Version 1.0.31

README.md

@@ -0,0 +1 @@
+[See the wiki](https://git.metabarcoding.org/obitools/sumaclust/wikis/home)

sumaclust.c

@@ -23,7 +23,7 @@
 #include "mtcompare_sumaclust.h"
 #include "sumaclust.h"
 
-#define VERSION "1.0.10"
+#define VERSION "1.0.31"
 
 
 /* ----------------------------------------------- */
@@ -73,9 +73,10 @@ static void PrintHelp()
         PP      " -f       : Output in FASTA format is deactivated.\n");
         PP      "\n");
         PP      "------------------------------------------------------------\n");
-        PP      " Argument : the nucleotide dataset to cluster\n");
+        PP      " Argument : the nucleotide dataset to cluster (or nothing   \n");
+        PP      "            if the standard input should be used).          \n");
         PP      "------------------------------------------------------------\n");
-        PP		" http://metabarcoding.org/sumatra\n");
+        PP		" http://metabarcoding.org/sumaclust\n");
         PP      "------------------------------------------------------------\n\n");
 }
 
@@ -584,7 +585,7 @@ void putSeqInCluster(fastaSeqPtr* seq, fastaSeqPtr* center, double score)
 }
 
 
-int compare(fastaSeqPtr* db,  int n, BOOL fastOption, double threshold, BOOL normalize, int reference, BOOL lcsmode,
+int compare(fastaSeqPtr* db, int n, BOOL fastOption, double threshold, BOOL normalize, int reference, BOOL lcsmode,
 		double max_ratio)
 {
 	double       score;
@@ -722,7 +723,7 @@ int compare(fastaSeqPtr* db,  int n, BOOL fastOption, double threshold, BOOL nor
 	free(iseq1-sizeForSeqs+lmax);
 	free(iseq2-sizeForSeqs+lmax);
 
-	if (normalize && reference == ALILEN)
+	if (normalize && (reference == ALILEN))
 		free(address);
 
 	return(k);
@@ -794,7 +795,6 @@ int main(int argc, char** argv)
 	BOOL			reverse		     = FALSE;
 	BOOL			onlyATGC	     = TRUE;
 	int             reference        = ALILEN;
-	int             ndb              = 0;
 	int				nproc            = 1;
 	BOOL			printBIOM        = FALSE;
 	BOOL			printOTUtable    = FALSE;
@@ -941,10 +941,6 @@ int main(int argc, char** argv)
 		}
 	}
 
-	ndb = argc - optind;
-	if (ndb != 1)
-        errflag++;
-
 	if (errflag)
 		ExitUsage(errflag);
 
@@ -965,6 +961,7 @@ int main(int argc, char** argv)
 
 	fprintf(stderr,"Reading dataset...");
 	db = seq_readAllSeq2(argv[optind], TRUE, onlyATGC);
+
 	fprintf(stderr,"\n%d sequences\n",db.count);
 
 	if (db.count == 0)
@@ -1040,7 +1037,6 @@ int main(int argc, char** argv)
 	// FASTA file
 	if (printFASTA)
 	{
-
 		if (printFASTAtofile)
 		{
 			FASTA_output = fopen(FASTA_file_name, "w");

sumaclust_user_manual.md

@@ -46,12 +46,12 @@ Sumaclust clusters sequences using the same clustering algorithm as UCLUST and C
 
 #### Input
 
-Input file must be in FASTA format.
+The input can be either the standard input (stdin), or a file in FASTA format.
 
 #### Usage
 
 ```
-sumaclust [-l|L|a|n|r|d|e|o|g|f] [-t threshold_value] [-s sorting_key] [-R maximum_ratio] [-p number_of_threads] [-B file_name_for_BIOM-formatted_output] [-O file_name_for_OTU_table-formatted_output] [-F file_name_for_FASTA-formatted_output] dataset
+sumaclust [-l|L|a|n|r|d|e|o|g|f] [-t threshold_value] [-s sorting_key] [-R maximum_ratio] [-p number_of_threads] [-B file_name_for_BIOM-formatted_output] [-O file_name_for_OTU_table-formatted_output] [-F file_name_for_FASTA-formatted_output] [dataset]
 ```
 
 Argument: the sequence dataset to cluster.