Added README file for Gitlab

itself.

README.md

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

sumatra.c

@@ -20,7 +20,7 @@
 #include "./sumalibs/libutils/utilities.h"
 #include "mtcompare_sumatra.h"
 
-#define VERSION "1.0.10"
+#define VERSION "1.0.20"
 
 
 /* ----------------------------------------------- */
@@ -57,7 +57,9 @@ static void PrintHelp()
         PP      " -g       : n's are replaced with a's (default: sequences with n's are discarded).\n");
         PP      " -x       : Adds four extra columns with the count and length of both sequences.\n");
         PP      "-----------------------------------------------------------------------------------------------------------------------------\n");
-        PP      " First argument  : the nucleotide dataset to analyze\n\n");
+        PP      " First argument  : the nucleotide dataset to analyze (or nothing   \n");
+        PP      "                   if there is only one dataset and the standard   \n");
+        PP		"                   input should be used).                        \n\n");
         PP      " Second argument : optionally the second nucleotide dataset\n");
         PP      "-----------------------------------------------------------------------------------------------------------------------------\n");
         PP      " Results table description : \n");
@@ -84,7 +86,7 @@ static void PrintHelp()
 static void ExitUsage(stat)
         int stat;
 {
-        PP      "usage: sumatra [-l|L|a|n|r|d|g|x] [-t threshold_value] [-p number of threads] dataset1 [dataset2]\n");
+        PP      "usage: sumatra [-l|L|a|n|r|d|g|x] [-t threshold_value] [-p number of threads] [dataset1] [dataset2]\n");
         PP      "type \"sumatra -h\" for help\n");
 
         if (stat)
@@ -425,8 +427,6 @@ int main(int argc, char **argv)
 	}
 
 	ndb = argc - optind;
-	if (ndb < 1)
-        errflag++;
 
 	if (errflag)
 		ExitUsage(errflag);

sumatra_user_manual.md

@@ -40,12 +40,12 @@ Sumatra computes the pairwise alignment scores from one dataset or between two d
 
 #### Input
 
-Files must be in FASTA format.
+If there is one dataset, the input can be either the standard input (stdin), or a file in FASTA format. If there are two datasets to compare, the input must be two files in FASTA format.
 
 #### Usage
 
 ```
-sumatra [-l|L|a|n|r|d|g|x] [-t threshold_value] [-p number of threads] dataset1 [dataset2] 
+sumatra [-l|L|a|n|r|d|g|x] [-t threshold_value] [-p number of threads] [dataset1] [dataset2]
 ```
 First argument: the sequence dataset in fasta format to analyse.