From 27ba10f8c9227e372367149a45ac08223b1a166e Mon Sep 17 00:00:00 2001
From: Anders Valind <anders.valind@gmail.com>
Date: Thu, 6 Mar 2025 14:01:15 +0100
Subject: [PATCH 1/4] Fixed deprecated JVM GC flag

UseParalellOldGC was deprecated in Java 15 (cf https://bugs.openjdk.org/browse/JDK-8235860), and the JVM suggests using UseParallelGC instead.
---
 R/impute.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/impute.R b/R/impute.R
index 783a2d1c..de831024 100644
--- a/R/impute.R
+++ b/R/impute.R
@@ -267,7 +267,7 @@ run.beagle5 = function(beaglejar,
     cmd <- paste0(javajre,
 		  " -Xmx",maxheap.gb,"g",
 		  " -Xms", maxheap.gb, "g",
-		  " -XX:+UseParallelOldGC",
+		  " -XX:+UseParallelGC",
                   " -jar ",beaglejar,
                   " gt=",vcfpath,
                   " ref=",reffile ,

From b1ec966b53e5dda9e502d9826ae9e2ede4401bb6 Mon Sep 17 00:00:00 2001
From: Anders Valind <anders.valind@gmail.com>
Date: Fri, 7 Mar 2025 09:48:45 +0100
Subject: [PATCH 2/4] BiocGenerics doesn't export rowSums

BiocGenerics does not export a function called rowSums. Reverting to rowSums() from base R.
---
 R/haplotype_external.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/haplotype_external.R b/R/haplotype_external.R
index 1f8c5930..b97cc4a2 100644
--- a/R/haplotype_external.R
+++ b/R/haplotype_external.R
@@ -208,7 +208,7 @@ get_multisample_phasing <- function(chrom, bbphasingprefixes, maxlag = 100, rela
     singlevcf <- vcfs_common[[vcfidx]]
     sid <- VariantAnnotation::samples(VariantAnnotation::header(singlevcf))
     adddf <- S4Vectors::DataFrame(Major = VariantAnnotation::geno(singlevcf)$GT[,1], #Major = as.integer(ifelse(test = grepl(pattern = "|", x = geno(singlevcf)$GT, fixed = T), substr(x = geno(singlevcf)$GT, 1, 1), NA)),
-                       BAF = VariantAnnotation::geno(singlevcf)$AD[,1,2]/BiocGenerics::rowSums(VariantAnnotation::geno(singlevcf)$AD[,1,]),
+                       BAF = VariantAnnotation::geno(singlevcf)$AD[,1,2]/rowSums(VariantAnnotation::geno(singlevcf)$AD[,1,]),
                        PS = VariantAnnotation::geno(singlevcf)$PS[,1])
     colnames(adddf) <- paste0(sid, "_", colnames(adddf))
     S4Vectors::mcols(loci) <- cbind(S4Vectors::mcols(loci), adddf)

From 0bd6fdaaee59d22991e886b4de98963396739eb4 Mon Sep 17 00:00:00 2001
From: Anders Valind <anders.valind@gmail.com>
Date: Sat, 8 Mar 2025 16:14:35 +0100
Subject: [PATCH 3/4] Update segmentation.R

Print()-debugging
---
 R/segmentation.R | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/R/segmentation.R b/R/segmentation.R
index 95f7cf42..ea27bab0 100644
--- a/R/segmentation.R
+++ b/R/segmentation.R
@@ -511,7 +511,8 @@ segment.baf.phased.multisample = function(samplename, inputfile, outputfile, pri
   # @param no_segmentation Do not perform segmentation. This step will switch the haplotype blocks, but then just takes the mean BAFphased as BAFsegm
   # @return A data.frame with columns Chromosome,Position,BAF,BAFphased,BAFseg
   run_pcf = function(BAFrawchr, presegment_chrom_start, presegment_chrom_end, gamma) {
-    
+    print("run_pcf input = ")
+    print(BAFrawchr)
     row.indices = which(BAFrawchr$Position >= presegment_chrom_start & 
                           BAFrawchr$Position <= presegment_chrom_end)
     
@@ -593,7 +594,8 @@ segment.baf.phased.multisample = function(samplename, inputfile, outputfile, pri
   BAFraw <- Reduce(f = function(...) merge(..., sort = F, all = F), x = lapply(X = inputfile, FUN = Battenberg:::read_baf))
   # BAFraw = as.data.frame(read_tsv(inputfile, col_types = paste0("ci", paste0(rep("n", length(samplename)), collapse = ""), collapse = "")))
   if (!is.null(prior_breakpoints_file)) { bkps = read.table(prior_breakpoints_file, header=T, stringsAsFactors=F) } else { bkps = NULL }
-  
+  print("BAFraw just after reading input files:")
+  print(BAFraw)
   BAFoutput = list()
   for (chr in unique(BAFraw[,1])) {
     print(paste0("Segmenting ", chr))

From 78597d548eeeca2858a18279500d2fc92c577b28 Mon Sep 17 00:00:00 2001
From: Anders Valind <anders.valind@gmail.com>
Date: Sun, 9 Mar 2025 06:58:45 +0100
Subject: [PATCH 4/4] Update fitcopynumber.R

More chromosome naming convention fixes
---
 R/fitcopynumber.R | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/R/fitcopynumber.R b/R/fitcopynumber.R
index 4b833a87..c1bebea3 100644
--- a/R/fitcopynumber.R
+++ b/R/fitcopynumber.R
@@ -676,6 +676,8 @@ merge_segments=function(subclones, bafsegmented, logR, rho, psi, platform_gamma,
   subclones=df2gr(subclones,'chr','startpos','endpos')
   str(bafsegmented)
   bafsegmented=df2gr(bafsegmented,'Chromosome','Position','Position')
+  #str(logR)
+  logR$Chromosome=paste("chr",logR$Chromosome,sep="")
   str(logR)
   logR=df2gr(logR,'Chromosome','Position','Position')
   names(GenomicRanges::mcols(logR))='logR'