void initenv ( int argc, char ** argv ) { int copt; int inpseq, outseq; extern char * optarg; char temp[100]; optind = 1; inpseq = outseq = 0; while ( ( copt = getopt ( argc, argv, "s:g:K:p:" ) ) != EOF ) { //printf("get option\n"); switch ( copt ) { case 's': inpseq = 1; sscanf ( optarg, "%s", shortrdsfile ); continue; case 'g': outseq = 1; sscanf ( optarg, "%s", graphfile ); // continue; case 'K': sscanf ( optarg, "%s", temp ); // overlaplen = atoi ( temp ); continue; case 'p': sscanf ( optarg, "%s", temp ); // thrd_num = atoi ( temp ); continue; default: if ( inpseq == 0 || outseq == 0 ) // { display_map_usage(); exit ( 1 ); } } } if ( inpseq == 0 || outseq == 0 ) // { //printf("need more\n"); display_map_usage(); exit ( 1 ); } }
void initenv ( int argc, char ** argv ) { int copt; int inpseq, outseq; extern char * optarg; char temp[100]; optind = 1; inpseq = outseq = 0; fprintf ( stderr, "Parameters: map " ); while ( ( copt = getopt ( argc, argv, "s:g:K:p:k:f" ) ) != EOF ) { //printf("get option\n"); switch ( copt ) { case 's': fprintf ( stderr, "-s %s ", optarg ); inpseq = 1; sscanf ( optarg, "%s", shortrdsfile ); break; case 'g': fprintf ( stderr, "-g %s ", optarg ); outseq = 1; sscanf ( optarg, "%s", graphfile ); break; case 'K': fprintf ( stderr, "-K %s ", optarg ); sscanf ( optarg, "%s", temp ); overlaplen = atoi ( temp ); break; case 'p': fprintf ( stderr, "-p %s ", optarg ); sscanf ( optarg, "%s", temp ); thrd_num = atoi ( temp ); break; case 'k': fprintf ( stderr, "-k %s ", optarg ); sscanf ( optarg, "%s", temp ); smallKmer = atoi ( temp ); break; case 'f': fill = 1; fprintf ( stderr, "-f " ); break; default: if ( inpseq == 0 || outseq == 0 ) { display_map_usage (); exit ( 1 ); } } } fprintf ( stderr, "\n\n" ); if ( inpseq == 0 || outseq == 0 ) { display_map_usage (); exit ( 1 ); } }