From 73236c72a85da621a32a39bef008f05c61c9a333 Mon Sep 17 00:00:00 2001
From: Celine Mercier <celine.mercier@metabarcoding.org>
Date: Tue, 22 Jan 2019 15:51:43 +0100
Subject: [PATCH] version 0.5: ecoPrimers can now read *.ldx files (local taxa)

---
 VERSION                |  2 +-
 src/ecoprimer.c        |  2 +-
 src/libecoPCR/ecoPCR.h |  2 +-
 src/libecoPCR/ecotax.c | 41 +++++++++++++++++++++++++++++++----------
 4 files changed, 34 insertions(+), 13 deletions(-)

diff --git a/VERSION b/VERSION
index e6adf3f..ea2303b 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-0.4
\ No newline at end of file
+0.5
\ No newline at end of file
diff --git a/src/ecoprimer.c b/src/ecoprimer.c
index 628e7c4..b5ab37f 100644
--- a/src/ecoprimer.c
+++ b/src/ecoprimer.c
@@ -20,7 +20,7 @@
 #include"libthermo/thermostats.h"
 
 
-#define VERSION "0.4"
+#define VERSION "0.5"
   /* TR: by default, statistics are made on species level*/
 #define DEFAULTTAXONRANK "species"
 
diff --git a/src/libecoPCR/ecoPCR.h b/src/libecoPCR/ecoPCR.h
index 237ec32..f2fe663 100644
--- a/src/libecoPCR/ecoPCR.h
+++ b/src/libecoPCR/ecoPCR.h
@@ -219,7 +219,7 @@ econameidx_t     *read_nameidx(const char *filename,ecotaxonomy_t *taxonomy);
 	 * @return pointer to a taxonomy index structure
 	 */
 
-ecotxidx_t       *read_taxonomyidx(const char *filename);
+ecotxidx_t       *read_taxonomyidx(const char *filename,const char *filename2);
 
 ecotaxonomy_t    *read_taxonomy(const char *prefix,int32_t readAlternativeName);
 
diff --git a/src/libecoPCR/ecotax.c b/src/libecoPCR/ecotax.c
index a0ade86..95b304e 100644
--- a/src/libecoPCR/ecotax.c
+++ b/src/libecoPCR/ecotax.c
@@ -10,23 +10,41 @@ static ecotx_t *readnext_ecotaxon(FILE *f,ecotx_t *taxon);
  * @param	pointer to the database (.tdx file)
  * @return	a ecotxidx_t structure
  */
-ecotxidx_t     *read_taxonomyidx(const char *filename)
+ecotxidx_t     *read_taxonomyidx(const char *filename,const char *filename2)
 {
 	int32_t      count;
+	int32_t      count2;
 	FILE         *f;
+	FILE         *f2;
 	ecotxidx_t *index;
 	int32_t      i;
 
-	f = open_ecorecorddb(filename,&count,1);
+	f  = open_ecorecorddb(filename,&count,1);
+	f2 = open_ecorecorddb(filename2,&count2,0);
 
-	index = (ecotxidx_t*) ECOMALLOC(sizeof(ecotxidx_t) + sizeof(ecotx_t) * (count-1),
+
+
+	index = (ecotxidx_t*) ECOMALLOC(sizeof(ecotxidx_t) + sizeof(ecotx_t) * (count+count2-1),
 	                                  "Allocate taxonomy");
 
-	index->count=count;
+	index->count=count+count2;
+
+	fprintf(stderr,"Reading %d taxa...\n",count);
 	for (i=0; i < count; i++){
 		readnext_ecotaxon(f,&(index->taxon[i]));
-		index->taxon[i].parent=index->taxon + (size_t)index->taxon[i].parent;
+		index->taxon[i].parent=index->taxon + (int32_t)index->taxon[i].parent;
 	}
+
+	if (count2>0)
+		fprintf(stderr,"Reading %d local taxa...\n",count2);
+	else
+		fprintf(stderr,"No local taxon\n");
+
+	for (i=0; i < count2; i++){
+		readnext_ecotaxon(f2,&(index->taxon[count+i]));
+		index->taxon[count+i].parent=index->taxon + (int32_t)index->taxon[count+i].parent;
+	}
+
 	return index;
 }
 
@@ -111,33 +129,36 @@ ecotaxonomy_t    *read_taxonomy(const char *prefix,int32_t readAlternativeName)
 {
 	ecotaxonomy_t *tax;
 	char          *filename;
+	char          *filename2;
 	int           buffsize;
 
 	tax = ECOMALLOC(sizeof(ecotaxonomy_t),
-	                "Allocate taxonomy structure");
+					"Allocate taxonomy structure");
 
 	buffsize = strlen(prefix)+10;
 
 	filename = ECOMALLOC(buffsize,
-	                     "Allocate filename");
+						 "Allocate filename");
+	filename2= ECOMALLOC(buffsize,
+						 "Allocate filename");
 
 	snprintf(filename,buffsize,"%s.rdx",prefix);
 
 	tax->ranks = read_rankidx(filename);
 
 	snprintf(filename,buffsize,"%s.tdx",prefix);
+	snprintf(filename2,buffsize,"%s.ldx",prefix);
 
-	tax->taxons = read_taxonomyidx(filename);
+	tax->taxons = read_taxonomyidx(filename,filename2);
 
 	if (readAlternativeName)
 	{
-  	   snprintf(filename,buffsize,"%s.ndx",prefix);
+	   snprintf(filename,buffsize,"%s.ndx",prefix);
 	   tax->names=read_nameidx(filename,tax);
 	}
 	else
 	   tax->names=NULL;
 	return tax;
-
 }