Actualiser src/global.mk

.gitignore

@@ -1,16 +1,15 @@
-
+*.o
-# /src/
 /src/*.P
 /src/*.a
 /src/ecoPrimer
-
-# /src/libecoPCR/
 /src/libecoPCR/*.P
 /src/libecoPCR/*.a
-
+/src/libecoPCR/*.o
-# /src/libecoprimer/
 /src/libecoprimer/*.P
 /src/libecoprimer/*.a
-
+/src/libecoprimer/*.o
-# /src/libthermo/
 /src/libthermo/*.P
+/src/libthermo/*.a
+/src/libthermo/*.o
+phylonorway.*
+src/ecoPrimers

VERSION

@@ -1 +1 @@
-0.4
+0.5

src/Makefile

@@ -28,7 +28,7 @@ all: $(EXEC)
 # executable compilation and link
 
 ecoPrimers: $(PRIMER_OBJ) $(LIBFILE) 
-	$(CC) -g $(LDFLAGS) -O5 -m64 -o $@ $< $(LIBPATH) $(LIB)
+	$(CC) $(LDFLAGS) -O5 -o $@ $< $(LIBPATH) $(LIB)
 	
 
 ########

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"
 
@@ -171,13 +171,9 @@ void printapair(int32_t index,ppair_t pair, poptions_t options)
 	bool_t good2=pair->p2->good;
 	bool_t goodtmp;
 	bool_t strand;
-	uint32_t i, j;
+	uint32_t i;
-	float temp;
-	CNNParams nnparams;
 
-	//nparam_InitParams(&nnparams, DEF_CONC_PRIMERS,DEF_CONC_SEQUENCES,DEF_SALT,SALT_METHOD_SANTALUCIA);
+	const char *c;
-
-	char *c;
 	char p1[32];
 	char p2[32];
 
@@ -376,21 +372,20 @@ uint32_t filterandsortpairs(ppair_t* sortedpairs,uint32_t count, poptions_t opti
 void printpairs (ppairtree_t pairs, poptions_t options,ecotaxonomy_t *taxonomy, pecodnadb_t seqdb)
 {
    ppair_t* sortedpairs;
-   ppair_t* index;
+   // ppair_t* index;
    ppairlist_t pl;
    size_t i,j;
    size_t count;
    char *taxon[]={"taxon","taxa"};
    ecotx_t    *current_taxon;
    //pairset pair_sets;
-   pairset *pset = NULL;
 
    //printf("Index\tPrimer1\tPrimer2\tGB\tInexampleCount\tOutexampleCount\tYule\tIntaxaCount\tOuttaxaCount\tCoverage\tSpecificity\tMinAmplifiedLength\tMaxAmplifiedLength\tAvgAmplifiedLength\n");
 
    fprintf(stderr,"Total pair count : %d\n",pairs->count);
 
    sortedpairs = ECOMALLOC(pairs->count*sizeof(ppair_t),"Cannot Allocate ordered pairs");
-   index=sortedpairs;
+   // index=sortedpairs;
    pl=pairs->first;
    j=0;
    while(pl->next)
@@ -475,10 +470,10 @@ void printpairs (ppairtree_t pairs, poptions_t options,ecotaxonomy_t *taxonomy,
 
    if (options->filter_on_links)
    {
-		fprintf (stderr, "Old size: %d, ", count);
+		fprintf (stderr, "Old size: %ld, ", count);
 		count = primers_changeSortedArray (&sortedpairs, count, options);
 		//count = primers_filterWithGivenLinks (&sortedpairs, count, options);
-		fprintf (stderr, "New size: %d\n", count);
+		fprintf (stderr, "New size: %ld\n", count);
 
 		if (count == 0)
 		{
@@ -799,13 +794,17 @@ int main(int argc, char **argv)
    		}
 
 	}
+
+	if (errflag) {
+		ExitUsage(1);
+	}
     options.pnparm = &nnparams;
     if (options.saltmethod != 2) //if not SALT_METHOD_OWCZARZY
     	options.saltmethod = SALT_METHOD_SANTALUCIA; //then force SALT_METHOD_SANTALUCIA
 
