resolved merge conflicts

yannchristinat · Feb 9, 2021 · 3d328ce · 3d328ce
2 parents 053a69c + 1a78a08
commit 3d328ce
Show file tree

Hide file tree

Showing 3 changed files with 7 additions and 1 deletion.
diff --git a/R/input.R b/R/input.R
@@ -432,11 +432,12 @@ adjust_loh <- function(segments){
         #new_loh$cn.type <- cntype.loh
         #new_loh$cn.subtype <- cntype.loh
 
+
         loh.toadd <- append(loh.toadd, new_loh)
         loh.todelete <- append(loh.todelete, loh)
       }
     }
-    #adj <- c(segs.loh[!(segs.loh %in% loh.todelete)], loh.toadd)
+
     adj <- union(setdiff(segs.loh, loh.todelete), loh.toadd)
     if(length(adj)>0){
       adj$cn <- NA

diff --git a/R/scores.R b/R/scores.R
@@ -165,7 +165,9 @@ score_loh <- function(segments, kit.coverage, armlevel.loh, armlevel.hetloss){
     chromnames <- unique(unlist(strsplit(as.character(seqnames(kit.coverage)), '[pq]')))
     arms_found.to_ban <- lapply(chromnames, function(chrom){
       arms <- paste0(chrom, c('p','q'))
+
       arms.covered <- intersect(arms, as.vector(seqnames(kit.coverage)))
+
       arms.found <- unique(intersect(arms.covered, armlevel.loh))
       if(length(arms.found) == length(arms.covered)){
         return(as.character(arms.covered))
@@ -180,7 +182,9 @@ score_loh <- function(segments, kit.coverage, armlevel.loh, armlevel.hetloss){
     chromnames <- unique(unlist(strsplit(as.character(seqnames(kit.coverage)), '[pq]')))
     arms_found.to_ban <- lapply(chromnames, function(chrom){
       arms <- paste0(chrom, c('p','q'))
+
       arms.covered <- intersect(arms, as.vector(seqnames(kit.coverage)))
+
       arms.found <- unique(intersect(arms.covered, armlevel.hetloss))
       if(length(arms.found) == length(arms.covered)){
         return(as.character(arms.covered))

diff --git a/tests/testthat/test-workflow.R b/tests/testthat/test-workflow.R
@@ -117,5 +117,6 @@ test_that("Oncoscan workflow returns the correct structure", {
   gender.test <- dat[['gender']] == 'M'
   file.test <- dat[['file']] == basename(segs.filename)
   #print(c(armlevel.nametest, scores.nametest, gender.test, file.test))
+
   expect_true(sum(c(armlevel.nametest, scores.nametest, gender.test, file.test))==4)
 })