Potential fix for lima1#225.

DESCRIPTION

@@ -2,8 +2,8 @@ Package: PureCN
 Type: Package
 Title: Copy number calling and SNV classification using
     targeted short read sequencing
-Version: 2.1.8
-Date: 2022-02-11
+Version: 2.1.9
+Date: 2022-02-25
 Authors@R: c(person("Markus", "Riester",
                     role = c("aut", "cre"),
                     email = "[email protected]",

NEWS

@@ -24,6 +24,8 @@ BUGFIXES
     o Fix for a crash when there are no off-target reads in off-target regions
       (#209).
     o Fixed parsing of base quality scores in Mutect 2.2   
+    o Fixed crash in GenomicsDB parsing when there were no variants in contig
+      (#225)
 
 
 Changes in version 2.0.0

R/calculateMappingBiasVcf.R

@@ -188,6 +188,7 @@ calculateMappingBiasGatk4 <- function(workspace, reference.genome,
     genomicsdb::disconnect(db)
     flog.info("Collecting variant information...")
     # concat with minimal memory overhead
+    parsed_ad_list <- parsed_ad_list[!sapply(parsed_ad_list, is.null)]
     m_alt <- as.matrix(rbindlist(lapply(parsed_ad_list, function(x) data.frame(x$alt)), fill = TRUE))
     for (i in seq_along(parsed_ad_list)) parsed_ad_list[[i]]$alt <- NULL
     m_ref <- as.matrix(rbindlist(lapply(parsed_ad_list, function(x) data.frame(x$ref)), fill = TRUE))
@@ -214,6 +215,7 @@ calculateMappingBiasGatk4 <- function(workspace, reference.genome,
 }
 
 .parseADGenomicsDb <- function(query, AF.info.field = "AF") {
+    if (!nrow(query)) return(NULL)
     ref <-  dcast(query, CHROM + POS + END + REF + ALT ~ SAMPLE, value.var = "AD")
     af <-  dcast(query, CHROM + POS + END + REF + ALT ~ SAMPLE, value.var = AF.info.field)
     gr <- GRanges(seqnames = ref$CHROM, IRanges(start = ref$POS, end = ref$END),