File Changes for kent

v251_preview to v251_preview2 (2011-04-26 to 2011-05-03) v251

• src/hg/hgTracks/container.c
  • lines changed 3, context: html, text, full: html, text
    Making it so that only visible subtracks are used in the autoScale calcs.
• src/hg/hgTracks/multiWig.c
  • lines changed 3, context: html, text, full: html, text
    Making it so that only visible subtracks are used in the autoScale calcs.
  • lines changed 13, context: html, text, full: html, text
    Fixing Katrina's 7) Rainbow tracks: when Display mode is set to 'dense' and the Overlay method is set to 'none,' in hgTracks the labels are shifted down, resulting in partially cutting-off the bottom-most label.
• src/hg/hgc/peakClusters.c
  • lines changed 196, context: html, text, full: html, text
    Making it so that the DNase clusters can get their metadata from an associated table rather than rummaging through groups and trackDb, following same pattern did for factorSource tracks. It turns out the ENCODE tracks change so much, having one depend on another just is an invitation to problems.
  • lines changed 177, context: html, text, full: html, text
    More work on DNAse and TFBS cluster tracks' details page. Making newer system, where a minimal amount of metadata is in an associated table that goes with the track, include full metadata if the input track is still available. Making older system just omit a row in the table rather than crashing if the input track has gone missing.
• src/hg/inc/hui.h
  • lines changed 3, context: html, text, full: html, text
    Fixing it so that 16 as the max smoothing window appears only one place.
• src/hg/lib/clusterInputDnase.as
  • lines changed 10, context: html, text, full: html, text
    Adding more metadata fields to the DNase inputs table.
• src/hg/lib/clusterInputDnase.sql
  • lines changed 16, context: html, text, full: html, text
    Adding more metadata fields to the DNase inputs table.
• src/hg/makeDb/doc/hg19.txt
  • lines changed 5, context: html, text, full: html, text
    Adding more metadata fields to the DNase inputs table.
  • lines changed 1, context: html, text, full: html, text
    More work on DNAse and TFBS cluster tracks' details page. Making newer system, where a minimal amount of metadata is in an associated table that goes with the track, include full metadata if the input track is still available. Making older system just omit a row in the table rather than crashing if the input track has gone missing.
  • lines changed 15, context: html, text, full: html, text
    Renaming Caltech RNA components of wgEncodeReg to start with their parent track name, wgEncodeRegTxn, to keep it consistent with everything else and keep various scripts working. Adjusting default visibilities and view limits on rainbows. Defining sourceObj metadata tag and adding it to pooled Caltech RNAs.
• src/hg/makeDb/hgBedsToBedExps/hgBedsToBedExps.c
  • lines changed 1, context: html, text, full: html, text
    Changing strand from '+' to '.' since it really is unknown.
• src/hg/makeDb/trackDb/README
  • lines changed 8, context: html, text, full: html, text
    Updating inputTrackTable description and depreciating inputTracksSubgroupDisplay, which proved too fragile of a method.
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 11, context: html, text, full: html, text
    Renaming Caltech RNA components of wgEncodeReg to start with their parent track name, wgEncodeRegTxn, to keep it consistent with everything else and keep various scripts working. Adjusting default visibilities and view limits on rainbows. Defining sourceObj metadata tag and adding it to pooled Caltech RNAs.
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    Making word before histone mark in rainbow tracks be 'layered' as per Bob's suggestion. Moving ENCODE to end of some short labels.
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeReg.ra
  • lines changed 7, context: html, text, full: html, text
    Fixing compositeTrack tag.
  • lines changed 72, context: html, text, full: html, text
    Adding metadata for high level DNase and TFBS tracks.
  • lines changed 28, context: html, text, full: html, text
    Renaming Caltech RNA components of wgEncodeReg to start with their parent track name, wgEncodeRegTxn, to keep it consistent with everything else and keep various scripts working. Adjusting default visibilities and view limits on rainbows. Defining sourceObj metadata tag and adding it to pooled Caltech RNAs.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.ra
  • lines changed 1, context: html, text, full: html, text
    Hiding genometype track by default.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra
  • lines changed 6, context: html, text, full: html, text
    Making word before histone mark in rainbow tracks be 'layered' as per Bob's suggestion. Moving ENCODE to end of some short labels.
  • lines changed 3, context: html, text, full: html, text
    Making it so that the DNase clusters can get their metadata from an associated table rather than rummaging through groups and trackDb, following same pattern did for factorSource tracks. It turns out the ENCODE tracks change so much, having one depend on another just is an invitation to problems.
  • lines changed 23, context: html, text, full: html, text
    Renaming Caltech RNA components of wgEncodeReg to start with their parent track name, wgEncodeRegTxn, to keep it consistent with everything else and keep various scripts working. Adjusting default visibilities and view limits on rainbows. Defining sourceObj metadata tag and adding it to pooled Caltech RNAs.
• src/hg/makeDb/trackDb/human/hg19/wgEncodeRegTxn.html
  • lines changed 3, context: html, text, full: html, text
    Adding text about the pooling and normalization in the description of RNA seq.
• src/hg/makeDb/trackDb/loadTracks
  • lines changed 2, context: html, text, full: html, text
    Changing some /cluster/data to the newer /hive/data/genomes since /cluster/data is just now a symbolic link to /hive/data/genomes the last few years, and the /cluster file system was being flaky.
• src/hg/oneShot/freen/freen.c
  • lines changed 15, context: html, text, full: html, text
    Freen tests new ra handling a bit.
• src/inc/ra.h
  • lines changed 3, context: html, text, full: html, text
    Adding raTagVals function.
• src/lib/ra.c
  • lines changed 19, context: html, text, full: html, text
    Adding raTagVals function.