obitools/ecopcr
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Patch a bug inducing that sequences were considered as circular whatever

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the -c option was present or not.
This commit is contained in:
Eric Coissac
2020-04-27 12:07:28 +02:00
parent c4321036be
commit 9deb30a8c4
1 changed files with 9 additions and 4 deletions
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13
src/ecopcr.c
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@ -614,8 +614,10 @@ int main(int argc, char **argv)
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) else {
length = posj + apatseq->seqlen - posi - o1->patlen - o2->patlen; if (circular > 0)
length = posj + apatseq->seqlen - posi - o1->patlen - o2->patlen;
}
if ((length>0) && // For when primers touch or overlap if ((length>0) && // For when primers touch or overlap
(!lmin || (length >= lmin)) && (!lmin || (length >= lmin)) &&
(!lmax || (length <= lmax))) (!lmax || (length <= lmax)))
@ -648,7 +650,7 @@ int main(int argc, char **argv)
} }
o1cHits = ManberAll(apatseq,o1c,3,begin,length); o1cHits = ManberAll(apatseq,o1c,3,begin,length);
printf("circular= %d\n",circular);
if (o1cHits) if (o1cHits)
for (i=0; i < o2Hits;i++) for (i=0; i < o2Hits;i++)
{ {
@ -668,8 +670,11 @@ 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 : deleted by <EC> (prior to the OBITools3) */ length = posj - posi + 1 - o2->patlen - o1->patlen; /* - o1->patlen : deleted by <EC> (prior to the OBITools3) */
if (posj < posi) else {
if (circular > 0)
length = posj + apatseq->seqlen - posi - o1->patlen - o2->patlen; length = posj + apatseq->seqlen - posi - o1->patlen - o2->patlen;
}
if ((length>0) && // For when primers touch or overlap if ((length>0) && // For when primers touch or overlap
(!lmin || (length >= lmin)) && (!lmin || (length >= lmin)) &&
(!lmax || (length <= lmax))) (!lmax || (length <= lmax)))