Automatically recognize BED vs TSV files and add the option -C, --coords

The program was working with 1-based coordinates only. In this commit
we make it automatically recognize BED files by .bed, .bed.gz suffix
(case-insensitive).

The new option -C, --coords allows to override the program's decision

Author: pd3

annot-tsv.c

@@ -1,5 +1,5 @@
 /*
-    Copyright (C) 2018-2024 Genome Research Ltd.
+    Copyright (C) 2018-2025 Genome Research Ltd.
 
     Author: Petr Danecek <[email protected]>
 
@@ -72,6 +72,7 @@ typedef struct
     cols_t *core, *match, *transfer, *annots;
     int *core_idx, *match_idx, *transfer_idx, *annots_idx;
     int *nannots_added; // for --max-annots: the number of annotations added
+    int coor_base[2];   // 0 or 1-indexed beg,end?
     char delim;
     int grow_n;
     kstring_t line;     // one buffered line, a byproduct of reading the header
@@ -102,7 +103,7 @@ typedef struct
 {
     nbp_t *nbp;
     dat_t dst, src;
-    char *core_str, *match_str, *transfer_str, *annots_str, *headers_str, *delim_str;
+    char *core_str, *coords_str, *match_str, *transfer_str, *annots_str, *headers_str, *delim_str;
     char *temp_dir, *out_fname;
     BGZF *out_fp;
     int allow_dups, max_annots, mode, no_write_hdr, overlap_either;
@@ -301,6 +302,13 @@ int parse_tab_with_payload(const char *line, char **chr_beg, char **chr_end, hts
     *end = strtod(ptr, &tmp);
     if ( tmp==ptr ) error("Expected numeric value, found \"%s\": %s\n",ptr,line);
 
+    // NB: for indexing we leave the coordinates 1-based when 1-based, otherwise 0-coordinate would underflow. This
+    // means the biggest hts coordinate will overflow, which is less common than the 0 underflow. This does not affect the output,
+    // only indexing.
+    // The following code will make beg+=1 for BED file (-C 01)
+    (*beg) -= dat->coor_base[0] - 1;
+    (*end) -= dat->coor_base[1] - 1;
+
     if ( *end < *beg )
     {
         if ( !beg_end_warned )
@@ -484,6 +492,26 @@ void sanity_check_columns(char *fname, hdr_t *hdr, cols_t *cols, int **col2idx,
         (*col2idx)[i] = idx;
     }
 }
+void parse_coor_base(args_t *args, char *str, dat_t *dat)
+{
+    int len = strlen(dat->fname);
+    int beg = 1, end = 1;
+    if ( *str )
+    {
+        if ( str[0]=='0' ) beg = 0;
+        else if ( str[0]=='1' ) beg = 1;
+        else error("Could not parse: --coords %s\n",args->coords_str);
+
+        if ( str[1]=='0' ) end = 0;
+        else if ( str[1]=='1' ) end = 1;
+        else error("Could not parse: --coords %s\n",args->coords_str);
+    }
+    else if ( len>=4 && !strcasecmp(".bed",dat->fname+len-4) ) beg = 0;
+    else if ( len>=7 && !strcasecmp(".bed.gz",dat->fname+len-7) ) beg = 0;
+    dat->coor_base[0] = beg;
+    dat->coor_base[1] = end;
+}
+
 void init_data(args_t *args)
 {
     if ( !args->delim_str )
@@ -521,6 +549,13 @@ void init_data(args_t *args)
     if ( args->src.core->n!=3 || args->dst.core->n!=3 ) error("Expected three columns: %s\n", args->core_str);
     cols_destroy(tmp);
 
