Preparing caller based on the new NB probs

Snakefile

@@ -304,9 +304,7 @@ rule mosaiClassifier_make_call:
     output:
         "sv_calls/{sample}/{windows}.{bpdens}/simpleCalls.txt"
     shell:
-        """
-        Rscript utils/mosaiClassifier.makeCall.R {input} {output}
-        """
+        "utils/mosaiClassifier_call.snakemake.R"
 
 rule mosaiClassifier_calc_probs:
     input:

utils/mosaiClassifier_call.snakemake.R

+library(data.table)
+source("utils/mosaiClassifier/makeSVcalls.R")
+
+probs = readRDS(snakemake@input[["probs"]])
+llr   = as.numeric(snakemake@params[["llr"]])
+
+tab <- makeSVCallSimple(probs)
+
+write.table(tab, file = snakemake@output[[1]], sep = "\t", quote=F, row.names = F, col.names = T)