fixed top_priority_effect for ExonicSpliceSite #235
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…d VCF writing reference name
julia326
reviewed
Oct 11, 2018
varcode/effects/effect_ordering.py
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| IntronicSpliceSite, | ||
| # exonic variants near a splice boundary | ||
| ExonicSpliceSite, | ||
| # modification or deletion of stop codon |
| @@ -125,13 +124,31 @@ def effect_sort_key(effect): | |||
| effect_class_priority = effect_priority(effect) | |||
| return (effect_class_priority, cds_length, transcript_length) | |||
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| def select_between_exonic_splice_site_and_alternate_effect(effect): | |||
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can you add some comments here? this functionality is kinda non-obvious
varcode/vcf_output.py
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| @@ -248,9 +249,11 @@ def get_sample_names(): | |||
| headers += ['FORMAT'] + sample_names | |||
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| unique_variants_list = merge_duplicate_variants() | |||
| # can't have more than one reference in VCF so pick the first one and pray | |||
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instead of praying, throw an error? when would we ever want to support combining VCFs created against different references?
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I'm imagining hg19 vs. GRCh37 type differences but you're probably right: better to raise an exception
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Changed it to check for a unique reference
iskandr
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fix-effect-ordering-and-top-priority-for-exonic-splice-site
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Currently, if an
ExonicSpliceSiteeffect has analternate_effectwhich is more interesting (e.g.StopGain), it doesn't come up as the top priority. This changes thetop_priority_effectlogic to return thealternate_effectif it's higher priority than a potential exonic splice site change.Other changes:
Silentin the effect ordering.Fixes: #233