Tiny bug fixed: ClinCNV does not crash when baseline is copied from t…

…he IGV
imgag · Dec 9, 2022 · 94c271d · 94c271d
1 parent 721a258
commit 94c271d
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Showing 4 changed files with 4 additions and 6 deletions.
diff --git a/clinCNV.R b/clinCNV.R
@@ -1,7 +1,7 @@
 #!/usr/bin/env Rscript
 set.seed(100)
 options(warn=-1)
-clincnvVersion = paste0("ClinCNV version: v1.18.1")
+clincnvVersion = paste0("ClinCNV version: v1.18.2")
 
 ## CHECK R VERSION
 if (!( (as.numeric(version$major) >= 3 & as.numeric(version$minor) > 2.0) |  as.numeric(version$major) >= 4) ) {

diff --git a/germline/helpersGermline.R b/germline/helpersGermline.R
@@ -732,12 +732,10 @@ calculateLocationAndScale <- function(bedFile, coverage, genderOfSamples, autoso
     print(chrom)
     coveragesToDealWith = coverage[which(bedFile[,1] == chrom),,drop=F]
     if (chrom == "chrX") {
-      if (length(which(genderOfSamples == "F")) > 0.4 * length(which(genderOfSamples == "M"))) {
-        print("The number of females is too few for accurate PAR estimation, we use males for chrX which leads to wrong PAR calling.")
-      }
       if (length(which(genderOfSamples == "F")) > 0.4 * length(which(genderOfSamples == "M"))) {
         whichSamplesUsed = which(genderOfSamples == "F")
       } else {
+        print("The number of females is too few for accurate PAR estimation, we use males for chrX which leads to wrong PAR calling.")
         whichSamplesUsed = which(genderOfSamples == "M")
       }
     } else if (chrom == "chrY") {

diff --git a/germline/mCNVhelpers.R b/germline/mCNVhelpers.R
@@ -60,7 +60,7 @@ likelihoodOfGaussianMixture <- function(location, value , sd_to_start, robustPer
         locationTmp[l] = sum(weights[,l] * value) / cluster_weights[l]
       }
       multiplierForLocation = locationTmp[which.max(cluster_weights[l])] / location[which.max(cluster_weights[l])]
-      if (abs(log2(initLocation / (location * multiplierForLocation))) < 0.1) {
+      if (abs(log2(initLocation / (location * multiplierForLocation)))[1] < 0.1) {
         location = location * multiplierForLocation
       } 
       sd_counter_tmp = sqrt(sum(sapply(1:length(location), 

diff --git a/somatic/helpersSomatic.R b/somatic/helpersSomatic.R
@@ -930,7 +930,7 @@ determine_potential_states = function(sampleLogFold, local_cn_states, sampleLogF
 
 find_baseline_level <- function(allowedChromsBafSample, matrixOfLogFoldSample, bedFileForCluster, matrixOfLogFoldOffSample=NULL, bedFileForClusterOff=NULL) {
   if (!is.null(opt$guideBaseline)) {
-    splitted = strsplit(opt$guideBaseline, ":")
+    splitted = strsplit(gsub(",","",opt$guideBaseline), ":")
     chrom = splitted[[1]][1]
     splitted = strsplit(splitted[[1]][2], "-")
     start = as.numeric(splitted[[1]][1])