Commits for braney

v291_preview2 to v291_base (2013-10-14 to 2013-10-21) v291

• take out verbose flag on rsyncs to eurotoad
  • src/hg/makeDb/genbank/etc/euronode-copy - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/euronode-dbload - lines changed 2, context: html, text, full: html, text
• check in some changes to the GWAS otto scripts
  • src/hg/utils/otto/gwas/checkGwas.sh - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/otto/gwas/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/otto/gwas/perlParser.pl - lines changed 4, context: html, text, full: html, text
  • src/hg/utils/otto/gwas/validateGwas.sh - lines changed 1, context: html, text, full: html, text
• fix a problem in pslOpen that caused a hang is the psl file only hadcomments. Add tests to pslPretty to validate
  
  • src/hg/pslPretty/makefile - lines changed 20, context: html, text, full: html, text
  • src/hg/pslPretty/test/expected/bad.axt - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/pslPretty/test/expected/bad.output - lines changed 2, context: html, text, full: html, text
  • src/hg/pslPretty/test/expected/dnax.axt - lines changed 8, context: html, text, full: html, text
  • src/hg/pslPretty/test/expected/empty.axt - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/pslPretty/test/expected/empty.output - lines changed 1, context: html, text, full: html, text
  • src/hg/pslPretty/test/expected/justComments.axt - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/pslPretty/test/expected/justComments.output - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/pslPretty/test/input/bad.psl - lines changed 1, context: html, text, full: html, text
  • src/hg/pslPretty/test/input/empty.psl - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/pslPretty/test/input/justComments.psl - lines changed 2, context: html, text, full: html, text
  • src/lib/psl.c - lines changed 14, context: html, text, full: html, text
• implement maf output in table browser
  • src/hg/hgTables/hal.c - lines changed 64, context: html, text, full: html, text
  • src/hg/hgTables/hgTables.c - lines changed 4, context: html, text, full: html, text
  • src/hg/hgTables/hgTables.h - lines changed 3, context: html, text, full: html, text
  • src/hg/hgTables/joining.c - lines changed 12, context: html, text, full: html, text
  • src/hg/hgTables/mainPage.c - lines changed 8, context: html, text, full: html, text
  • src/hg/hgTables/makefile - lines changed 1, context: html, text, full: html, text
• reorganize the genbank db lists to be prioritized
  • src/hg/makeDb/genbank/etc/hgwbeta.dbs - lines changed 138, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/hgwdev.dbs - lines changed 161, context: html, text, full: html, text