angie: changes by file

branch to review (2009-07-07 to 2009-07-15) v210

• src/hg/hgTables/correlate.c
  • 1.78 lines changed: 5, context: html, text, full: html, text
    Moved connection-freeing into the block that originally allocated the connection.
• src/hg/hgTables/identifiers.c
  • 1.28 lines changed: 5, context: html, text, full: html, text
    Fix for corner case in explainIdentifiers: when xrefTable is the selected table, and its idField happens to be the same as its alias field for the main table (e.g. refLink), don't refer to the field twice (thanks Katrina).
• src/hg/hgc/hgc.c
  • 1.1560 lines changed: 1, context: html, text, full: html, text
    Updated link to IUPAC codes to Ann's new goldenPath/help page.
  • 1.1559 lines changed: 2, context: html, text, full: html, text
    In printSnpAlleleRows, don't reverse-complement refUCSC if it is like '(1000bp insertion)'.
• src/hg/lib/hdb.c
  • 1.405 lines changed: 23, context: html, text, full: html, text
    Oops, backing out the previous changes because they trigger both mrna and all_mrna trackDb records to display, and an upstream fix in hgFind.c fixed the original problem.
  • 1.404 lines changed: 29, context: html, text, full: html, text
    Added some special cases to support tracks all_{mrna,est} in a database that could have split tables.
• src/hg/lib/hgFind.c
  • 1.220 lines changed: 11, context: html, text, full: html, text
    When searching all_{mrna,est}, strip off the all_ only if there are split tables; otherwise all_{mrna,est} is the trackDb track name too.
• src/hg/lib/jaxAllelePheno.as
  • 1.1 lines changed: 7, context: html, text, full: html, text
    Meant to check these in a long time ago (thanks Brooke!).
• src/hg/lib/jaxAllelePheno.sql
  • 1.1 lines changed: 15, context: html, text, full: html, text
    Meant to check these in a long time ago (thanks Brooke!).
• src/hg/lib/snp125Coding.as
  • 1.1 lines changed: 15, context: html, text, full: html, text
    Functional annotations including mapped coords.
• src/hg/lib/snp125Coding.sql
  • 1.1 lines changed: 23, context: html, text, full: html, text
    Functional annotations including mapped coords.
• src/hg/makeDb/trackDb/mouse/trackDb.ra
  • 1.156 lines changed: 6, context: html, text, full: html, text
    Adding search on jaxQtl (just like the old one on jaxQTL, thanks Brooke).
  • 1.155 lines changed: 1, context: html, text, full: html, text
    Shortening shortLabel of jaxRepTranscript to 16 chars.
• src/hg/utils/automation/doHgNearBlastp.pl
  • 1.9 lines changed: 2, context: html, text, full: html, text
    Correcting comment.
  • 1.8 lines changed: 42, context: html, text, full: html, text
    Added back the varying blastp -e params that I lost when writing this. Have been using 0.01 for all blastp runs, but the original process used 0.001, 0.005, 0.01 depending on clade distance. Thanks Hiram and b0b!
• src/inc/common.mk
  • 1.62 lines changed: 6, context: html, text, full: html, text
    Fix to SAMPATH setting: for MACHTYPE other than x86_64, look for a MACHTYPE subdir lib. Also let user's SAMPATH env variable take preference if set.