Commits for kent

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

• Adding HepG2 cell line to wgEncodeReg tracks. Making room for this in the rainbow color scheme.
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra - lines changed 65, context: html, text, full: html, text
• Freen does some colorful stuff.
  • src/hg/oneShot/freen/freen.c - lines changed 49, 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.
  • src/hg/lib/hui.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/hgTrackUi/hgTrackUi.c - lines changed 1, context: html, text, full: html, text
• Adding inputTrackList build, and removing some old no longer used steps from the part on the wgEncodeReg clusters.
  • src/hg/makeDb/doc/hg18.txt - lines changed 82, 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/hgTracks/wigTrack.c - lines changed 7, context: html, text, full: html, text
  • src/hg/lib/hui.c - lines changed 7, 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/hgc/peakClusters.c - lines changed 17, context: html, text, full: html, text
• Adding inputTrackTable tags to wgEncodeReg subtracks that need it.
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra - 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/README - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 1, 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/factorSource.c - lines changed 12, context: html, text, full: html, text
• Defining a new table type for benefit of factorSource type tracks.
  • src/hg/lib/clusterInputTrackTable.as - lines changed 2, context: html, text, full: html, text
  • src/hg/lib/clusterInputTrackTable.sql - lines changed 4, context: html, text, full: html, text
• Adding clusterInputTrackTable.as and sql file to support regulatory cluster tracks.
  • src/hg/lib/clusterInputTrackTable.as - lines changed 6, context: html, text, full: html, text
  • src/hg/lib/clusterInputTrackTable.sql - lines changed 14, context: html, text, full: html, text
• Second pass through wgEncodeReg build doc.
  • src/hg/makeDb/doc/hg18.txt - lines changed 712, context: html, text, full: html, text
• Adding -dupeLetterOk option. Closing a file left dangling open.
  • src/hg/makeDb/hgBedsToBedExps/hgBedsToBedExps.c - lines changed 12, 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/encodeMergeReplicates/encodeMergeReplicates.c - lines changed 27, context: html, text, full: html, text
• Adding tabList and cellLetter options. Mistakenly checked in test case for cellLetter with previous commit.
  • src/hg/regulate/regClusterBedExpCfg/regClusterBedExpCfg.c - lines changed 61, context: html, text, full: html, text
• Improved comment.
  • src/hg/regulate/regClusterBedExpCfg/cellLetter.tab - lines changed 25, context: html, text, full: html, text
  • src/hg/utils/mdbQuery/mdbQuery.c - lines changed 1, context: html, text, full: html, text
• Working on program that will set up batch file to merge replicates.
  • src/hg/encode/encodeMergeReplicatesBatch/encodeMergeReplicatesBatch.c - lines changed 207, context: html, text, full: html, text
  • src/hg/encode/encodeMergeReplicatesBatch/expected.ra - lines changed 410, context: html, text, full: html, text
  • src/hg/encode/encodeMergeReplicatesBatch/expected.sh - lines changed 83, context: html, text, full: html, text
  • src/hg/encode/encodeMergeReplicatesBatch/makefile - lines changed 23, context: html, text, full: html, text
  • src/hg/encode/encodeMergeReplicatesBatch/test.in - lines changed 972, context: html, text, full: html, text
• Turning 3col to 4col output.
  • src/hg/utils/mdbQuery/mdbQuery.c - lines changed 6, context: html, text, full: html, text
• Making metaObject be a synonym for obj in selects.
  • src/hg/utils/mdbQuery/mdbQuery.c - lines changed 3, context: html, text, full: html, text
• Making ra output use metaObject rather than obj.
  • src/hg/utils/mdbQuery/mdbQuery.c - lines changed 1, context: html, text, full: html, text
• Improving some comments and a function name.
  • src/hg/utils/mdbQuery/mdbQuery.c - lines changed 7, context: html, text, full: html, text
• Adding error message when no from clause.
  • src/hg/utils/mdbQuery/mdbQuery.c - lines changed 12, context: html, text, full: html, text