fixed bad tests in match.rb

[biopieces.git] / code_c / Maasha / src / bed_sort.c

diff --git a/code_c/Maasha/src/bed_sort.c b/code_c/Maasha/src/bed_sort.c
index d8e84eb8a6f13f3321b9e39f84e1d34529662be2..6c7bf6927a9c463074660c7ccfb823151e6b8576 100644 (file)
--- a/code_c/Maasha/src/bed_sort.c
+++ b/code_c/Maasha/src/bed_sort.c
@@ -4,19 +4,105 @@
 #include "list.h"
 #include "ucsc.h"
 
+static void usage()
+{
+    fprintf( stderr, 
+        "\n"
+        "bed_sort - sorts a BED file.\n"
+        "\n"
+        "Usage: bed_sort [options] <BED file>\n"
+        "\n"
+        "Options:\n"
+        "   [-s <int> | --sort <int>]   # 1: chr AND chr_beg.\n"
+        "                               # 2: chr AND strand AND chr_beg.\n"
+        "                               # 3: chr_beg.\n"
+        "                               # 4: strand AND chr_beg.\n"
+        "   [-c <int> | --cols <int>]   # Number of columns to read (default all).\n"
+        "   [-d <dir> | --dir <dir> ]   # Directory to use for file bound sorting.\n"
+        "\n"
+        "Examples:\n"
+        "   bed_sort test.bed > test.bed.sort\n"
+        "\n"
+        );
+
+    exit( EXIT_FAILURE );
+}
+
+
+static struct option longopts[] = {
+    { "sort",  required_argument, NULL, 's' },
+    { "cols",  required_argument, NULL, 'c' },
+    { "dir",   required_argument, NULL, 'd' },
+    { NULL,    0,                 NULL,  0  }
+};
+
 
 int main( int argc, char *argv[] )
 {
+    int      opt     = 0;
+    int      sort    = 1;
+    int      cols    = 0;
+    char    *dir     = NULL;
     char    *file    = NULL;
     list_sl *entries = NULL;
 
-    file = argv[ 1 ];
+    while ( ( opt = getopt_long( argc, argv, "n:l", longopts, NULL ) ) != -1 )
+    {
+        switch ( opt ) {
+            case 's': sort = strtol( optarg, NULL, 0 ); break;
+            case 'c': cols = strtol( optarg, NULL, 0 ); break;
+            case 'd': dir  = optarg;                    break;          
+            default:                                    break;
+        }
+    }
+
+    fprintf( stderr, "sort: %d  cols: %d   dir: %s\n", sort, cols, dir );
+
+    argc -= optind;
+    argv += optind;
+
+    if ( sort < 1 || sort > 4 )
+    {
+        fprintf( stderr, "ERROR: argument to --sort must be 1, 2, 3 or 4 - not: %d\n", sort );
+        abort();
+    }
+
+    if ( cols != 0 && cols != 3 && cols != 4 && cols != 5 && cols != 6 && cols != 12 )
+    {
+        fprintf( stderr, "ERROR: argument to --cols must be 3, 4, 5, 6 or 12 - not: %d\n", cols );
+        abort();
+    }
+
+    if ( ( sort == 2 || sort == 4 ) && ( cols > 0 && cols < 6 ) )
+    {
+        fprintf( stderr, "ERROR: cannot sort on strand with cols (%d) less than 6\n", cols );
+        abort();
+    }
+
+    if ( dir != NULL )
+    {
+        fprintf( stderr, "ERROR: directory: %s does not exists\n", dir );
+        abort();
+    }
+
+    if ( argc < 1 ) {
+        usage();
+    }
+
+    file = argv[ argc - 1 ];
 
-    entries = bed_entries_get( file, 3 );
+    entries = bed_entries_get( file, cols );
 
-    list_sl_sort( &entries, cmp_bed_sort_chr_beg );
+    switch ( sort )
+    {
+        case 1: list_sl_sort( &entries, cmp_bed_sort_chr_beg );        break;
+        case 2: list_sl_sort( &entries, cmp_bed_sort_chr_strand_beg ); break;
+        case 3: list_sl_sort( &entries, cmp_bed_sort_beg );            break;
+        case 4: list_sl_sort( &entries, cmp_bed_sort_strand_beg );     break;
+        default: break;
+    }
 
-    bed_entries_put( entries, 3 );
+    bed_entries_put( entries, cols );
 
     return EXIT_SUCCESS;
 }