[Genabel-commits] r1159 - pkg/OmicABEL/src

[noreply at r-forge.r-project.org]

Author: dfabregat
Date: 2013-03-19 16:43:41 +0100 (Tue, 19 Mar 2013)
New Revision: 1159

Modified:
   pkg/OmicABEL/src/CLAK_GWAS.c
Log:
CLAK-GWAS usage (as printed with -h option) is more clear now.


Modified: pkg/OmicABEL/src/CLAK_GWAS.c
===================================================================
--- pkg/OmicABEL/src/CLAK_GWAS.c	2013-03-19 15:42:11 UTC (rev 1158)
+++ pkg/OmicABEL/src/CLAK_GWAS.c	2013-03-19 15:43:41 UTC (rev 1159)
@@ -143,18 +143,19 @@
 
 void usage( void ) 
 {
-    fprintf(stderr, "\nUsage: HP-GWAS [options]\n\n");
-    fprintf(stderr, "Following options may be given:\n\n");
-    fprintf(stderr, "  -var     [chol | eigen] Default is chol.\n");
-    fprintf(stderr, "  -cov     base path to covariates file \n");
-    fprintf(stderr, "  -phi     base path to kinship? file \n");
-    fprintf(stderr, "  -snp     base path to SNPs file \n");
-    fprintf(stderr, "  -pheno   base path to phenotypes file \n");
-    fprintf(stderr, "  -out     base path to output file \n");
-    fprintf(stderr, "  -nths    # Default is 1 thread.\n");
-    fprintf(stderr, "  -thres   # Default is 95%%.\n");
+    fprintf(stderr, "\nUsage: CLAK-GWAS <arguments> [options]\n\n");
+    fprintf(stderr, "Following arguments are mandatory:\n\n");
+    fprintf(stderr, "  -cov <path>    base path to the file containing the covariates\n");
+    fprintf(stderr, "  -phi <path>    base path to the file containing the relationship matrix\n");
+    fprintf(stderr, "  -snp <path>    base path to the file containing the SNPs\n");
+    fprintf(stderr, "  -pheno <path>  base path to the file containing the phenotypes\n");
+    fprintf(stderr, "  -out <path>    base path to the file where the output will be stored\n\n");
+    fprintf(stderr, "Following options might be given:\n\n");
+    fprintf(stderr, "  -var [chol | eigen] Default is chol.\n");
+    fprintf(stderr, "  -nths <num>         Default is 1 thread.\n");
+    fprintf(stderr, "  -thres <num>        Default is 95(%%).\n");
 	/*fprintf(stderr, "  -no-output               Default is to write the output files.\n");*/
-    fprintf(stderr, "  -h       Show this help and exit\n\n");
+    fprintf(stderr, "  -h                  Show this help and exit\n\n");
 }
 
 int parse_input( int argc, char *argv[], char *var, 
@@ -378,16 +379,17 @@
 	
 	// Paths provided?
 	if ( strcmp( phi_base, "" ) == 0 || strcmp( cov_base, "" ) == 0 || 
-			strcmp( snp_base, "" ) == 0 || strcmp( pheno_base, "" ) == 0 )
+			 strcmp( snp_base, "" ) == 0 || strcmp( pheno_base, "" ) == 0 ||
+			(strcmp( out_base, "" ) == 0 && write_output) )
 	{
-		fprintf( stderr, "You must provide all of -cov -phi -snp -pheno\n\n" );
+		fprintf( stderr, "You must provide all mandatory arguments (see -h option for details)\n\n" );
 		exit( EXIT_FAILURE );
 	}
-	if ( strcmp( out_base, "" ) == 0 && write_output )
-	{
-		fprintf( stderr, "Output base path required\n\n" );
-		exit( EXIT_FAILURE );
-	}
+//	if ( strcmp( out_base, "" ) == 0 && write_output )
+//	{
+//		fprintf( stderr, "Output base path required (see -h option for details)\n\n" );
+//		exit( EXIT_FAILURE );
+//	}
 			
 	// Phi data
     snprintf( cf->Phi_data_path, STR_BUFFER_SIZE, "%s.fvd", phi_base );