 13, context: html, text, full: html, text
    Split testGitRename into two modules.
  • lines changed 14, context: html, text, full: html, text
    Split testGitRename into two modules.
  • lines changed 38, 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/upperFile.c
  • lines changed 20, context: html, text, full: html, text
    Merged two files.
  • lines changed 4, 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.
  • lines changed 2, context: html, text, full: html, text
    Split testGitRename into two modules.
  • lines changed 19, context: html, text, full: html, text
    Split testGitRename into two modules.
• src/oneShot/testGitRename/upperFile.h
  • lines changed 4, 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.