diff --git a/sumaclust.c b/sumaclust.c index a86a72f..e3e9e49 100644 --- a/sumaclust.c +++ b/sumaclust.c @@ -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) diff --git a/sumaclust_user_manual.md b/sumaclust_user_manual.md index e46072a..e6700b1 100644 --- a/sumaclust_user_manual.md +++ b/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. diff --git a/sumaclust_user_manual.pdf b/sumaclust_user_manual.pdf index de53660..1ab0b51 100644 Binary files a/sumaclust_user_manual.pdf and b/sumaclust_user_manual.pdf differ