-    if (options.salt < 0.01 || options.salt > 0.3) //if salt value out of literature values
+    if (options.salt < 0.01 || options.salt > 0.3) {//if salt value out of literature values
     	options.salt = DEF_SALT; //set to default
-
+	}
 	nparam_InitParams(&nnparams, DEF_CONC_PRIMERS,DEF_CONC_SEQUENCES,options.salt,options.saltmethod);
 
     fprintf(stderr,"Reading taxonomy database ...");
@@ -851,7 +850,7 @@ int main(int argc, char **argv)
     fprintf(stderr,"\nIndexing words in sequences\n");
 
     words = lookforStrictPrimer(seqdb,seqdbsize,insamples,&options);
-    fprintf(stderr,"\n  Strict primer count : %d\n",words->size);
+    fprintf(stderr,"\n  Strict primer count : %lld\n",words->size);
     
     /*/TR Testing
     fprintf(stderr,"\nReducing for debugging\n");
@@ -871,7 +870,7 @@ int main(int argc, char **argv)
     if (options.no_multi_match)
     {
     	(void)filterMultiStrictPrimer(words);
-    	fprintf(stderr,"\n  Strict primer with single match count : %d\n",words->size);
+    	fprintf(stderr,"\n  Strict primer with single match count : %lld\n",words->size);
     }
 
 
@@ -921,7 +920,7 @@ pwordcount_t reduce_words_to_debug (pwordcount_t words, poptions_t options)
 {
 	uint32_t i, k;
 	pwordcount_t new_words;
-	char *rwrd;
+	const char *rwrd;
 	char dwrd[20];
 	/*char *strict_words[DEBUG_WORDS_CNT] = {"GAGTCTCTGCACCTATCC", "GCAATCCTGAGCCAAATC", "ACCCCTAACCACAACTCA", 
 			"TCCGAACCGACTGATGTT", "GAAGCTTGGGTGAAACTA", "GGAGAACCAGCTAGCTCT", "GCTGGTTCTCCCCGAAAT",
@@ -981,7 +980,7 @@ pwordcount_t reduce_words_to_debug (pwordcount_t words, poptions_t options)
 
 void print_wordwith_positions (primer_t prm, uint32_t seqdbsize, poptions_t options)
 {
-	char *wrd;
+	const char *wrd;
 	uint32_t i, j;
 	char *twrd = "GCCTGTTTACCAAAAACA";
 

src/global.mk

@@ -1,9 +1,9 @@
-MACHINE=MAC_OS_X
+MACHINE=LINUX
-LIBPATH= -LlibecoPCR -Llibecoprimer -Llibthermo
+LIBPATH= -LlibecoPCR -Llibecoprimer -Llibthermo -L/usr/local/lib
 MAKEDEPEND = gcc -D$(MACHINE) -M $(CPPFLAGS) -o $*.d $<
 
 CC=gcc
-CFLAGS= -W -Wall -m64 -g
+CFLAGS= -W -Wall -O5
 #CFLAGS= -W -Wall -O5 -m64 -g
 #CFLAGS= -W -Wall -O0 -m64  -g
 #CFLAGS= -W -Wall -O5 -fast -g

src/libecoPCR/ecoMalloc.c

@@ -2,7 +2,7 @@
 #include <stdlib.h>
 
 static int eco_log_malloc = 0;
-static size_t eco_amount_malloc=0;
+//static size_t eco_amount_malloc=0;
 static size_t eco_chunk_malloc=0;
 
 void    eco_trace_memory_allocation()
@@ -37,7 +37,7 @@ void   *eco_malloc(int64_t chunksize,
 
 	if (eco_log_malloc)
 		fprintf(stderr,
-			    "Memory segment located at %p of size %d is allocated (file : %s [%d])",
+			    "Memory segment located at %p of size %lld is allocated (file : %s [%d])",
 			    chunk,
 			    chunksize,
 			    filename,
@@ -65,7 +65,7 @@ void   *eco_realloc(void *chunk,
 
