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MOD: In the printRepeat function, corrected rdelta and ldelta management

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git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@417 60f365c0-8329-0410-b2a4-ec073aeeaa1d
This commit is contained in:
Frédéric Boyer
2012-05-07 09:14:09 +00:00
parent 93c530e090
commit 2a118eedda
1 changed files with 18 additions and 10 deletions
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28
src/ecopcr.c
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@ -146,7 +146,7 @@ void printRepeat(ecoseq_t *seq,
AC = seq->AC; AC = seq->AC;
seqlength = seq->SQ_length; seqlength = seq->SQ_length;
main_taxon = &taxonomy->taxons->taxon[seq->taxid]; main_taxon = &taxonomy->taxons->taxon[seq->taxid];
taxid = main_taxon->taxid; taxid = main_taxon->taxid;
@ -201,20 +201,29 @@ void printRepeat(ecoseq_t *seq,
superkingdom_name = "###"; superkingdom_name = "###";
} }
ldelta=(pos1 <= delta)?pos1:delta; ldelta=(pos1 <= delta)?pos1:delta;
rdelta=(pos2+delta>=seqlength)?seqlength-pos2-1:delta;
/*rdelta=((pos2+delta)>=seqlength)?seqlength-pos2-1:delta; */
rdelta=((pos2+delta)>=seqlength)?seqlength-pos2:delta;
amplifia = getSubSequence(seq->SQ,pos1-ldelta,pos2+rdelta); amplifia = getSubSequence(seq->SQ,pos1-ldelta,pos2+rdelta);
amplength= strlen(amplifia)-rdelta-ldelta; amplength= strlen(amplifia)-rdelta-ldelta;
if (strand=='R') if (strand=='R')
{ {
ecoComplementSequence(amplifia);
strncpy(oligo1,amplifia+ rdelta ,o2->patlen); ecoComplementSequence(amplifia);
strncpy(oligo1,amplifia + rdelta ,o2->patlen);
oligo1[o2->patlen]=0; oligo1[o2->patlen]=0;
error1=err2; error1=err2;
strncpy(oligo2,amplifia + ldelta + amplength - o1->patlen,o1->patlen); strncpy(oligo2, amplifia + rdelta + amplength - o1->patlen,o1->patlen);
oligo2[o1->patlen]=0; oligo2[o1->patlen]=0;
error2=err1; error2=err1;
@ -227,13 +236,13 @@ void printRepeat(ecoseq_t *seq,
rdelta=delta+o1->patlen; rdelta=delta+o1->patlen;
} }
} }
else else /* strand == 'D' */
{ {
strncpy(oligo1,amplifia+ldelta,o1->patlen); strncpy(oligo1,amplifia+ldelta,o1->patlen);
oligo1[o1->patlen]=0; oligo1[o1->patlen]=0;
error1=err1; error1=err1;
strncpy(oligo2,amplifia + rdelta + amplength - o2->patlen,o2->patlen); strncpy(oligo2,amplifia + ldelta + amplength - o2->patlen,o2->patlen);
oligo2[o2->patlen]=0; oligo2[o2->patlen]=0;
error2=err2; error2=err2;
@ -247,7 +256,6 @@ void printRepeat(ecoseq_t *seq,
} }
ecoComplementSequence(oligo2); ecoComplementSequence(oligo2);
if(delta==0) if(delta==0)
@ -257,7 +265,7 @@ void printRepeat(ecoseq_t *seq,
delta=ldelta+rdelta+amplength-o1->patlen-o2->patlen; delta=ldelta+rdelta+amplength-o1->patlen-o2->patlen;
for (i=0;i<ldelta;i++) for (i=0;i<ldelta;i++)
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; amplifia[delta]=0;