Commit fcb9dbcf by Celine Mercier

Input can now be stdin

parent 9ed2385f
......@@ -23,7 +23,7 @@
#include "mtcompare_sumaclust.h"
#include "sumaclust.h"
#define VERSION "1.0.10"
#define VERSION "1.0.20"
/* ----------------------------------------------- */
......@@ -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");
}
......@@ -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)
......
......@@ -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.
......
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