 	if (!newchunk)
            {
-        fprintf(stderr,"Requested memory : %d\n",newsize);
+        fprintf(stderr,"Requested memory : %lld\n",newsize);
 		ecoError(ECO_MEM_ERROR,error_message,filename,line);
            }
 	if (!chunk)
@@ -73,7 +73,7 @@ void   *eco_realloc(void *chunk,
 
 	if (eco_log_malloc)
 		fprintf(stderr,
-			    "Old memory segment %p is reallocated at %p with a size of %d (file : %s [%d])",
+			    "Old memory segment %p is reallocated at %p with a size of %lld (file : %s [%d])",
 			    chunk,
 			    newchunk,
 			    newsize,

src/libecoPCR/ecoPCR.h

@@ -21,8 +21,8 @@ typedef struct {
 	int32_t  taxid;
 	char     AC[20];
 	int32_t  DE_length;
-	int32_t  SQ_length;
+	uint32_t  SQ_length;
-	int32_t  CSQ_length; /*what is this CSQ_length ? */
+	uint32_t  CSQ_length; /*what is this CSQ_length ? */
 
 	char     data[1];
 
@@ -30,7 +30,7 @@ typedef struct {
 
 typedef struct {
 	int32_t taxid;
-	int32_t SQ_length;
+	uint32_t SQ_length;
 	int32_t isexample;
 	char    *AC;
 	char    *DE;
@@ -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);
 

src/libecoPCR/ecorank.c

@@ -12,14 +12,14 @@ ecorankidx_t     *read_rankidx(const char *filename)
 	int32_t      i;
 	int32_t      rs;
 	char         *buffer;
-	
+
 	f = open_ecorecorddb(filename,&count,1);
-	
+
 	index = (ecorankidx_t*) ECOMALLOC(sizeof(ecorankidx_t) + sizeof(char*) * (count-1),
 	                                  "Allocate rank index");
-	 
+
-	index->count=count;                                 
+	index->count=count;
-	          
+
 	for (i=0; i < count; i++)
 		{
 			buffer = read_ecorecord(f,&rs);
@@ -27,21 +27,18 @@ ecorankidx_t     *read_rankidx(const char *filename)
 			                                  "Allocate rank label");
 			strncpy(index->label[i],buffer,rs);
 		}
-		
+
 	return index;
 }
 
 int32_t rank_index(const char* label,ecorankidx_t* ranks)
 {
 	char **rep;
-	
+        fprintf(stderr,"Looking for rank -%s-... ",label);
 	rep = bsearch(label,ranks->label,ranks->count,sizeof(char*),compareRankLabel);
-	
+
 	if (rep)
 		return rep-ranks->label;
-	else
-		ECOERROR(ECO_NOTFOUND_ERROR,"Rank label not found");
-		
 	return -1;
 }
 

src/libecoPCR/ecoseq.c

@@ -2,6 +2,7 @@
 #include <stdlib.h>
 #include <string.h>
 #include <zlib.h>
+#include <ctype.h>
 #include <string.h>
 #include <stdio.h>
 
@@ -194,7 +195,7 @@ ecoseq_t *ecoseq_iterator(const char *prefix)
 {
 	static FILE    *current_seq_file= NULL;
 	static int32_t current_file_idx = 1;
-	static char    current_prefix[1024];
+	static char    current_prefix[1025];
 	ecoseq_t       *seq;
 
 	if (prefix)

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;
 }
 
@@ -94,7 +112,7 @@ ecotx_t *readnext_ecotaxon(FILE *f,ecotx_t *taxon)
 		raw->taxid      = swap_int32_t(raw->taxid);
 	}
 
-	taxon->parent = (ecotx_t*)(size_t)raw->parent;
+	taxon->parent = (ecotx_t*)raw->parent;
 	taxon->taxid  = raw->taxid;
 	taxon->rank   = raw->rank;
 
