angie: changes by commit

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

• Meant to check these in a long time ago (thanks Brooke!).
  • src/hg/lib/jaxAllelePheno.as 1.1 - lines changed: 7, context: html, text, full: html, text
  • src/hg/lib/jaxAllelePheno.sql 1.1 - lines changed: 15, context: html, text, full: html, text
• Shortening shortLabel of jaxRepTranscript to 16 chars.
  • src/hg/makeDb/trackDb/mouse/trackDb.ra 1.155 - lines changed: 1, context: html, text, full: html, text
• Adding search on jaxQtl (just like the old one on jaxQTL, thanks Brooke).
  • src/hg/makeDb/trackDb/mouse/trackDb.ra 1.156 - lines changed: 6, context: html, text, full: html, text
• Functional annotations including mapped coords.
  • src/hg/lib/snp125Coding.as 1.1 - lines changed: 15, context: html, text, full: html, text
  • src/hg/lib/snp125Coding.sql 1.1 - lines changed: 23, 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/hdb.c 1.404 - lines changed: 29, 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/hgTables/identifiers.c 1.28 - lines changed: 5, 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/hgFind.c 1.220 - lines changed: 11, 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.
  • src/hg/lib/hdb.c 1.405 - lines changed: 23, 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/hg/utils/automation/doHgNearBlastp.pl 1.8 - lines changed: 42, context: html, text, full: html, text
• Correcting comment.
  • src/hg/utils/automation/doHgNearBlastp.pl 1.9 - lines changed: 2, context: html, text, full: html, text
• In printSnpAlleleRows, don't reverse-complement refUCSC if it is like '(1000bp insertion)'.
  • src/hg/hgc/hgc.c 1.1559 - lines changed: 2, context: html, text, full: html, text
• Moved connection-freeing into the block that originally allocated the connection.
  • src/hg/hgTables/correlate.c 1.78 - lines changed: 5, context: html, text, full: html, text
• Updated link to IUPAC codes to Ann's new goldenPath/help page.
  • src/hg/hgc/hgc.c 1.1560 - lines changed: 1, 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.
  • src/inc/common.mk 1.62 - lines changed: 6, context: html, text, full: html, text