Commits for markd

v240_preview to v240_base (2010-09-07 to 2010-09-14) v240

• move gtfToGenePred to hg/utils so that it doesn't cause grief for people trying to compile without mysql
  • src/hg/utils/gtfToGenePred/gtfToGenePred.c - lines changed 188, context: html, text, full: html, text
  • src/hg/utils/gtfToGenePred/makefile - lines changed 21, context: html, text, full: html, text
  • src/hg/utils/gtfToGenePred/tests/expected/basic.gp - lines changed 4, context: html, text, full: html, text
  • src/hg/utils/gtfToGenePred/tests/expected/basic.info - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/gtfToGenePred/tests/expected/dups.gp - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/gtfToGenePred/tests/expected/dups.out - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/gtfToGenePred/tests/expected/ensembl.gp - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/gtfToGenePred/tests/expected/ensembl.info - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/gtfToGenePred/tests/expected/geneNameAsName2.gp - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/gtfToGenePred/tests/expected/impliedStop.gp - lines changed 6, context: html, text, full: html, text
  • src/hg/utils/gtfToGenePred/tests/expected/impliedStop.info - lines changed 7, context: html, text, full: html, text
  • src/hg/utils/gtfToGenePred/tests/expected/splitStop.gp - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/gtfToGenePred/tests/expected/srcPre.gp - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/gtfToGenePred/tests/expected/srcPre.info - lines changed 4, context: html, text, full: html, text
  • src/hg/utils/gtfToGenePred/tests/input/basic.gtf - lines changed 14, context: html, text, full: html, text
  • src/hg/utils/gtfToGenePred/tests/input/dups.gtf - lines changed 19, context: html, text, full: html, text
  • src/hg/utils/gtfToGenePred/tests/input/ensembl.gtf - lines changed 12, context: html, text, full: html, text
  • src/hg/utils/gtfToGenePred/tests/input/flybase.gtf - lines changed 56, context: html, text, full: html, text
  • src/hg/utils/gtfToGenePred/tests/input/split.gtf - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/gtfToGenePred/tests/input/splitStop.gtf - lines changed 34, context: html, text, full: html, text
  • src/hg/utils/gtfToGenePred/tests/makefile - lines changed 56, context: html, text, full: html, text
  • src/hg/utils/makefile - lines changed 2, context: html, text, full: html, text
  • src/makefile - lines changed 2, context: html, text, full: html, text
  • src/utils/gtfToGenePred/gtfToGenePred.c - lines changed 188, context: html, text, full: html, text
  • src/utils/gtfToGenePred/makefile - lines changed 21, context: html, text, full: html, text
  • src/utils/gtfToGenePred/tests/expected/basic.gp - lines changed 4, context: html, text, full: html, text
  • src/utils/gtfToGenePred/tests/expected/basic.info - lines changed 5, context: html, text, full: html, text
  • src/utils/gtfToGenePred/tests/expected/dups.gp - lines changed 2, context: html, text, full: html, text
  • src/utils/gtfToGenePred/tests/expected/dups.out - lines changed 3, context: html, text, full: html, text
  • src/utils/gtfToGenePred/tests/expected/ensembl.gp - lines changed 2, context: html, text, full: html, text
  • src/utils/gtfToGenePred/tests/expected/ensembl.info - lines changed 3, context: html, text, full: html, text
  • src/utils/gtfToGenePred/tests/expected/geneNameAsName2.gp - lines changed 2, context: html, text, full: html, text
  • src/utils/gtfToGenePred/tests/expected/impliedStop.gp - lines changed 6, context: html, text, full: html, text
  • src/utils/gtfToGenePred/tests/expected/impliedStop.info - lines changed 7, context: html, text, full: html, text
  • src/utils/gtfToGenePred/tests/expected/splitStop.gp - lines changed 2, context: html, text, full: html, text
  • src/utils/gtfToGenePred/tests/expected/srcPre.gp - lines changed 3, context: html, text, full: html, text
  • src/utils/gtfToGenePred/tests/expected/srcPre.info - lines changed 4, context: html, text, full: html, text
  • src/utils/gtfToGenePred/tests/input/basic.gtf - lines changed 14, context: html, text, full: html, text
  • src/utils/gtfToGenePred/tests/input/dups.gtf - lines changed 19, context: html, text, full: html, text
  • src/utils/gtfToGenePred/tests/input/ensembl.gtf - lines changed 12, context: html, text, full: html, text
  • src/utils/gtfToGenePred/tests/input/flybase.gtf - lines changed 56, context: html, text, full: html, text
  • src/utils/gtfToGenePred/tests/input/split.gtf - lines changed 5, context: html, text, full: html, text
  • src/utils/gtfToGenePred/tests/input/splitStop.gtf - lines changed 34, context: html, text, full: html, text
  • src/utils/gtfToGenePred/tests/makefile - lines changed 56, context: html, text, full: html, text
  • src/utils/makefile - lines changed 1, context: html, text, full: html, text
• fix incorrect use of printf detect by gcc 4.4.3
  • src/hg/lib/hui.c - lines changed 1, context: html, text, full: html, text
• fixed make error caused by directory move
  • src/hg/utils/gtfToGenePred/tests/makefile - lines changed 1, context: html, text, full: html, text
• fixed C99 incompatiblities
  • src/hg/mouseStuff/bedCoverage/bedCoverage.c - lines changed 2, context: html, text, full: html, text
  • src/hg/mouseStuff/mafCoverage/mafCoverage.c - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/refSeqGet/refSeqVerInfo.c - lines changed 4, context: html, text, full: html, text
• hack around some systems complaining about read result not being used even with cast
  • src/lib/pipeline.c - lines changed 4, context: html, text, full: html, text