Commits for angie
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v246_base to v247_preview (2011-01-25 to 2011-02-01) v247
- Track #1684 (SNPs 132 (dbSNP)): Added hg19 overrides for new tracks snp132{Common,Patient,NonUnique}.
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 30, context: html, text, full: html, text
- Track #1684 (SNPs 132 (dbSNP)): Got rid of a couple of the new exceptionsthat were basically echoes of bitfield column values (GenotypeConflict and
ClusterNonOverlappingAlleles). Initially I thought it would be nice to
include those in exceptions for easier filtering, but it's easy enough to
filter on bitfields as well as exceptions. Moreover, it's nice to keep
exceptions UCSC-only, and bitfields dbSNP-only; otherwise it's hard to
explain why we have separate columns for those. Reloaded snp132,
snp132ExceptionDesc, and subsets snp132{Common,Patient,NonUnique,Misc}.
- src/hg/makeDb/doc/hg19.txt - lines changed 49, context: html, text, full: html, text
- src/hg/snp/snpLoad/snpNcbiToUcsc.c - lines changed 19, context: html, text, full: html, text
- Track #1684 (SNPs 132 (dbSNP)): Added new coloring and filtering optionsfor new columns exceptions and bitfields. Fixed remaining hardcoded cart
var names to use track name, keeping backwards compat with old sessions.
Lots of refactoring -- got rid of snp125Extended business (mostly so I
wouldn't have to make a snp132Extended); color is stored in snp->weight
now, and extraName stuff overwrites name. Added new color-sorting in
squish mode so the most interesting SNPs appear at the top. Also added
new trackDb var defaultMaxWeight for the NonUnique subset (so its items
aren't invisible by default).
- src/hg/hgTrackUi/hgTrackUi.c - lines changed 263, context: html, text, full: html, text
- src/hg/hgTracks/variation.c - lines changed 471, context: html, text, full: html, text
- src/hg/hgTracks/variation.h - lines changed 5, context: html, text, full: html, text
- src/hg/lib/snp125Ui.c - lines changed 177, context: html, text, full: html, text
- src/hg/makeDb/trackDb/tagTypes.tab - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/trackDb.ra - lines changed 1, context: html, text, full: html, text
- Merge branch 'master' of angie@hgwdev.cse.ucsc.edu:/data/git/kent
- Track #1684 (SNPs 132 (dbSNP)): Changed snp132's shortLabel to"All SNPs (132)"; added new coloring/filtering options and field
descriptions to snp132.html.
- src/hg/makeDb/trackDb/snp132.html - lines changed 169, context: html, text, full: html, text
- src/hg/makeDb/trackDb/trackDb.ra - lines changed 1, context: html, text, full: html, text
- Track #1684 (SNPs 132 (dbSNP)): Descriptions for new subset tracks.These are pretty much duplicates of snp132.html, but with brief
descriptions of each subset. Also, default max weight for
snp132NonUnique is 3 (1 for all others).
- src/hg/makeDb/trackDb/snp132Common.html - lines changed 365, context: html, text, full: html, text
- src/hg/makeDb/trackDb/snp132NonUnique.html - lines changed 366, context: html, text, full: html, text
- src/hg/makeDb/trackDb/snp132Patient.html - lines changed 367, context: html, text, full: html, text
- Track #1684 (SNPs 132 (dbSNP)): updated all.joiner: added newsubset tracks, removed nonexistent table snp132Exceptions.
- src/hg/makeDb/schema/all.joiner - lines changed 8, context: html, text, full: html, text
- Track #1684 (SNPs 132 (dbSNP)): minor prettying up of near-genefunctional annotation.
- Track #1684 (SNPs 132 (dbSNP)): Added some missing settings forsubset tracks (snpSeq, snpSeqFile) and fixed some visibilities.
- src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 5, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 2, context: html, text, full: html, text
- src/hg/makeDb/trackDb/trackDb.ra - lines changed 3, context: html, text, full: html, text
- Track #1684 (SNPs 132 (dbSNP)): Adding another warning about unreliablebitfield. Sending bug report to dbSNP...
- src/hg/makeDb/trackDb/snp132.html - lines changed 3, context: html, text, full: html, text
- src/hg/makeDb/trackDb/snp132Common.html - lines changed 3, context: html, text, full: html, text
- src/hg/makeDb/trackDb/snp132NonUnique.html - lines changed 3, context: html, text, full: html, text
- src/hg/makeDb/trackDb/snp132Patient.html - lines changed 3, context: html, text, full: html, text
- Feature #1638 (Add "this SNP also maps to" text to hgdpGeo track).
- Added no-op clean target to txGeneValidation/makefile to get rid ofstderr complaint from make about lack of clean target.
- src/hg/txGene/txGeneValidation/makefile - lines changed 3, context: html, text, full: html, text
- hgTables' schema page displays the SQL type of each column, whichcan be a very long unbroken string when the column is an enum or
set with many values. That makes the HTML table painfully wide.
So when the SQL type contains single-quoted comma-separated items,
add a space after each comma so that the HTML cell can break the
list into multiple lines to maintain a reasonable width.
- src/hg/hgTables/schema.c - lines changed 8, context: html, text, full: html, text
- Track #34 (dbVar for human): Fetched ISCA Retrospective dataset fromdbVar and loaded as bed8 plus attributes. Next step: recognize the
new bed8Attrs track type and make a nice track handler.
- src/hg/makeDb/doc/hg18.txt - lines changed 38, context: html, text, full: html, text
- src/hg/makeDb/doc/hg19.txt - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 9, context: html, text, full: html, text
- Track #34 (dbVar for human): Added new track type gvf with basichandlers in hgTracks and hgc. dbVar's GVF attributes are recognized,
esp. var_type is used to color items, and items are sorted using
the Parent keyword so that parents appear immediately before their
children, and children are sorted by var_type. Attributes are
displayed in hgc; need to do a bit better for the Start_range and
End_range (e.g. translate "." to "inner start unknown" etc.).
- src/hg/hgTracks/gvfTrack.c - lines changed 122, context: html, text, full: html, text
- src/hg/hgTracks/hgTracks.h - lines changed 3, context: html, text, full: html, text
- src/hg/hgTracks/makefile - lines changed 1, context: html, text, full: html, text
- src/hg/hgTracks/simpleTracks.c - lines changed 4, context: html, text, full: html, text
- src/hg/inc/bed8Attrs.h - lines changed 67, context: html, text, full: html, text
- src/hg/lib/bed8Attrs.as - lines changed 15, context: html, text, full: html, text
- src/hg/lib/bed8Attrs.c - lines changed 211, context: html, text, full: html, text
- src/hg/lib/bed8Attrs.sql - lines changed 23, context: html, text, full: html, text
- src/hg/lib/trackDbCustom.c - lines changed 2, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/trackDb/tagTypes.tab - lines changed 1, context: html, text, full: html, text
- Track #34 (dbVar for human): oops, forgot to subtract 1 from starts.
- src/hg/makeDb/doc/hg18.txt - lines changed 1, context: html, text, full: html, text
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