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delta bug

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git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@309 60f365c0-8329-0410-b2a4-ec073aeeaa1d
This commit is contained in:
Eric Coissac
2011-06-30 15:12:38 +00:00
parent f53cc6d500
commit ae528e48f4
3 changed files with 16 additions and 9 deletions
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11
src/ecopcr.c
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@ -262,6 +262,9 @@ void printRepeat(ecoseq_t *seq,
amplifia[i]|=32; amplifia[i]|=32;
for (i=1;i<rdelta;i++) for (i=1;i<rdelta;i++)
amplifia[delta-i]|=32; amplifia[delta-i]|=32;
amplifia[delta]=0;
} }
if (compute_tm) if (compute_tm)
@ -636,9 +639,9 @@ 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 : suppress by <EC> */ length=posj - posi - o1->patlen - o2->patlen;
if (posj < posi) if (posj < posi)
length= posj + apatseq->seqlen - posi - o1->patlen; length= posj + apatseq->seqlen - posi - o1->patlen - o2->patlen;
if (length && if (length &&
(!lmin || (length >= lmin)) && (!lmin || (length >= lmin)) &&
(!lmax || (length <= lmax))) (!lmax || (length <= lmax)))
@ -689,9 +692,9 @@ int main(int argc, char **argv)
length = 0; length = 0;
if (posj > posi) if (posj > posi)
length=posj - posi + 1 - o2->patlen; /* - o1->patlen : suppress by <EC> */ length=posj - posi + 1 - o2->patlen - o1->patlen; /* - o1->patlen : suppress by <EC> */
if (posj < posi) if (posj < posi)
length= posj + apatseq->seqlen - posi - o1->patlen; length= posj + apatseq->seqlen - posi - o1->patlen - o2->patlen;
if (length && if (length &&
(!lmin || (length >= lmin)) && (!lmin || (length >= lmin)) &&

3
src/libecoPCR/ecodna.c
View File

@ -104,6 +104,9 @@ char *ecoComplementSequence(char *nucAcSeq)
char *getSubSequence(char* nucAcSeq,int32_t begin,int32_t end) char *getSubSequence(char* nucAcSeq,int32_t begin,int32_t end)
/*
extract subsequence from nucAcSeq [begin,end[
*/
{ {
static char *buffer = NULL; static char *buffer = NULL;
static int32_t buffSize= 0; static int32_t buffSize= 0;

11
src/libecoPCR/ecofilter.c
View File

@ -10,10 +10,11 @@ int eco_is_taxid_included( ecotaxonomy_t *taxonomy,
taxon = eco_findtaxonbytaxid(taxonomy, taxid); taxon = eco_findtaxonbytaxid(taxonomy, taxid);
for (i=0; i < tab_len; i++) if (taxon)
if ( (taxon->taxid == restricted_taxid[i]) || for (i=0; i < tab_len; i++)
(eco_isundertaxon(taxon, restricted_taxid[i])) ) if ( (taxon->taxid == restricted_taxid[i]) ||
return 1; (eco_isundertaxon(taxon, restricted_taxid[i])) )
return 1;
return 0; return 0;
} }