File Changes for kate

v304_preview2 to v304_base (2014-08-04 to 2014-08-11) v304

• src/hg/inc/gtexData.h
  • lines changed 64, context: html, text, full: html, text
    Tool to load GTEx (NIH Common Fund Gene Tissue Expression). Quite similar to microarray table organization.
• src/hg/inc/gtexSample.h
  • lines changed 69, context: html, text, full: html, text
    Tool to load GTEx (NIH Common Fund Gene Tissue Expression). Quite similar to microarray table organization.
• src/hg/lib/bed5SourceVals.as
  • lines changed 12, context: html, text, full: html, text
    Generalize sourceScores, per Angie's suggestion
• src/hg/lib/gtexData.as
  • lines changed 7, context: html, text, full: html, text
    Tool to load GTEx (NIH Common Fund Gene Tissue Expression). Quite similar to microarray table organization.
• src/hg/lib/gtexData.c
  • lines changed 156, context: html, text, full: html, text
    Tool to load GTEx (NIH Common Fund Gene Tissue Expression). Quite similar to microarray table organization.
• src/hg/lib/gtexSample.as
  • lines changed 8, context: html, text, full: html, text
    Tool to load GTEx (NIH Common Fund Gene Tissue Expression). Quite similar to microarray table organization.
• src/hg/lib/gtexSample.c
  • lines changed 155, context: html, text, full: html, text
    Tool to load GTEx (NIH Common Fund Gene Tissue Expression). Quite similar to microarray table organization.
• src/hg/lib/wgEncodeRegDnaseClusteredSources.as
  • lines changed 6, context: html, text, full: html, text
    Renaming cells table to sources and adding .as. refs #13490
  • lines changed 1, context: html, text, full: html, text
    Correct tablename mismatch
• src/hg/makeDb/doc/encodeRegHg19.txt
  • lines changed 12, context: html, text, full: html, text
    Adding source table that describes sourceIds in main bed table. Not currently used by hgc (which still uses inputTrackTable). It is there for VAI. refs 13490
  • lines changed 8, context: html, text, full: html, text
    Rename Cells table to Sources. refs #13490
  • lines changed 1, context: html, text, full: html, text
    Renaming cells table to sources and adding .as. refs #13490
• src/hg/makeDb/outside/hgGtex/expected/gtexTest.tab
  • lines changed 3, context: html, text, full: html, text
    Add trivial test to Gtex loader
• src/hg/makeDb/outside/hgGtex/expected/gtexTestSamples.tab
  • lines changed 2921, context: html, text, full: html, text
    Add trivial test to Gtex loader
• src/hg/makeDb/outside/hgGtex/hgGtex.c
  • lines changed 231, context: html, text, full: html, text
    Tool to load GTEx (NIH Common Fund Gene Tissue Expression). Quite similar to microarray table organization.
  • lines changed 68, context: html, text, full: html, text
    Minor cleanup
  • lines changed 70, context: html, text, full: html, text
    Add sample grouping of Gtex data
  • lines changed 59, context: html, text, full: html, text
    Medians basically works
  • lines changed 4, context: html, text, full: html, text
    Add debug
  • lines changed 4, context: html, text, full: html, text
    Fix problem with median compute (lost last sample in set)
  • lines changed 2, context: html, text, full: html, text
    Fix another off by one err
• src/hg/makeDb/outside/hgGtex/input/samples.txt
  • lines changed 4502, context: html, text, full: html, text
    Add trivial test to Gtex loader
  • lines changed 4502, context: html, text, full: html, text
    Aim GTex tests at real data
• src/hg/makeDb/outside/hgGtex/input/small.gct
  • lines changed 6, context: html, text, full: html, text
    Add trivial test to Gtex loader
  • lines changed 6, context: html, text, full: html, text
    Aim GTex tests at real data
• src/hg/makeDb/outside/hgGtex/makefile
  • lines changed 3, context: html, text, full: html, text
    Tool to load GTEx (NIH Common Fund Gene Tissue Expression). Quite similar to microarray table organization.
  • lines changed 9, context: html, text, full: html, text
    Add trivial test to Gtex loader
  • lines changed 5, context: html, text, full: html, text
    Aim GTex tests at real data
• src/hg/makeDb/outside/hgGtex/samples.txt
  • lines changed 4502, context: html, text, full: html, text
    Tool to load GTEx (NIH Common Fund Gene Tissue Expression). Quite similar to microarray table organization.
  • lines changed 4502, context: html, text, full: html, text
    Add trivial test to Gtex loader
• src/hg/makeDb/outside/hgGtex/test.gct
  • lines changed 6, context: html, text, full: html, text
    Tool to load GTEx (NIH Common Fund Gene Tissue Expression). Quite similar to microarray table organization.
  • lines changed 6, context: html, text, full: html, text
    Add trivial test to Gtex loader
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeRegDnaseClustered.ra
  • lines changed 12, context: html, text, full: html, text
    Adding cell table/file to V3 DNase Clusters. refs #13490
  • lines changed 9, context: html, text, full: html, text
    Renaming cells table to sources and adding .as. refs #13490
• src/hg/makeDb/trackDb/human/hg19/wgEncodeReg.ra
  • lines changed 1, context: html, text, full: html, text
    Adding source table that describes sourceIds in main bed table. Not currently used by hgc (which still uses inputTrackTable). It is there for VAI. refs 13490
  • lines changed 1, context: html, text, full: html, text
    Rename Cells table to Sources. refs #13490