Make sure -h -1 does not loose the first line

jkbonfield · May 9, 2024 · b204d55 · b204d55
1 parent 80bf6b8
commit b204d55
Show file tree

Hide file tree

Showing 2 changed files with 5 additions and 2 deletions.
diff --git a/annot-tsv.c b/annot-tsv.c
@@ -373,12 +373,13 @@ void parse_header(dat_t *dat, char *fname, int nth_row, int autodetect)
         buf[nbuf++] = strdup(dat->line.s);
     }
 
+    int keep_line = 0;
     if ( nth_row < 0 )
     {
         if ( nbuf!=-nth_row )
             error("Found %d header lines in %s, cannot fetch N=%d from the end\n",nbuf,fname,-nth_row);
         cols = cols_split(buf[0], NULL, dat->delim);
-
+        keep_line = 1;
     }
     else
         cols = cols_split(dat->line.s, NULL, dat->delim);
@@ -400,6 +401,7 @@ void parse_header(dat_t *dat, char *fname, int nth_row, int autodetect)
         cols = cols_split(str.s, NULL, dat->delim);
         free(str.s);
         dat->hdr.dummy = 1;
+        keep_line = 1;
     }
 
     dat->hdr.name2idx = khash_str2int_init();
@@ -421,7 +423,7 @@ void parse_header(dat_t *dat, char *fname, int nth_row, int autodetect)
         khash_str2int_set(dat->hdr.name2idx, cols->off[i], i);
     }
     dat->hdr.cols = cols;
-    if ( !dat->hdr.dummy ) dat->line.l = 0;
+    if ( !keep_line ) dat->line.l = 0;
 
     for (i=0; i<nbuf; i++) free(buf[i]);
     free(buf);

diff --git a/test/test.pl b/test/test.pl
@@ -1416,6 +1416,7 @@ sub test_annot_tsv
     run_annot_tsv($opts,src=>'src.10.txt',dst=>'dst.10.txt',out=>'out.10.6.txt',args=>'-m smpl -x');
     run_annot_tsv($opts,src=>'src.11.txt',dst=>'dst.11.txt',out=>'out.11.1.txt',args=>'-c 1,2,3:1,2,3 -f 4:5 -h 0:0');
     run_annot_tsv($opts,src=>'src.11.txt',dst=>'dst.11.txt',out=>'out.11.1.txt',args=>'-c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -II');
+    run_annot_tsv($opts,src=>'src.11.txt',dst=>'dst.11.txt',out=>'out.11.1.txt',args=>'-c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:-1 -II');
     run_annot_tsv($opts,src=>'src.11.txt',dst=>'dst.11.txt',out=>'out.11.2.txt',args=>'-c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2');
     run_annot_tsv($opts,src=>'src.11.txt',dst=>'dst.11.txt',out=>'out.11.2.txt',args=>'-c chr2,beg2,end2:chr,beg,end -f smpl2:src_smpl -h 3:2');
     run_annot_tsv($opts,src=>'src.11.txt',dst=>'dst.11.txt',out=>'out.11.3.txt',args=>'-c chr1,beg1,end1:chr,beg,end -f smpl1:src_smpl -h 2:2 -I');