Fix bug #19
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Fix bug #19
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mmoisse
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Jun 25, 2019
Fix bug issue ding-lab#19
fernanda-rodrigues
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Aug 15, 2019
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If override = True, the ref and alt for genomic variants would be wrongly changed for minus strand transcripts. Because in splitHGVSc, it only replaced the ref and alt without considering the strand. There is no need to replace the ref and alt here. |
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For insertion and deletion, the start, stop, ref and alt were transformed in the readVCF: Lines 257 to 265 in b4a13b1 In the getMacClinVarTSV, the variants should be processed in the same way to match. |
fernanda-rodrigues
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Sep 30, 2019
Changes include: - Fixed parseMacPathogenicity() to handle variants with multiple submitters that received both benign and pathogenic classifications, but no conflict is reported (i.e. `isPathogenic == 1 and isBenign == 1 and isConflicted == 0`) - Fixed bug reported in pull request #19: var.splitHGVSc, which doesn't consider strand information. When override = True, the ref and alt for genomic variants would be wrongly changed for minus strand transcripts. Changed to override = False - Fixed bug reported in pull request #19: fixed corrdinates in getMacClinVarTSV() to match readVCF().
Merged
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Issues fixed in release v0.5.3 |
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minPathogenicScore could be equal.
var.splitHGVScdoesn't consider strand information. Whenoverride = True, the ref and alt for genomic variants would be wrongly changed for minus strand transcripts.