@@ -111,6 +129,7 @@ ecotaxonomy_t    *read_taxonomy(const char *prefix,int32_t readAlternativeName)
 {
 	ecotaxonomy_t *tax;
 	char          *filename;
+	char          *filename2;
 	int           buffsize;
 
 	tax = ECOMALLOC(sizeof(ecotaxonomy_t),
@@ -120,14 +139,17 @@ ecotaxonomy_t    *read_taxonomy(const char *prefix,int32_t readAlternativeName)
 
 	filename = ECOMALLOC(buffsize,
 	                     "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)
 	{
@@ -319,6 +341,9 @@ ecotx_t *eco_getsuperkingdom(ecotx_t *taxon,
 	if (taxonomy && tax!=taxonomy)
 	{
 		rankindex = rank_index("superkingdom",taxonomy->ranks);
+                if (rankindex < 0) {
+		   rankindex = rank_index("domain",taxonomy->ranks);
+                }
 		tax=taxonomy;
 	}
 

src/libecoprimer/PrimerSets.c

@@ -1139,7 +1139,7 @@ void sets_by_SimulatedAnealing (pairset *pair_set,
 	{
 		pair_set = extend_set_randomly (NULL, &params, 3);
 		printf("\nStart Random seed set for Simulated :\n");
-		print_set_info (&pair_set, &params);
+		print_set_info (pair_set, &params);
 	}
 	min_spc = max_spc = pair_set->set_specificity;
 	min_cov = max_cov = pair_set->set_coverage;
@@ -1566,7 +1566,8 @@ int32_t *addinset (int32_t *set, int32_t i, int32_t j, int32_t* slots, int32_t *
 size_t primers_changeSortedArray (ppair_t ** pairs,
 		size_t sorted_count, poptions_t options)
 {
-	int32_t i, j, k, l, total_links;
+	int32_t i, k, total_links;
+	uint32_t j;
 	int *owi;
 	int *iwi;
 	int allowedtaxa;
@@ -1579,14 +1580,14 @@ size_t primers_changeSortedArray (ppair_t ** pairs,
 	idx_set = ECOMALLOC(slots*sizeof (int32_t),
 		            "Could not allocate memory for index set.");
 
-	for (i=0; i<sorted_count; i++)
+	for (i=0; ((uint32_t)i)<sorted_count; i++)
 	{
 		owi = sortedpairs[i]->wellIdentifiedSeqs;
 		passed = FALSE;
 
 		for (j=0; j<sorted_count; j++)
 		{
-			if (i == j) continue;
+			if ((uint32_t)i == j) continue;
 
 			iwi = sortedpairs[j]->wellIdentifiedSeqs;
 			total_links = 0;
@@ -1610,9 +1611,10 @@ size_t primers_changeSortedArray (ppair_t ** pairs,
 			if (options->max_links_percent > 0)
 			{
 				allowedtaxa = options->max_links_percent;
-				if (total_links > allowedtaxa)
+				if (total_links > allowedtaxa){
 					passed = TRUE;
-					break;
+					}
+				break;
 			}
 			else
 			if (!(total_links > 5 && total_links <= allowedtaxa))
@@ -1630,7 +1632,7 @@ size_t primers_changeSortedArray (ppair_t ** pairs,
 	for (j=0; j<sorted_count; j++)
 	{
 		for (k=0; k<index; k++)
-			if (j == idx_set[k]) break;
+			if (j == (uint32_t)(idx_set[k])) break;
 		//need to remove this element
 		if (k == index)
 		{
@@ -1711,9 +1713,9 @@ int32_t *addinset_withLinks (int32_t *set, int32_t i, int32_t* slots, int32_t *i
 size_t primers_filterWithGivenLinks (ppair_t ** pairs,
 		size_t sorted_count, poptions_t options)
 {
-	int32_t i, j, k;
+	int32_t i,  k;
+	uint32_t j;
 	ppair_t *sortedpairs = *pairs;
-	bool_t passed;
 
 	int32_t *idx_set = NULL;
 	int32_t slots=50, index=0;
@@ -1732,7 +1734,7 @@ size_t primers_filterWithGivenLinks (ppair_t ** pairs,
 	for (j=0; j<sorted_count; j++)
 	{
 		for (k=0; k<index; k++)
-			if (j == idx_set[k]) break;
+			if (j == (uint32_t) (idx_set[k])) break;
 		//need to remove this element
 		if (k == index)
 		{
@@ -1755,7 +1757,7 @@ size_t primers_filterWithGivenLinks (ppair_t ** pairs,
 	else i=sorted_count;
 
