Commits for angie
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v290_preview2 to v290_base (2013-09-23 to 2013-09-30) v290
- Major restructuring of gpFx.c, to accomodate large deletions thatcan knock out entire exons. Now, instead of iterating through
exons and building a new genePred along with a sequence that has
one exon's modification, we project the variant start and end onto
cDNA and CDS coords up front. Then there is only one modification
to make per allele, and in fact we only care about the actual
modification when there's a CDS change.
A new SO term, exon_loss, has been incorporated into gpFx and
hgVai's/annoGratorGpVar's filtering.
fixes #11771
- src/hg/inc/annoGratorGpVar.h - lines changed 1, context: html, text, full: html, text
- src/hg/lib/annoFormatVep.c - lines changed 47, context: html, text, full: html, text
- src/hg/lib/annoGratorGpVar.c - lines changed 54, context: html, text, full: html, text
- src/hg/lib/tests/expected/annoGrator/vepOut.txt - lines changed 1, context: html, text, full: html, text
- Code review feedback, thanks Tim.refs #11800
- src/lib/annoStreamVcf.c - lines changed 4, context: html, text, full: html, text
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