Commits for markd

v372_preview2 to v372_base (2018-09-24 to 2018-10-01) v372

ee6b3270d5a37e7e28c7af65aead341fa682295f Thu Sep 27 17:09:26 2018 -0700

• Fixed GTF conversion problem where final CDS exon had incorrect frame. occurred when The CDS started in the exon that contains the last codon before the stop codon. The stop code was either spliced or the only codon in the exon. This changed 44 gencode V28 transcripts, many of which were manually validated in the browser.
  • src/hg/lib/genePred.c - lines changed 16, context: html, text, full: html, text
  • src/hg/utils/gtfToGenePred/tests/expected/splitStop.gp - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/gtfToGenePred/tests/input/splitStop.gtf - lines changed 26, context: html, text, full: html, text

676da6b57134c0641578e9277776fb40101424c9 Sat Sep 29 14:46:42 2018 -0700

• switch loading gencode from GTFs to GFF3 so as not to need to debug yet another issue with GTF stop codon outside of CDS
  • src/hg/makeDb/outside/gencode/gencodeLoad.mk - lines changed 19, context: html, text, full: html, text