 
-	for (j=0; j<i; j++)
+	for (j=0; j<(uint32_t)i; j++)
 		for (k=0; k<options->dbsize; k++)
 			if ((*pairs)[j]->coveredSeqs[k] == 1)
 				cov[k] = 1;

src/libecoprimer/ahocorasick.c

@@ -213,7 +213,6 @@ pprimercount_t ahoc_lookforStrictPrimers (pecodnadb_t database, uint32_t seqdbsi
 	char *base;
 	int8_t code;
 	uint32_t   goodPrimers=0;
-	static int iii=0;
 
 
 	//inSequenceQuorum = (uint32_t)floor((float)exampleCount * options->sensitivity_quorum);

src/libecoprimer/apat_search.c

@@ -36,10 +36,10 @@ int32_t ManberNoErr(pecoseq_t pseq,ppattern_t pat,
         ppatternParam_t param,
         StackiPtr stkpos)
 {
-        int32_t     pos;
+        uint32_t     pos;
         uint32_t    smask, r;
         uint8_t     *data;
-        int32_t    end;
+        uint32_t    end;
 
         end = (size_t)(pseq->SQ_length);
 
@@ -84,11 +84,11 @@ int32_t ManberSub(pecoseq_t pseq,ppattern_t pat,
         StackiPtr stkpos)
 {
         int       e, found;
-        int32_t     pos;
+        uint32_t     pos;
         uint32_t    smask, cmask, sindx;
         uint32_t    *pr, r[2 * MAX_PAT_ERR + 2];
         uint8_t     *data;
-        int32_t    end;
+        uint32_t    end;
 
         end = (size_t)(pseq->SQ_length);
 

src/libecoprimer/aproxpattern.c

@@ -59,7 +59,7 @@ void encodeSequence(ecoseq_t *seq)
      data = (uint8_t*)(seq->SQ);
      cseq = seq->SQ;
 
-     for (i=0;i<seq->SQ_length;i++,data++,cseq++)
+     for (i=0;i<(int)(seq->SQ_length);i++,data++,cseq++)
      {
          *data = encoder[(IS_UPPER(*cseq) ? *cseq : 'Z') - 'A'];
      }
@@ -201,7 +201,7 @@ pprimercount_t lookforAproxPrimer(pecodnadb_t database, uint32_t seqdbsize,uint3
 		data[w].good = data[w].inexample >= inSequenceQuorum && data[w].outexample <= outSequenceQuorum;
 		goodPrimers+=data[w].good? 1:0;
 
-		fprintf(stderr,"Primers %5d/%d analyzed  => sequence : %s in %d example and %d counterexample sequences       \r",
+		fprintf(stderr,"Primers %5d/%lld analyzed  => sequence : %s in %d example and %d counterexample sequences       \r",
 				i+1,words->size,ecoUnhashWord(data[w].word,options->primer_length),
 				data[w].inexample,data[w].outexample);
 
@@ -224,8 +224,8 @@ pprimercount_t lookforAproxPrimer(pecodnadb_t database, uint32_t seqdbsize,uint3
 		ECOFREE(data[w].reversePos,"Free direct count table");
 	}
 
-	fprintf(stderr,"\n\nOn %d analyzed primers %d respect quorum conditions\n",words->size,goodPrimers);
+	fprintf(stderr,"\n\nOn %lld analyzed primers %d respect quorum conditions\n",words->size,goodPrimers);
-	fprintf(stderr,"Conserved primers for further analysis : %d/%d\n",w,words->size);
+	fprintf(stderr,"Conserved primers for further analysis : %d/%lld\n",w,words->size);
 
 	primers = ECOMALLOC(sizeof(primercount_t),"Cannot allocate memory for primer table");
 	primers->primers=ECOREALLOC(data,

src/libecoprimer/hashencoder.h

@@ -8,14 +8,6 @@
 #ifndef HASHENCODER_H_
 #define HASHENCODER_H_
 
-static int8_t encoder[] = {0,                                            // A
+extern int8_t encoder[];
-		                   -1,                                           // b
-		                   1,                                            // C
-	       	               -1,-1,-1,                                     // d, e, f
-		                   2,                                            // G
-		                   -1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,          // h,i,j,k,l,m,n,o,p,q,r,s
-		                   3,3,                                           // T,U
-		                   -1,-1,-1,-1,-1};                              // v,w,x,y,z
-
 
