Commit 1cae92e9 by Eric Coissac

Add minus -R option to localize aplicon over one of the sequence database.

This option add two column on the right of the output table with the primers location 
and the barcode sequence    

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@219 60f365c0-8329-0410-b2a4-ec073aeeaa1d
parent 3a617890
......@@ -160,6 +160,10 @@ void printapair(int32_t index,ppair_t pair, poptions_t options)
bool_t good1=pair->p1->good;
bool_t good2=pair->p2->good;
bool_t goodtmp;
bool_t strand;
uint32_t i;
char *c;
if (!asdirect1)
w1=ecoComplementWord(w1,options->primer_length);
......@@ -211,9 +215,9 @@ void printapair(int32_t index,ppair_t pair, poptions_t options)
if (options->refseq && pair->refsequence >=0)
{
printf("\t%s:",options->reference);
strand = pair->pcr.amplifias[pair->refsequence].strand;
if (pair->pcr.amplifias[pair->refsequence].strand)
if (strand)
printf("join(");
else
printf("complement(");
......@@ -226,6 +230,14 @@ void printapair(int32_t index,ppair_t pair, poptions_t options)
printf(")");
printf("\t");
for (c=pair->pcr.amplifias[pair->refsequence].amplifia,
i=pair->pcr.amplifias[pair->refsequence].begin;
i<=pair->pcr.amplifias[pair->refsequence].end;
i++,
c+=(strand)? 1:-1)
printf("%c","acgt"[(strand)? (*c):(~*c)&3]);
}
printf("\n");
......
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