Commit 68c47433 authored by Eric Coissac's avatar Eric Coissac

added print help

git-svn-id: 60f365c0-8329-0410-b2a4-ec073aeeaa1d
parent 035495b2
......@@ -25,9 +25,59 @@
static void PrintHelp()
PP "------------------------------------------\n");
PP " ecoPrimer Version %s\n", VERSION);
PP "------------------------------------------\n");
PP "------------------------------------------\n");
PP " ecoPrimer Version %s\n", VERSION);
PP "------------------------------------------\n");
PP "synopsis : finding primers and measureing the quality of primers and barcode region\n");
PP "usage: ./ecoPrimer [options] \n");
PP "------------------------------------------\n");
PP "options:\n");
PP "-d : [D]atabase : to match the expected format, the database\n");
PP " has to be formated first by the program located.\n");
PP " in the ecoPCR/tools directory.\n");
PP " creates three file types :\n");
PP " .sdx : contains the sequences\n");
PP " .tdx : contains information concerning the taxonomy\n");
PP " .rdx : contains the taxonomy rank\n\n");
PP " ecoPrimer needs all the file type. As a result, you have to write the\n");
PP " database radical without any extension. For example /ecoPrimerDB/fstvert\n\n");
PP "-e : [E]rror : max error allowed by oligonucleotide (0 by default)\n\n");
PP "-h : [H]elp - print <this> help\n\n");
PP "-i : [I]gnore the given taxonomy id.\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\n");
PP "-c : Consider that the database sequences are [c]ircular\n\n");
PP "-3 : Three prime strict match\n\n");
PP "-q : Strict matching [q]uorum, percentage of the sequences in which strict primers are found. By default it is 70\n\n");
PP "-s : [S]ensitivity quorum\n\n");
PP "-t : required [t]axon level for results, by default the results are computed at species level\n\n");
PP "-x : false positive quorum\n\n");
PP "-D : set in [d]ouble strand mode\n\n");
PP "-S : Set in [s]ingle strand mode\n\n");
PP "-U : No multi match\n\n");
PP "\n");
PP "------------------------------------------\n");
PP "Table result description : \n");
PP "column 1 : serial number\n");
PP "column 2 : primer1\n");
PP "column 3 : primer2\n");
PP "column 4 : good/bad\n");
PP "column 5 : in sequence count\n");
PP "column 6 : out sequence count\n");
PP "column 7 : yule\n");
PP "column 8 : in taxa count\n");
PP "column 9 : out taxa count\n");
PP "column 10 : coverage\n");
PP "column 11 : specificity\n");
PP "column 12 : minimum amplified length\n");
PP "column 13 : maximum amplified length\n");
PP "column 14 : average amplified length\n");
PP "------------------------------------------\n");
PP "\n");
PP "------------------------------------------\n\n");
PP "\n");
static void ExitUsage(int stat)
......@@ -180,6 +230,8 @@ void printpairs (ppairtree_t pairs, poptions_t options)
size_t i,j;
int32_t count;
fprintf(stderr,"Total pair count : %d\n",pairs->count);
sortedpairs = ECOMALLOC(pairs->count*sizeof(ppair_t),"Cannot Allocate ordered pairs");
......@@ -374,9 +426,9 @@ int main(int argc, char **argv)
/* -------------------- */
case 'h': /* help */
/* -------------------- */
/* ------------------------- */
case 'l': /* min amplification lenght */
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