obitools/ecopcr
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Fixed a bug when primers would touch or overlap, producing amplicons of

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size <= 0
This commit is contained in:
Celine Mercier
2018-07-26 19:03:59 +02:00
parent f0cca648ea
commit bd1db764d4
1 changed files with 23 additions and 18 deletions
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41
src/ecopcr.c
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@ -6,7 +6,7 @@
#include <getopt.h> #include <getopt.h>
#define VERSION "0.8.0" #define VERSION "1.0.0"
/* ----------------------------------------------- */ /* ----------------------------------------------- */
@ -80,7 +80,7 @@ static void PrintHelp()
PP "column 21 : sequence\n"); PP "column 21 : sequence\n");
PP "column 22 : definition\n"); PP "column 22 : definition\n");
PP "------------------------------------------\n"); PP "------------------------------------------\n");
PP " http://www.grenoble.prabi.fr/trac/ecoPCR/\n"); PP " https://git.metabarcoding.org/obitools/ecopcr/wikis/home\n");
PP "------------------------------------------\n\n"); PP "------------------------------------------\n\n");
PP "\n"); PP "\n");
@ -566,11 +566,11 @@ int main(int argc, char **argv)
) )
{ {
scname = taxonomy->taxons->taxon[seq->taxid].name; //scname = taxonomy->taxons->taxon[seq->taxid].name;
strncpy(head,seq->SQ,10); //strncpy(head,seq->SQ,10);
head[10]=0; //head[10]=0;
strncpy(tail,seq->SQ+seq->SQ_length-10,10); //strncpy(tail,seq->SQ+seq->SQ_length-10,10);
tail[10]=0; //tail[10]=0;
apatseq=ecoseq2apatseq(seq,apatseq,circular); apatseq=ecoseq2apatseq(seq,apatseq,circular);
@ -613,15 +613,17 @@ int main(int argc, char **argv)
errj =apatseq->hiterr[1]->val[j]; errj =apatseq->hiterr[1]->val[j];
length = 0; length = 0;
if (posj > posi) if (posj > posi)
length=posj - posi - o1->patlen - o2->patlen; length = posj - posi - o1->patlen - o2->patlen;
if (posj < posi) if (posj < posi)
length= posj + apatseq->seqlen - posi - o1->patlen - o2->patlen; //length = posj + apatseq->seqlen - posi - o1->patlen - o2->patlen; // TODO
if (length && length = posi - posj - o1->patlen - o2->patlen;
if ((length>0) && // For when primers touch or overlap
(!lmin || (length >= lmin)) && (!lmin || (length >= lmin)) &&
(!lmax || (length <= lmax))) (!lmax || (length <= lmax)))
{
printRepeat(seq,oligo1,oligo2,&tparm,o1,o2c,'D',kingdom_mode,posi,posj,erri,errj,taxonomy,delta); printRepeat(seq,oligo1,oligo2,&tparm,o1,o2c,'D',kingdom_mode,posi,posj,erri,errj,taxonomy,delta);
//printf("%s\tD\t%s...%s (%d)\t%d\t%d\t%d\t%d\t%s\n",seq->AC,head,tail,seq->SQ_length,o1Hits,o2cHits,posi,posj,scname); //printf("%s\tD\t%s...%s (%d)\t%d\t%d\t%d\t%d\t%s\n",seq->AC,head,tail,seq->SQ_length,o1Hits,o2cHits,posi,posj,scname);
}
} }
} }
} }
@ -666,15 +668,18 @@ int main(int argc, char **argv)
length = 0; length = 0;
if (posj > posi) if (posj > posi)
length=posj - posi + 1 - o2->patlen - o1->patlen; /* - o1->patlen : suppress by <EC> */ //length = posj - posi + 1 - o2->patlen - o1->patlen; /* - o1->patlen : deleted by <EC> (prior to the OBITools3) */ TODO ????
length = posj - posi - o2->patlen - o1->patlen;
if (posj < posi) if (posj < posi)
length= posj + apatseq->seqlen - posi - o1->patlen - o2->patlen; //length = posj + apatseq->seqlen - posi - o1->patlen - o2->patlen; TODO ????
length = posi - posj - o2->patlen - o1->patlen;
if (length && if ((length>0) && // For when primers touch or overlap
(!lmin || (length >= lmin)) && (!lmin || (length >= lmin)) &&
(!lmax || (length <= lmax))) (!lmax || (length <= lmax)))
{
printRepeat(seq,oligo1,oligo2,&tparm,o2,o1c,'R',kingdom_mode,posi,posj,erri,errj,taxonomy,delta); printRepeat(seq,oligo1,oligo2,&tparm,o2,o1c,'R',kingdom_mode,posi,posj,erri,errj,taxonomy,delta);
//printf("%s\tR\t%s...%s (%d)\t%d\t%d\t%d\t%d\t%s\n",seq->AC,head,tail,seq->SQ_length,o2Hits,o1cHits,posi,posj,scname); //printf("%s\tR\t%s...%s (%d)\t%d\t%d\t%d\t%d\t%s\n",seq->AC,head,tail,seq->SQ_length,o2Hits,o1cHits,posi,posj,scname);
}
} }
} }
} }