From ae528e48f471014a10fd18975b81c9eedf5b2608 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric.coissac@metabarcoding.org>
Date: Thu, 30 Jun 2011 15:12:38 +0000
Subject: [PATCH] delta bug

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@309 60f365c0-8329-0410-b2a4-ec073aeeaa1d
---
 src/ecopcr.c              | 11 +++++++----
 src/libecoPCR/ecodna.c    |  3 +++
 src/libecoPCR/ecofilter.c | 11 ++++++-----
 3 files changed, 16 insertions(+), 9 deletions(-)

diff --git a/src/ecopcr.c b/src/ecopcr.c
index 1cb5ac4..ff2d830 100644
--- a/src/ecopcr.c
+++ b/src/ecopcr.c
@@ -262,6 +262,9 @@ void printRepeat(ecoseq_t *seq,
 			amplifia[i]|=32;
 		for (i=1;i<rdelta;i++)
 			amplifia[delta-i]|=32;
+
+		amplifia[delta]=0;
+
 	}
 	
 	if (compute_tm)
@@ -636,9 +639,9 @@ int main(int argc, char **argv)
 										errj  =apatseq->hiterr[1]->val[j];
 										length = 0;
 										if (posj > posi)
-											length=posj - posi  - o1->patlen; /* - o2->patlen : suppress by <EC> */
+											length=posj - posi  - o1->patlen - o2->patlen; 
 										if (posj < posi)
-											length= posj + apatseq->seqlen - posi - o1->patlen;
+											length= posj + apatseq->seqlen - posi - o1->patlen - o2->patlen;
 										if (length &&
 											(!lmin || (length >= lmin)) &&
 										    (!lmax || (length <= lmax)))
@@ -689,9 +692,9 @@ int main(int argc, char **argv)
 
 										length = 0;
 										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)
-											length= posj + apatseq->seqlen - posi - o1->patlen;
+											length= posj + apatseq->seqlen - posi - o1->patlen - o2->patlen;
 
 										if (length &&
 											(!lmin || (length >= lmin)) &&
diff --git a/src/libecoPCR/ecodna.c b/src/libecoPCR/ecodna.c
index 7d29a0e..86d2012 100644
--- a/src/libecoPCR/ecodna.c
+++ b/src/libecoPCR/ecodna.c
@@ -104,6 +104,9 @@ char *ecoComplementSequence(char *nucAcSeq)
 
 
 char *getSubSequence(char* nucAcSeq,int32_t begin,int32_t end)
+/*
+   extract subsequence from nucAcSeq [begin,end[
+*/
 {
 	static char *buffer  = NULL;
 	static int32_t buffSize= 0;
diff --git a/src/libecoPCR/ecofilter.c b/src/libecoPCR/ecofilter.c
index 8a7dbb1..64276c0 100644
--- a/src/libecoPCR/ecofilter.c
+++ b/src/libecoPCR/ecofilter.c
@@ -10,10 +10,11 @@ int eco_is_taxid_included(	ecotaxonomy_t *taxonomy,
 	
 	taxon = eco_findtaxonbytaxid(taxonomy, taxid);
 	
-	for (i=0; i < tab_len; i++)
-		if ( (taxon->taxid == restricted_taxid[i]) ||
-			 (eco_isundertaxon(taxon, restricted_taxid[i])) )
-			return 1;
+	if (taxon)
+		for (i=0; i < tab_len; i++)
+			if ( (taxon->taxid == restricted_taxid[i]) ||
+				 (eco_isundertaxon(taxon, restricted_taxid[i])) )
+				return 1;
 	
 	return 0;
-}
\ No newline at end of file
+}