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Fixed deprecated JVM GC flag #147

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Fixed deprecated JVM GC flag #147

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27ba10f
Fixed deprecated JVM GC flag
avalind Mar 6, 2025
b1ec966
BiocGenerics doesn't export rowSums
avalind Mar 7, 2025
0bd6fda
Update segmentation.R
avalind Mar 8, 2025
78597d5
Update fitcopynumber.R
avalind Mar 9, 2025
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2 changes: 2 additions & 0 deletions R/fitcopynumber.R
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Expand Up @@ -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'
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2 changes: 1 addition & 1 deletion R/haplotype_external.R
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Expand Up @@ -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)
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2 changes: 1 addition & 1 deletion R/impute.R
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Expand Up @@ -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 ,
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6 changes: 4 additions & 2 deletions R/segmentation.R
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Expand Up @@ -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)

Expand Down Expand Up @@ -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))
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