From d683eb44bf99d335b9937f91286df707ea5548c6 Mon Sep 17 00:00:00 2001 From: pdiakumis Date: Fri, 11 Oct 2024 19:00:22 +1100 Subject: [PATCH] tsov2: use alias for VCF parsing (fixes #143) --- R/tsov2.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/R/tsov2.R b/R/tsov2.R index 5e3e3a7..8ec5175 100644 --- a/R/tsov2.R +++ b/R/tsov2.R @@ -161,7 +161,7 @@ Wf_tso_ctdna_tumor_only_v2 <- R6::R6Class( #' @description Read `cnv.vcf` file. #' @param x Path to file. read_cnv = function(x) { - dat <- bcftools_parse_vcf(x, only_pass = FALSE, alias = FALSE) + dat <- bcftools_parse_vcf(x, only_pass = FALSE, alias = TRUE) tibble::tibble(name = "cnv", data = list(dat)) }, #' @description Read `exon_cov_report.tsv` file. @@ -190,7 +190,7 @@ Wf_tso_ctdna_tumor_only_v2 <- R6::R6Class( #' @description Read `hard-filtered.vcf` file. #' @param x Path to file. read_hardfilt = function(x) { - dat <- bcftools_parse_vcf(x, only_pass = FALSE, alias = FALSE) + dat <- bcftools_parse_vcf(x, only_pass = FALSE, alias = TRUE) tibble::tibble(name = "hardfilt", data = list(dat)) }, #' @description Read `microsat_output.json` file.