# HG changeset patch
# User jackcurragh
# Date 1663943447 0
# Node ID 14ae3bb73e02aef2b9a8e1f160abc07e7ba23f67
# Parent  ecf172071e80762f6c54dc76edb552258f36cd60
Uploaded

diff -r ecf172071e80 -r 14ae3bb73e02 get_chrom_sizes/get_chrom_sizes.xml
--- a/get_chrom_sizes/get_chrom_sizes.xml	Fri Sep 23 14:19:34 2022 +0000
+++ b/get_chrom_sizes/get_chrom_sizes.xml	Fri Sep 23 14:30:47 2022 +0000
@@ -3,8 +3,7 @@
     <command>
 
         #if $refGenomeSource.genomeSource == "builtin":
-            cat "#chrom\tlength" > $output1
-            cat ${refGenomeSource.input1_builtin.fields.path} | awk '$0 ~ ">" {if (NR > 1) {print c;} c=0; printf ${input2} substr($0,2,100) "\t"; } $0 !~ ">" {c+=length($0);} END {print c; }' | cat >> $output1
+            cat ${refGenomeSource.input1_builtin.fields.path} | awk '$0 ~ ">" {if (NR > 1) {print c;} c=0; printf ${input2} substr($0,2,100) "\t"; } $0 !~ ">" {c+=length($0);} END {print c; }' | cat > $output1
         #else:
             cat ${refGenomeSource.input1_file} | awk '$0 ~ ">" {if (NR > 1) {print c;} c=0; printf ${input2} substr($0,2,100) "\t"; } $0 !~ ">" {c+=length($0);} END {print c; }' | cat > $output1
         #end if