Commits for angie
switch to files view, user index
v363_base to v364_preview (2018-03-26 to 2018-04-02) v364
Show details
e83a6e8aac3501b503ca69156cfae2187ebd619a Fri Mar 23 12:36:04 2018 -0700
- Make vpTranscriptToGpFx more consistent with gpFxPredEffect for frameshift variants by including full sequences for {codon,aa}{Old,New}.
refs #21142
- src/hg/lib/variantProjector.c - lines changed 42, context: html, text, full: html, text
205d43b94283eb56c77a64f5e86e2a77295ab750 Mon Mar 12 10:38:40 2018 -0700
- hgVai: Add options for HGVS output from Gencode Basic/Comp tracks (not just RefSeq). Use variantProjector instead of gpFx to do predictions for genePreds by converting to PSL+CDS.
refs #21142
The use of variantProjector resulted in significant changes to hg/lib/tests results:
pgSnpKgDbToGpFx.txt: right-shifting, 'Z' -> '*'
vepIndelTrimOut.txt:
* right-shifting
* per-allele consequences even for variants where allele doesn't affect consequence
e.g. intron... this is a drawback, would be good to filter these after the fact to
reduce to a single consequence
* right-shifting intron -> splice_region for gene LSP1
* right-shifting coding_sequence_variant into just 3_prime_UTR_variant for ORJ81
* recognition of genome missing a base for EI24 (so insC restores frame and restores
missing codon from genome-compensating transcripts)
* exon numbers changing due to not counting too-short introns
- src/hg/lib/annoGratorGpVar.c - lines changed 216, context: html, text, full: html, text
- src/hg/lib/tests/expected/annoGrator/pgSnpKgDbToGpFx.txt - lines changed 20, context: html, text, full: html, text
- src/hg/lib/tests/expected/annoGrator/vepOutIndelTrim.txt - lines changed 89, context: html, text, full: html, text
0894a7b7b123ba04bc474582e17b8af408cbb1af Mon Mar 26 11:40:05 2018 -0700
- gp was freed -- but it is used later during the draw stage for baseColoring, so don't free it here.
- src/hg/hgTracks/gencodeTracks.c - lines changed 1, context: html, text, full: html, text
switch to files view, user index