From 8cbbb5ac3d344e8219732dd01f23bb8e36f792c0 Mon Sep 17 00:00:00 2001 From: Masahiro Kanai Date: Wed, 18 Nov 2020 17:20:38 -0500 Subject: [PATCH 1/2] fix liftover_expr --- gnomad/utils/liftover.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/gnomad/utils/liftover.py b/gnomad/utils/liftover.py index f6646ae98..6aabbd0f3 100644 --- a/gnomad/utils/liftover.py +++ b/gnomad/utils/liftover.py @@ -98,7 +98,9 @@ def liftover_expr( original_locus=locus, original_alleles=alleles, locus_fail_liftover=hl.is_missing(lifted_over_locus), - ref_allele_mismatch=lifted_over_locus.result.sequence_context() + ref_allele_mismatch=lifted_over_locus.result.sequence_context( + after=hl.len(alleles[0]) - 1 + ) != lifted_over_alleles[0], ) From 5f275708bec53d4b940510fcee724734c8a9cf4e Mon Sep 17 00:00:00 2001 From: Masahiro Kanai Date: Wed, 18 Nov 2020 17:49:31 -0500 Subject: [PATCH 2/2] add CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 8b200ac7c..bd8d11f31 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -18,6 +18,7 @@ * Add reference genome to call of `has_liftover` in `get_liftover_genome` [(#259)](https://github.com/broadinstitute/gnomad_methods/pull/259) * Added fix for MQ calculation in `_get_info_agg_expr`, switched `RAW_MQ` and `MQ_DP` in calculation [(#262)](https://github.com/broadinstitute/gnomad_methods/pull/262) * Fix for error in `default_lift_data` caused by missing `results` field in `new_locus` [(#270)](https://github.com/broadinstitute/gnomad_methods/pull/270) +* Fix for incorrect `ref_allele_mismatch` error in `liftover_expr` when the original reference allele has more than one bp [(#273)](https://github.com/broadinstitute/gnomad_methods/pull/273) ## Version 0.4.0 - July 9th, 2020