File Changes for galt

v292_preview2 to v292_base (2013-11-04 to 2013-11-11) v292

• src/hg/encode3/validateManifest/validateManifest.c
  • lines changed 6, context: html, text, full: html, text
    oops must allow "10" which is 2 digits long
• src/hg/hgTables/gffOut.c
  • lines changed 72, context: html, text, full: html, text
    fixes #12107. This fixes the hgTables gtf-output frame column, at least for tables that have exonFrames column available like non-ancient refGene and other genePredExt tables usually do.
• src/hg/hgTracks/hgTracks.c
  • lines changed 6, context: html, text, full: html, text
    adding IUPAC support to the oligoMatch utility (which was cloned from hgTracks originally and then forgotten)
• src/hg/lib/hdb.c
  • lines changed 1, context: html, text, full: html, text
    fixes #11651. Accidentally failover was looking for backupcentral.database instead of backupcentral.db which is what all of our configurations have been using. Wow! Busted since 2009.
• src/hg/makeDb/schema/all.joiner
  • lines changed 9, context: html, text, full: html, text
    adding phastBias to tablesIgnored
• src/hg/utils/oligoMatch/oligoMatch.c
  • lines changed 29, context: html, text, full: html, text
    adding IUPAC support to the oligoMatch utility (which was cloned from hgTracks originally and then forgotten)
• src/hg/utils/oligoMatch/tests/expected/basicTest.bed
  • lines changed 16, context: html, text, full: html, text
    adding IUPAC support to the oligoMatch utility (which was cloned from hgTracks originally and then forgotten)
• src/hg/utils/oligoMatch/tests/input/oligos.fa
  • lines changed 6, context: html, text, full: html, text
    adding IUPAC support to the oligoMatch utility (which was cloned from hgTracks originally and then forgotten)
• src/hg/utils/oligoMatch/tests/input/sequence.fa
  • lines changed 4, context: html, text, full: html, text
    adding IUPAC support to the oligoMatch utility (which was cloned from hgTracks originally and then forgotten)
• src/hg/utils/oligoMatch/tests/makefile
  • lines changed 17, context: html, text, full: html, text
    adding IUPAC support to the oligoMatch utility (which was cloned from hgTracks originally and then forgotten)