 #endif /* HASHENCODER_H_ */

src/libecoprimer/hashsequence.c

@@ -12,6 +12,16 @@ static int cmpword(const void *x,const void *y);
 
 #include "hashencoder.h"
 
+int8_t encoder[] = {0,                                            // A
+		                   -1,                                           // b
+		                   1,                                            // C
+	       	               -1,-1,-1,                                     // d, e, f
+		                   2,                                            // G
+		                   -1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,          // h,i,j,k,l,m,n,o,p,q,r,s
+		                   3,3,                                           // T,U
+		                   -1,-1,-1,-1,-1};                              // v,w,x,y,z
+
+
 uint32_t ecoWordCount(uint32_t wordsize, uint32_t circular, ecoseq_t *seq)
 {
 	uint32_t wordcount;
@@ -257,6 +267,6 @@ uint32_t ecoFindWord(pwordcount_t table,word_t word)
 
 char ecoComplementChar(char base)
 {
-	return (base < 4)? !base & 3: 4;
+	return (base < 4)? ~base & 3: 4;
 }
 

src/libecoprimer/libstki.c

@@ -250,8 +250,7 @@ void CursiToTop(StackiPtr stki)
 
 } /* end of CursiToTop */
 
-void CursiToBottom(stki)
+void CursiToBottom(StackiPtr stki)
-        StackiPtr stki;
 {
         stki->cursor = 0;
 

src/libecoprimer/libstki.h

@@ -16,6 +16,7 @@
 
 
 #include "ecotype.h"
+#include <stdint.h>
 
 /* ==================================================== */
 /* Constantes de dimensionnement                        */
@@ -85,5 +86,6 @@ bool_t            SearchDownStacki   (StackiPtr  stki  , int32_t sval       );
 bool_t            BinSearchStacki    (StackiPtr  stki  , int32_t sval       );
 bool_t            SameStacki         (StackiPtr  stki1 , StackiPtr stki2  );
 bool_t            ReverseStacki      (StackiPtr  stki                     );
+void              CursiToBottom      (StackiPtr stki  );
 
 #endif /* _H_libstki */

src/libecoprimer/merge.c

@@ -41,7 +41,7 @@ void ecomerge(pwordcount_t data,uint32_t s1,uint32_t s2,uint32_t remainingSeq,ui
 	uint32_t  currentcount,tmpcount;
 	int       same;
 	queue_t   queue;
-	int       nsame=0;
+	// int       nsame=0;
 	uint32_t  maxcount=0;
 	bool_t    writed=TRUE;
 
@@ -103,7 +103,7 @@ void ecomerge(pwordcount_t data,uint32_t s1,uint32_t s2,uint32_t remainingSeq,ui
 		 * record if the two words in the both subtable are the same
 		 */
 		same = (source != S2) && (WORD(currentword) == WORD(merged.words[merged.read2]));
-		nsame+=same;
+		// nsame+=same;
 
 //		DEBUG_LOG("Merging : r1 = %d s1 = %d r2 = %d size = %d word = %s source=%u same=%u",merged.read1,s1,merged.read2-s1,merged.size,ecoUnhashWord(currentword,18),source,same)
 

