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

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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
This commit is contained in:
Eric Coissac
2009-06-24 08:09:39 +00:00
parent 3a617890ca
commit 1cae92e963
1 changed files with 14 additions and 2 deletions
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16
src/ecoprimer.c
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@ -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");