Commits for kent
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v251_preview to v251_preview2 (2011-04-26 to 2011-05-03) v251
- Making it so that only visible subtracks are used in the autoScale calcs.
- src/hg/hgTracks/container.c - lines changed 3, context: html, text, full: html, text
- src/hg/hgTracks/multiWig.c - lines changed 3, 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/hg18/trackDb.wgEncode.ra - lines changed 2, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra - lines changed 6, context: html, text, full: html, text
- Fixing compositeTrack tag.
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeReg.ra - lines changed 7, context: html, text, full: html, text
- Adding more metadata fields to the DNase inputs table.
- src/hg/lib/clusterInputDnase.as - lines changed 10, context: html, text, full: html, text
- src/hg/lib/clusterInputDnase.sql - lines changed 16, context: html, text, full: html, text
- src/hg/makeDb/doc/hg19.txt - lines changed 5, context: html, text, full: html, text
- Adding raTagVals function.
- 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.
- src/hg/hgc/peakClusters.c - lines changed 196, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra - lines changed 3, context: html, text, full: html, text
- Adding metadata for high level DNase and TFBS tracks.
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeReg.ra - lines changed 72, 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/hgc/peakClusters.c - lines changed 177, context: html, text, full: html, text
- src/hg/makeDb/doc/hg19.txt - lines changed 1, context: html, text, full: html, text
- Freen tests new ra handling a bit.
- src/hg/oneShot/freen/freen.c - lines changed 15, context: html, text, full: html, text
- Hiding genometype track by default.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibGenotype.ra - lines changed 1, 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/hgTracks/multiWig.c - lines changed 13, context: html, text, full: html, text
- Fixing it so that 16 as the max smoothing window appears only one place.
- Updating inputTrackTable description and depreciating inputTracksSubgroupDisplay, which proved too fragile of a method.
- src/hg/makeDb/trackDb/README - lines changed 8, 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/doc/hg19.txt - lines changed 15, context: html, text, full: html, text
- src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 11, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeReg.ra - lines changed 28, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra - lines changed 23, 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/makeDb/trackDb/loadTracks - lines changed 2, context: html, text, full: html, text
- Changing strand from '+' to '.' since it really is unknown.
- src/hg/makeDb/hgBedsToBedExps/hgBedsToBedExps.c - lines changed 1, context: html, text, full: html, text
- Adding text about the pooling and normalization in the description of RNA seq.
- src/hg/makeDb/trackDb/human/hg19/wgEncodeRegTxn.html - lines changed 3, context: html, text, full: html, text
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