+    // -C, --coordinates, 0 or 1-based
+    if ( !args->coords_str ) args->coords_str = ":";
+    tmp = cols_split(args->coords_str, NULL, ':');
+    parse_coor_base(args, tmp->off[0], &args->src);
+    parse_coor_base(args, tmp->n==2 ? tmp->off[1] : tmp->off[0], &args->dst);
+    cols_destroy(tmp);
+
     // -m, match columns
     if ( args->match_str )
     {
@@ -881,6 +916,7 @@ static const char *usage_text(void)
         "                             frac .. fraction of the target region with an\n"
         "                                       overlap\n"
         "                             nbp  .. number of source base pairs in the overlap\n"
+        "   -C, --coords SRC:TGT    Are coordinates 0 or 1-based, BED=01, TSV=11 [11]\n"
         "   -d, --delim SRC:TGT     Column delimiter in SRC and TGT file\n"
         "   -h, --headers SRC:TGT   Header row line number, 0:0 is equivalent to -H, negative\n"
         "                             value counts from the end of comment line block [1:1]\n"
@@ -923,6 +959,7 @@ int main(int argc, char **argv)
     static struct option loptions[] =
     {
         {"core",required_argument,NULL,'c'},
+        {"coords",required_argument,NULL,'C'},
         {"transfer",required_argument,NULL,'f'},
         {"match",required_argument,NULL,'m'},
         {"output",required_argument,NULL,'o'},
@@ -945,7 +982,7 @@ int main(int argc, char **argv)
     char *tmp = NULL;
     int c;
     int reciprocal = 0;
-    while ((c = getopt_long(argc, argv, "c:f:m:o:s:t:a:HO:rxh:Id:",loptions,NULL)) >= 0)
+    while ((c = getopt_long(argc, argv, "c:C:f:m:o:s:t:a:HO:rxh:Id:",loptions,NULL)) >= 0)
     {
         switch (c)
         {
@@ -966,6 +1003,7 @@ int main(int argc, char **argv)
             case 'H': args->headers_str = "0:0"; break;
             case 'r': reciprocal = 1; break;
             case 'c': args->core_str  = optarg; break;
+            case 'C': args->coords_str  = optarg; break;
             case 't': args->dst.fname = optarg; break;
             case 'm': args->match_str = optarg; break;
             case 'a': args->annots_str = optarg; break;

test/annot-tsv/dst.14.txt

@@ -0,0 +1,2 @@
+1	1	2
+1	6	7

test/annot-tsv/out.14.1.txt

@@ -0,0 +1,2 @@
+1	1	2
+1	6	7

test/annot-tsv/out.14.2.txt

@@ -0,0 +1 @@
+1	1	2

test/annot-tsv/src.14.txt

@@ -0,0 +1,2 @@
+1	1	2
+1	5	6

test/test.pl

@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 #
-#    Copyright (C) 2012-2024 Genome Research Ltd.
+#    Copyright (C) 2012-2025 Genome Research Ltd.
 #
 #    Author: Petr Danecek <[email protected]>
 #
@@ -1515,4 +1515,6 @@ sub test_annot_tsv
     run_annot_tsv($opts,src=>'src.13.txt',dst=>'src.13.txt',out=>'out.13.2.txt',args=>q[-c 1,2,3 -f 4:5 -O 0.5,0.5]);
     run_annot_tsv($opts,src=>'src.13.txt',dst=>'src.13.txt',out=>'out.13.3.txt',args=>q[-c 1,2,3 -f 4:5 -O 0,1]);
     run_annot_tsv($opts,src=>'src.13.txt',dst=>'src.13.txt',out=>'out.13.4.txt',args=>q[-c 1,2,3 -f 4:5 -O 1,0]);
+    run_annot_tsv($opts,src=>'src.14.txt',dst=>'dst.14.txt',out=>'out.14.1.txt',args=>q[-c 1,2,3 -C 11:11]);        # 1-based coordinates
+    run_annot_tsv($opts,src=>'src.14.txt',dst=>'dst.14.txt',out=>'out.14.2.txt',args=>q[-c 1,2,3 -C 01:01]);        # interpret as bed coordinates
 }