Commits for markd

v310_base to v311_preview (2015-01-05 to 2015-01-12) v311

• GFF3 allows CDS as a child of transcript as well as mRNA, support create genePred with CDS annotation from such GFF3 files
  • src/hg/utils/gff3ToGenePred/gff3ToGenePred.c - lines changed 33, context: html, text, full: html, text
  • src/hg/utils/gff3ToGenePred/tests/expected/transcriptCdsParentTest.gp - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/gff3ToGenePred/tests/input/transcriptCdsParent.gff3 - lines changed 7, context: html, text, full: html, text
  • src/hg/utils/gff3ToGenePred/tests/makefile - lines changed 5, context: html, text, full: html, text
• have axtChain error on PSLs with explicty target, which it does not support
  • src/hg/mouseStuff/axtChain/axtChain.c - lines changed 2, context: html, text, full: html, text
• build pslPosTarget as a standard tool
  • src/utils/makefile - lines changed 1, context: html, text, full: html, text
  • src/utils/pslPosTarget/pslPosTarget.c - lines changed 21, context: html, text, full: html, text