File Changes for kent

v234_base to v235_preview (2010-06-22 to 2010-06-29) v235

• src/hg/encode/encodeMergeReplicates/encodeMergeReplicates.c
  • lines changed 27, context: html, text, full: html, text
    Improving readability by adding comments and moving a few lines around in response to Brian's review.
• src/hg/encode/encodeMergeReplicatesBatch/encodeMergeReplicatesBatch.c
  • lines changed 207, context: html, text, full: html, text
    Working on program that will set up batch file to merge replicates.
• src/hg/encode/encodeMergeReplicatesBatch/expected.ra
  • lines changed 410, context: html, text, full: html, text
    Working on program that will set up batch file to merge replicates.
• src/hg/encode/encodeMergeReplicatesBatch/expected.sh
  • lines changed 83, context: html, text, full: html, text
    Working on program that will set up batch file to merge replicates.
• src/hg/encode/encodeMergeReplicatesBatch/makefile
  • lines changed 23, context: html, text, full: html, text
    Working on program that will set up batch file to merge replicates.
• src/hg/encode/encodeMergeReplicatesBatch/test.in
  • lines changed 972, context: html, text, full: html, text
    Working on program that will set up batch file to merge replicates.
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 1, context: html, text, full: html, text
    Fixing order of subtracks of supertracks in hgTrackUi so works for both wgEncodeReg and for wgEncodeHistone....
• src/hg/hgTracks/factorSource.c
  • lines changed 12, context: html, text, full: html, text
    Making it so that in dense mode the darker, higher scoring, items are drawn on top of lighter items.
• src/hg/hgTracks/wigTrack.c
  • lines changed 7, context: html, text, full: html, text
    Making log transform for wig more apparent in graph, and clarifying it's really ln(x+1) rather than the log(x) you might expect.
• src/hg/hgc/peakClusters.c
  • lines changed 17, context: html, text, full: html, text
    Getting list of tracks that are being clustered from a database table (defined by an inputTrackTable trackDb tag) rather than trying to figure them out from the trackDb subGroup data. This fixes a problem that sometimes caused tracks that should have appeared in the details page to be missed after the HudsonAlpha data integration into the wgEncodeRegTfbs track.
• src/hg/lib/clusterInputTrackTable.as
  • lines changed 2, context: html, text, full: html, text
    Defining a new table type for benefit of factorSource type tracks.
  • lines changed 6, context: html, text, full: html, text
    Adding clusterInputTrackTable.as and sql file to support regulatory cluster tracks.
• src/hg/lib/clusterInputTrackTable.sql
  • lines changed 4, context: html, text, full: html, text
    Defining a new table type for benefit of factorSource type tracks.
  • lines changed 14, context: html, text, full: html, text
    Adding clusterInputTrackTable.as and sql file to support regulatory cluster tracks.
• src/hg/lib/hui.c
  • lines changed 1, context: html, text, full: html, text
    Making it so that subtracks of composites without priorities are sorted by a case-insensitive comparision rather than a case sensitive comparison of label, which is consistent to how tracks are sorted elsewhere.
  • lines changed 7, context: html, text, full: html, text
    Making log transform for wig more apparent in graph, and clarifying it's really ln(x+1) rather than the log(x) you might expect.
• src/hg/makeDb/doc/hg18.txt
  • lines changed 82, context: html, text, full: html, text
    Adding inputTrackList build, and removing some old no longer used steps from the part on the wgEncodeReg clusters.
  • lines changed 712, context: html, text, full: html, text
    Second pass through wgEncodeReg build doc.
• src/hg/makeDb/hgBedsToBedExps/hgBedsToBedExps.c
  • lines changed 12, context: html, text, full: html, text
    Adding -dupeLetterOk option. Closing a file left dangling open.
• src/hg/makeDb/trackDb/README
  • lines changed 3, context: html, text, full: html, text
    Adding inputTrackTable tag to trackDb, which is used by details page of factorSource type tracks.
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • lines changed 65, context: html, text, full: html, text
    Adding HepG2 cell line to wgEncodeReg tracks. Making room for this in the rainbow color scheme.
  • lines changed 3, context: html, text, full: html, text
    Adding inputTrackTable tags to wgEncodeReg subtracks that need it.
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    Adding inputTrackTable tag to trackDb, which is used by details page of factorSource type tracks.
• src/hg/oneShot/freen/freen.c
  • lines changed 49, context: html, text, full: html, text
    Freen does some colorful stuff.
• src/hg/regulate/regClusterBedExpCfg/cellLetter.tab
  • lines changed 25, context: html, text, full: html, text
    Improved comment.
• src/hg/regulate/regClusterBedExpCfg/regClusterBedExpCfg.c
  • lines changed 61, context: html, text, full: html, text
    Adding tabList and cellLetter options. Mistakenly checked in test case for cellLetter with previous commit.
• src/hg/utils/mdbQuery/mdbQuery.c
  • lines changed 1, context: html, text, full: html, text
    Improved comment.
  • lines changed 6, context: html, text, full: html, text
    Turning 3col to 4col output.
  • lines changed 3, context: html, text, full: html, text
    Making metaObject be a synonym for obj in selects.
  • lines changed 1, context: html, text, full: html, text
    Making ra output use metaObject rather than obj.
  • lines changed 7, context: html, text, full: html, text
    Improving some comments and a function name.
  • lines changed 12, context: html, text, full: html, text
    Adding error message when no from clause.