From 7b0a72f1f8476ca5ff4439958c0d8214b2f6f64d Mon Sep 17 00:00:00 2001 From: Kent Riemondy Date: Mon, 21 Aug 2023 08:14:48 -0600 Subject: [PATCH] additional renaming --- R/calc_AEI.R | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/R/calc_AEI.R b/R/calc_AEI.R index 3287a02..4b32f82 100644 --- a/R/calc_AEI.R +++ b/R/calc_AEI.R @@ -167,7 +167,7 @@ calc_AEI <- function(bamfiles, res <- list() for(i in seq_along(bamfiles)) { bam_fn <- bamfiles[i] - aei <- .AEI_per_bam(bam_fn = bam_fn, fasta_fn = fasta, chroms = chroms, + aei <- .AEI_per_bam(bam_fn = bam_fn, fasta = fasta, chroms = chroms, alu_ranges = alu_ranges, snps = snps, param = param, genes_gr = genes_gr, verbose = verbose, BPPARAM = BPPARAM) res[[path(bam_fn)]] <- aei @@ -186,7 +186,7 @@ calc_AEI <- function(bamfiles, } -.AEI_per_bam <- function(bam_fn, fasta_fn, chroms, alu_ranges, snps, param, +.AEI_per_bam <- function(bam_fn, fasta, chroms, alu_ranges, snps, param, genes_gr, verbose, BPPARAM = BiocParallel::SerialParam()) { @@ -195,7 +195,7 @@ calc_AEI <- function(bamfiles, chroms, MoreArgs = list( bam_fn = bam_fn, - fasta_fn = fasta_fn, + fasta = fasta, alu_sites = alu_ranges, param = param, snp_gr = NULL, @@ -214,7 +214,7 @@ calc_AEI <- function(bamfiles, snps, MoreArgs = list( bam_fn = bam_fn, - fasta_fn = fasta_fn, + fasta = fasta, alu_sites = alu_ranges, param = param, genes_gr = genes_gr, @@ -257,7 +257,7 @@ calc_AEI <- function(bamfiles, list(AEI = aei_summary, AEI_per_chrom = aei_per_chrom) } -.calc_AEI_per_chrom <- function(bam_fn, fasta_fn, alu_sites, chrom, param, +.calc_AEI_per_chrom <- function(bam_fn, fasta, alu_sites, chrom, param, snp_gr, genes_gr, verbose) { if (verbose) { start <- Sys.time() @@ -267,7 +267,7 @@ calc_AEI <- function(bamfiles, param@only_keep_variants <- FALSE plp <- pileup_sites(bam_fn, - fasta = fasta_fn, + fasta = fasta, sites = alu_sites, chroms = chrom, param = param