fix pairs file header bug of imargi_distfilter.sh

Zhong-Lab-UCSD · Jul 24, 2020 · 0a22738 · 0a22738
1 parent a9bea76
commit 0a22738
Showing 1 changed file with 4 additions and 2 deletions.
diff --git a/src/imargi_distfilter.sh b/src/imargi_distfilter.sh
@@ -66,17 +66,19 @@ zcat $input_file |\
         if(NR % 1000000 == 0){print NR" records processed ..."}
         if($0 ~ /^#/){
             if($0 ~/^#columns/){
-                print "#samheader: @PG\tID:imargi_distfilter.sh\tPN:imargi_distfilter.sh\tCL:"commandline > output_file;
+                PP_ID = gensub(/.+ID:([^\t]+)\t.+/, "\\1", "g", previous_line);
+                print "#samheader: @PG\tID:imargi_distfilter.sh\tPN:imargi_distfilter.sh\tCL:"commandline"\tPP:"PP_ID > output_file;
                 print $0 > output_file;
                 if(filter_flag=="output"){
-                    print "#samheader: @PG\tID:imargi_distfilter.sh\tPN:imargi_distfilter.sh\tCL:"commandline > filterOut_file;
+                    print "#samheader: @PG\tID:imargi_distfilter.sh\tPN:imargi_distfilter.sh\tCL:"commandline"\tPP:"PP_ID > filterOut_file;
                     print $0 > filterOut_file;
                 }
             }else{
                 print $0 > output_file;
                 if(filter_flag=="output"){
                     print $0 > filterOut_file;
                 }
+                previous_line = $0;
             }
         }else{
             if($2!=$4){