src/libecoprimer/strictprimers.c

@@ -205,8 +205,8 @@ pwordcount_t lookforStrictPrimer(pecodnadb_t database, uint32_t seqdbsize,
     		}
     		else
     		{
-    			uint32_t s;
+//  			uint32_t s;
-    			s = strictprimers->size;
+//    			s = strictprimers->size;
 //    			DEBUG_LOG("stack size : %u",s);
     			addSeqToWordCountTable(strictprimers,options->primer_length,
     					                             options->circular,
@@ -223,7 +223,7 @@ pwordcount_t lookforStrictPrimer(pecodnadb_t database, uint32_t seqdbsize,
     			logfile = fopen(logfilename,"a");
     			seconde = timeval_subtract(&(usage.ru_utime),&(start.ru_utime)) +
     			          timeval_subtract(&(usage.ru_stime),&(start.ru_stime));
-    			fprintf(logfile,"%d\t%llu\t%lu\t%8.3f\t%8.3e\n",i,
+    			fprintf(logfile,"%d\t%llu\t%llu\t%8.3f\t%8.3e\n",i,
     					(long long unsigned)totallength,
 					strictprimers->size*(sizeof(int64_t)+sizeof(int32_t)),
     					seconde,seconde/(double)totallength);
@@ -248,9 +248,9 @@ pwordcount_t lookforStrictPrimer(pecodnadb_t database, uint32_t seqdbsize,
 										sizeof(word_t)*strictprimers->size,
 										"Cannot reallocate strict primer table");
 
-    if (neededWords)
+    if (neededWords){
     	ECOFREE(neededWords,"Clean needed word table");
-
+	}
 	//TR: Somehow for some primers strictcount value is extremely large hence invalid
 	//we need to remove these primers from the list
 	j = strictprimers->size+1;

src/libecoprimer/taxstats.c

@@ -231,8 +231,8 @@ static int cmpamp(const void *ampf1, const void* ampf2)
 	char cd1;
 	char cd2;
 	int len = 0;
-	char *ch1;
+	const char *ch1;
-	char *ch2;
+	const char *ch2;
 	int incr1;
 	int incr2;
 

src/libthermo/nnparams.c

@@ -17,6 +17,15 @@
 
 double forbidden_entropy;
 
+char bpencoder[] = {	1,							// A
+		                   	0,                          // b
+		                   	2,                          // C
+		                   	0,0,0,                      // d, e, f
+		                   	3,                          // G
+		                   	0,0,0,0,0,0,0,0,0,0,0,0,    // h,i,j,k,l,m,n,o,p,q,r,s
+		                   	4,0,                        // T,U
+		                   	0,0,0,0,0};                 // v,w,x,y,z
+
 
 double nparam_GetInitialEntropy(PNNParams nparm)
 {
@@ -470,7 +479,7 @@ int nparam_CountGCContent(char * seq ) {
 	return count;
 }
 
-void nparam_CleanSeq (char* inseq, char* outseq, int len)
+void nparam_CleanSeq (const char* inseq, char* outseq, int len)
 {
 	int seqlen = strlen (inseq);
 	int i, j;
@@ -508,7 +517,7 @@ void nparam_CleanSeq (char* inseq, char* outseq, int len)
 }
 
 //Calculate TM for given sequence against its complement
-double nparam_CalcSelfTM(PNNParams nparm, char* seq, int len)
+double nparam_CalcSelfTM(PNNParams nparm, const char* seq, size_t len)
 {
 	double thedH = 0;
 	//double thedS = nparam_GetInitialEntropy(nparm);
@@ -520,7 +529,7 @@ double nparam_CalcSelfTM(PNNParams nparm, char* seq, int len)
 	char c4;
 	unsigned int i;
 	char nseq[50];
-	char *useq = seq;
+	const char *useq = seq;
 
 	nparam_CleanSeq (seq, nseq, len);
 	useq = nseq;
@@ -533,7 +542,7 @@ double nparam_CalcSelfTM(PNNParams nparm, char* seq, int len)
 		c4 = GETNUMCODE(useq[i]);
 
 
-		thedH += nparm->dH[c3][c4][c1][c2];//nparam_GetEnthalpy(nparm, c3,c4,c1,c2);
+		thedH += nparm->dH[(uint8_t) c3][(uint8_t)c4][(uint8_t)c1][(uint8_t)c2];//nparam_GetEnthalpy(nparm, c3,c4,c1,c2);
 		thedS += nparam_GetEntropy(nparm, c3,c4,c1,c2);
 	}
 	//printf("------------------\n");
@@ -543,7 +552,7 @@ double nparam_CalcSelfTM(PNNParams nparm, char* seq, int len)
 	return mtemp;
 }
 
