From 194ec811f4a2fed8cf3e2a4961cf25f948b4f866 Mon Sep 17 00:00:00 2001 From: Celine Mercier Date: Tue, 19 May 2015 13:52:35 +0200 Subject: [PATCH] Fixes #2 by adding the missing -D option in the help --- src/ecopcr.c | 17 ++++++++++------- 1 file changed, 10 insertions(+), 7 deletions(-) diff --git a/src/ecopcr.c b/src/ecopcr.c index b12c272..0b533bd 100644 --- a/src/ecopcr.c +++ b/src/ecopcr.c @@ -23,6 +23,8 @@ static void PrintHelp() PP "usage: ecoPCR [options] \n"); PP "------------------------------------------\n"); PP "options:\n"); + PP "-a : Salt concentration in M for Tm computation (default 0.05 M)\n\n"); + PP "-c : Consider that the database sequences are [c]ircular\n\n"); PP "-d : [D]atabase : to match the expected format, the database\n"); PP " has to be formated first by the ecoPCRFormat.py program located.\n"); PP " in the tools directory.\n"); @@ -31,8 +33,11 @@ static void PrintHelp() PP " .tdx : contains information concerning the taxonomy\n"); PP " .rdx : contains the taxonomy rank\n\n"); PP " ecoPCR needs all the file type. As a result, you have to write the\n"); - PP " database radical without any extension. For example /ecoPCRDB/gbmam\n\n"); - PP "-e : [E]rror : max error allowed by oligonucleotide (0 by default)\n\n"); + PP " database radical without any extension. For example /ecoPCRDB/gbmam\n\n"); + PP "-D : Keeps the specified number of nucleotides on each side of the in silico \n"); + PP " amplified sequences (including the amplified DNA fragment plus the two target \n"); + PP " sequences of the primers).\n\n"); + PP "-e : [E]rror : max errors allowed by oligonucleotide (0 by default)\n\n"); PP "-h : [H]elp - print help\n\n"); PP "-i : [I]gnore the given taxonomy id.\n"); PP " Taxonomy id are available using the ecofind program.\n"); @@ -41,13 +46,11 @@ static void PrintHelp() PP " super kingdom mode by default.\n\n"); PP "-l : minimum [L]ength : define the minimum amplication length. \n\n"); PP "-L : maximum [L]ength : define the maximum amplicationlength. \n\n"); - PP "-r : [R]estricts the search to the given taxonomic id.\n"); - PP " Taxonomy id are available using the ecofind program.\n"); - PP " see its help typing ecofind -h for more information.\n"); - PP "-c : Consider that the database sequences are [c]ircular\n"); PP "-m : Salt correction method for Tm computation (SANTALUCIA : 1\n"); PP " or OWCZARZY:2, default=1)\n\n"); - PP "-a : Salt contentration in M for Tm computation (default 0.05 M)\n\n"); + PP "-r : [R]estricts the search to the given taxonomic id.\n"); + PP " Taxonomy id are available using the ecofind program.\n"); + PP " see its help typing ecofind -h for more information.\n\n"); PP "\n"); PP "------------------------------------------\n"); PP "first argument : oligonucleotide for direct strand\n\n");