Enable new segmentation

Snakefile

@@ -326,6 +326,7 @@ rule segmentation:
     shell:
         """
         {params.mc_command} segment \
+        --remove-none \
         -m 0.33 \
         -M 50000000 \
         -o {output} \

utils/helper.prepare_segments.R

@@ -5,6 +5,6 @@ qu
 d = fread(snakemake@input[[1]])
 d
 # type = 1 is important to get discrete values!
-d = d[, .SD[k == quantile(1:max(k), qu, type = 1)], by=chrom][,.(k, chrom, bps = breakpoint)]
+d = d[, .SD[k == quantile(1:max(k), qu, type = 1)], by=chrom][,.(k, chrom, bps)]
 d
 write.table(d, file = snakemake@output[[1]], row.names=F, quote=F, sep="\t")