File Changes for angie

v246_base to v247_preview (2011-01-25 to 2011-02-01) v247

• src/hg/hgTables/schema.c
  • lines changed 8, 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/hgTrackUi/hgTrackUi.c
  • lines changed 263, 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/hgTracks/gvfTrack.c
  • lines changed 122, 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/hgTracks.h
  • lines changed 3, 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/makefile
  • lines changed 1, 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/simpleTracks.c
  • lines changed 4, 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/variation.c
  • lines changed 471, 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/hgTracks/variation.h
  • lines changed 5, 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/hgc/gvfClick.c
  • lines changed 55, 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/hgc/hgc.c
  • lines changed 2, 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).
  • lines changed 4, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): minor prettying up of near-genefunctional annotation.
  • lines changed 46, context: html, text, full: html, text
    Feature #1638 (Add "this SNP also maps to" text to hgdpGeo track).
  • lines changed 4, 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/hgc/hgc.h
  • lines changed 4, context: html, text, full: html, text
    Feature #1638 (Add "this SNP also maps to" text to hgdpGeo track).
  • lines changed 3, 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/hgc/hgdpClick.c
  • lines changed 9, context: html, text, full: html, text
    Feature #1638 (Add "this SNP also maps to" text to hgdpGeo track).
• src/hg/hgc/makefile
  • lines changed 1, 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/inc/bed8Attrs.h
  • lines changed 67, 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/inc/snp125.h
  • lines changed 5, 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/inc/snp125Ui.h
  • lines changed 36, 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/lib/bed8Attrs.as
  • lines changed 15, 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/lib/bed8Attrs.c
  • lines changed 211, 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/lib/bed8Attrs.sql
  • lines changed 23, 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/lib/makefile
  • lines changed 1, 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/lib/snp125.c
  • lines changed 30, 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/lib/snp125Ui.c
  • lines changed 177, 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/lib/trackDbCustom.c
  • lines changed 2, 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/makeDb/doc/hg18.txt
  • lines changed 38, 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.
  • 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/hg19.txt
  • lines changed 49, 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}.
  • lines changed 1, 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/schema/all.joiner
  • lines changed 8, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): updated all.joiner: added newsubset tracks, removed nonexistent table snp132Exceptions.
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • lines changed 30, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): Added hg19 overrides for new tracks snp132{Common,Patient,NonUnique}.
  • lines changed 5, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): Added some missing settings forsubset tracks (snpSeq, snpSeqFile) and fixed some visibilities.
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 2, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): Added some missing settings forsubset tracks (snpSeq, snpSeqFile) and fixed some visibilities.
  • lines changed 9, 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.
  • lines changed 1, 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/makeDb/trackDb/snp132.html
  • lines changed 169, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): Changed snp132's shortLabel to"All SNPs (132)"; added new coloring/filtering options and field descriptions to snp132.html.
  • 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/snp132Common.html
  • lines changed 365, 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).
  • 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/snp132NonUnique.html
  • lines changed 366, 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).
  • 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/snp132Patient.html
  • lines changed 367, 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).
  • 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/tagTypes.tab
  • lines changed 1, 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).
  • lines changed 1, 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/makeDb/trackDb/trackDb.ra
  • lines changed 1, 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).
  • lines changed 1, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): Changed snp132's shortLabel to"All SNPs (132)"; added new coloring/filtering options and field descriptions to snp132.html.
  • lines changed 3, context: html, text, full: html, text
    Track #1684 (SNPs 132 (dbSNP)): Added some missing settings forsubset tracks (snpSeq, snpSeqFile) and fixed some visibilities.
• src/hg/snp/snpLoad/snpNcbiToUcsc.c
  • lines changed 19, 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/txGene/txGeneValidation/makefile
  • lines changed 3, context: html, text, full: html, text
    Added no-op clean target to txGeneValidation/makefile to get rid ofstderr complaint from make about lack of clean target.