Fixed a bug in collapsed gene count for .gene_count_multi_single

Author: mchaisso

SegDupAnalysis.snakefile

@@ -1688,7 +1688,7 @@ rule GetFullGeneCountTable:
         sd=SD
     shell:"""
 
-cat {input.depth_filt} | awk '{{ if (NR == 1) {{ print "gene\\tresolved\\tcollapsed"; }} else {{ cn=int($7)-1; if (cn < 0) {{ cn=0;}}  print $4"\\t1\\t"cn;}} }}' | bedtools groupby -header -g 1 -c 2,3 -o sum,sum > {output.gene_count_2column}
+cat {input.depth_filt} | awk '{{ if (NR == 1) {{ print "gene\\tresolved\\tcollapsed"; }} else {{ cn=int($7)-2; if (cn < 0) {{ cn=0;}}  print $4"\\t1\\t"cn;}} }}' | bedtools groupby -header -g 1 -c 2,3 -o sum,sum > {output.gene_count_2column}
 cat {output.gene_count_2column} | awk '{{ if (NR == 1) {{ print "gene\\tcopies";}} else {{  print $1"\\t"$2+$3;}} }}' > {output.gene_count}
 """