From 2a118eedda0a34792dab468b79376c65497fc3eb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Fr=C3=A9d=C3=A9ric=20Boyer?=
 <frederic.boyer@metabarcoding.org>
Date: Mon, 7 May 2012 09:14:09 +0000
Subject: [PATCH] MOD: In the printRepeat function, corrected rdelta and ldelta
 management

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@417 60f365c0-8329-0410-b2a4-ec073aeeaa1d
---
 src/ecopcr.c | 28 ++++++++++++++++++----------
 1 file changed, 18 insertions(+), 10 deletions(-)

diff --git a/src/ecopcr.c b/src/ecopcr.c
index fe40761..b12c272 100644
--- a/src/ecopcr.c
+++ b/src/ecopcr.c
@@ -146,7 +146,7 @@ void printRepeat(ecoseq_t *seq,
 
 	AC = seq->AC;
 	seqlength = seq->SQ_length;
-	
+
 	
 	main_taxon    = &taxonomy->taxons->taxon[seq->taxid];
 	taxid         = main_taxon->taxid;
@@ -201,20 +201,29 @@ void printRepeat(ecoseq_t *seq,
 			superkingdom_name  = "###";
 		}
 	
+
+
 	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);
 	amplength= strlen(amplifia)-rdelta-ldelta;
 	
 	if (strand=='R')
 	{
-		ecoComplementSequence(amplifia);
-		strncpy(oligo1,amplifia+ rdelta ,o2->patlen);
+
+	    ecoComplementSequence(amplifia);
+
+		strncpy(oligo1,amplifia + rdelta ,o2->patlen);
+
 		oligo1[o2->patlen]=0;
 		error1=err2;
-		
-		strncpy(oligo2,amplifia + ldelta + amplength - o1->patlen,o1->patlen);
+
+		strncpy(oligo2, amplifia + rdelta + amplength - o1->patlen,o1->patlen);
 		oligo2[o1->patlen]=0;
 		error2=err1;
 		
@@ -227,13 +236,13 @@ void printRepeat(ecoseq_t *seq,
 			rdelta=delta+o1->patlen;
 		}
 	}
-	else
+	else /* strand == 'D' */
 	{
 		strncpy(oligo1,amplifia+ldelta,o1->patlen);
 		oligo1[o1->patlen]=0;
 		error1=err1;
 		
-		strncpy(oligo2,amplifia + rdelta + amplength - o2->patlen,o2->patlen);
+		strncpy(oligo2,amplifia + ldelta + amplength - o2->patlen,o2->patlen);
 		oligo2[o2->patlen]=0;
 		error2=err2;
 		
@@ -247,7 +256,6 @@ void printRepeat(ecoseq_t *seq,
 		
 	}
 	
-
 	
 	ecoComplementSequence(oligo2);
 	if(delta==0)
@@ -257,7 +265,7 @@ void printRepeat(ecoseq_t *seq,
 		delta=ldelta+rdelta+amplength-o1->patlen-o2->patlen;
 		for (i=0;i<ldelta;i++)
 			amplifia[i]|=32;
-		for (i=1;i<rdelta;i++)
+		for (i=1;i<=rdelta;i++)
 			amplifia[delta-i]|=32;
 
 		amplifia[delta]=0;