diff --git a/sumatra.c b/sumatra.c index bf8ee9b..d9fe745 100644 --- a/sumatra.c +++ b/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" /* ----------------------------------------------- */ @@ -84,7 +84,7 @@ 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 +425,6 @@ int main(int argc, char **argv) } ndb = argc - optind; - if (ndb < 1) - errflag++; if (errflag) ExitUsage(errflag); diff --git a/sumatra_user_manual.md b/sumatra_user_manual.md index e28bf88..5c2425b 100644 --- a/sumatra_user_manual.md +++ b/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. diff --git a/sumatra_user_manual.pdf b/sumatra_user_manual.pdf index 229f03b..239e634 100644 Binary files a/sumatra_user_manual.pdf and b/sumatra_user_manual.pdf differ