-double nparam_CalcTwoTM(PNNParams nparm, char* seq1, char* seq2, int len)
+double nparam_CalcTwoTM(PNNParams nparm, const char* seq1, const char* seq2, size_t len)
 {
 	double thedH = 0;
 	//double thedS = nparam_GetInitialEntropy(nparm);
@@ -575,7 +584,7 @@ double nparam_CalcTwoTM(PNNParams nparm, char* seq1, char* seq2, int len)
 
 		//fprintf (stderr,"Primer : %s %f %f %d %d, %d %d %f\n",useq,thedH,thedS,(int)c3,(int)c4,(int)c1,(int)c2,nparam_GetEnthalpy(nparm, c3,c4,c1,c2));
 
-		thedH += nparm->dH[c3][c4][c1][c2];//nparam_GetEnthalpy(nparm, c3,c4,c1,c2);
+		thedH += nparm->dH[(uint8_t)c3][(uint8_t)c4][(uint8_t)c1][(uint8_t)c2];//nparam_GetEnthalpy(nparm, c3,c4,c1,c2);
 		thedS += nparam_GetEntropy(nparm, c3,c4,c1,c2);
 	}
 	//fprintf(stderr,"------------------\n");

src/libthermo/nnparams.h

@@ -13,11 +13,13 @@
 
 #include <math.h>
 #include <string.h>
+#include <stdint.h>
+
 //#include "../libecoprimer/ecoprimer.h"
 
 // following defines to simplify coding...
-#define ndH(a,b,c,d) nparm->dH[a][b][c][d]
+#define ndH(a,b,c,d) nparm->dH[(uint8_t) a][(uint8_t) b][(uint8_t) c][(uint8_t) d]
-#define ndS(a,b,c,d) nparm->dS[a][b][c][d]
+#define ndS(a,b,c,d) nparm->dS[(uint8_t) a][(uint8_t) b][(uint8_t) c][(uint8_t) d]
 #define forbidden_enthalpy 1000000000000000000.0f
 #define	R 1.987f
 #define	SALT_METHOD_SANTALUCIA 1
@@ -33,14 +35,7 @@
 
 extern double forbidden_entropy;
 
-static char bpencoder[] = {	1,							// A
+extern char bpencoder[];                 // v,w,x,y,z
-		                   	0,                          // b
-		                   	2,                          // C
-		                   	0,0,0,                      // d, e, f
-		                   	3,                          // G
-		                   	0,0,0,0,0,0,0,0,0,0,0,0,    // h,i,j,k,l,m,n,o,p,q,r,s
-		                   	4,0,                        // T,U
-		                   	0,0,0,0,0};                 // v,w,x,y,z
 
 
 typedef struct CNNParams_st
@@ -62,8 +57,8 @@ int nparam_CountGCContent(char * seq );
 double nparam_GetEntropy(PNNParams nparm, char x0, char x1, char y0, char y1);
 double nparam_GetEnthalpy(PNNParams nparm, char x0, char x1, char y0, char y1);
 double nparam_CalcTM(double entropy,double enthalpy);
-double nparam_CalcSelfTM(PNNParams nparm, char* seq, int len);
+double nparam_CalcSelfTM(PNNParams nparm, const char* seq, size_t len);
-double nparam_CalcTwoTM(PNNParams nparm, char* seq1, char* seq2, int len);
+double nparam_CalcTwoTM(PNNParams nparm, const char* seq1, const char* seq2, size_t len);
 
 double nparam_GetInitialEntropy(PNNParams nparm) ;
 double calculateMeltingTemperatureBasic (char * seq);

src/libthermo/thermostats.c

@@ -28,17 +28,15 @@ word_t extractSite(char* sequence, size_t begin, size_t length, bool_t strand)
 
 void getThermoProperties (ppair_t* pairs, size_t count, poptions_t options)
 {
-	size_t i, j,k,l;
+	size_t i, j;
 	uint32_t   bp1,bp2;
-	uint32_t   ep1,ep2;
 	word_t w1;
 	word_t w2;
 	bool_t strand;
 
-	char *sq,*sq1,*sq2,*c;
+	char *sq;
 	char prmrd[50];
 	char prmrr[50];
-	char sqsite[50];
 	double mtemp;
 
 	for (i = 0; i < count; i++)