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New version of pairing algorithm (alpha)

Browse Source 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/branches/eric-test@184 60f365c0-8329-0410-b2a4-ec073aeeaa1d
This commit is contained in:
Eric Coissac
2009-03-09 11:05:51 +00:00
parent 2be5f2659b
commit dffebd5826
31 changed files with 1015 additions and 211 deletions
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src/ecoPrimer
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23
src/ecoprimer.c
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@ -75,7 +75,7 @@ void printcurrenttime ()
/* Format and print the time, "ddd yyyy-mm-dd hh:mm:ss zzz" */
ts = localtime(&now);
strftime(buf, sizeof(buf), "%a %Y-%m-%d %H:%M:%S %Z", ts);
fprintf(stderr,"#%d#, %s\n",now, buf);
fprintf(stderr,"#%d#, %s\n",(int)now, buf);
}
void printcurrenttimeinmilli()
@ -90,6 +90,9 @@ void printcurrenttimeinmilli()
}
/*TR: Added*/
#ifdef MASKEDCODE
void printpairs (pairscount_t pairs, poptions_t options, int32_t rankdbstats, uint32_t seqdbsize)
{
uint32_t i;
@ -121,8 +124,11 @@ void printpairs (pairscount_t pairs, poptions_t options, int32_t rankdbstats, ui
}
}
#endif /* MASKEDCODE */
/*updateseqparams: This function counts the insample and outsample sequences
* and with each sequences adds a tag of the taxon to which the sequence beongs*/
void updateseqparams (pecodnadb_t seqdb, uint32_t seqdbsize, ecotaxonomy_t *taxonomy,
poptions_t options, int32_t *insamples, int32_t *outsamples)
{
@ -208,7 +214,9 @@ int32_t getrankdbstats(pecodnadb_t seqdb, uint32_t seqdbsize, ecotaxonomy_t *tax
return namesindex;
}
void setoktaxforspecificity (ppairscount_t pairs)
#ifdef MASKEDCODE
void setoktaxforspecificity (ppairtree_t pairs)
{
uint32_t i;
uint32_t j;
@ -251,6 +259,8 @@ void setoktaxforspecificity (ppairscount_t pairs)
}
}
#endif
int main(int argc, char **argv)
{
pecodnadb_t seqdb; /* of type ecoseq_t */
@ -267,7 +277,7 @@ int main(int argc, char **argv)
pwordcount_t words;
pprimercount_t primers;
pairscount_t pairs;
ppairtree_t pairs;
int32_t rankdbstats = 0;
@ -460,13 +470,14 @@ int main(int argc, char **argv)
/*TR: Added*/
pairs = buildPrimerPairs(seqdb, seqdbsize, primers, &options);
setoktaxforspecificity (&pairs);
printpairs (pairs, &options, rankdbstats, seqdbsize);
// setoktaxforspecificity (&pairs);
// printpairs (pairs, &options, rankdbstats, seqdbsize);
ECOFREE(pairs.pairs,"Free pairs table");
//ECOFREE(pairs.pairs,"Free pairs table");
return 0;
}

2
src/global.mk
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@ -3,7 +3,7 @@ LIBPATH= -Llibapat -LlibecoPCR -Llibecoprimer
MAKEDEPEND = gcc -D$(MACHINE) -M $(CPPFLAGS) -o $*.d $<
CC=gcc
CFLAGS= -W -Wall -O5 -m64 -fast -g
CFLAGS= -W -Wall -O3 -m64 -fast -g
#CFLAGS= -W -Wall -O0 -m64 -g
#CFLAGS= -W -Wall -O5 -fast -g

15
src/libecoPCR/ecoError.P Normal file
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@ -0,0 +1,15 @@
ecoError.o ecoError.P : ecoError.c ecoPCR.h /usr/include/stdio.h \
/usr/include/_types.h /usr/include/sys/_types.h \
/usr/include/sys/cdefs.h /usr/include/machine/_types.h \
/usr/include/i386/_types.h /usr/include/inttypes.h \
/usr/lib/gcc/i686-apple-darwin9/4.0.1/include/stdint.h \
/usr/include/stdlib.h /usr/include/available.h /usr/include/sys/wait.h \
/usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
/usr/include/machine/signal.h /usr/include/i386/signal.h \
/usr/include/i386/_structs.h /usr/include/sys/_structs.h \
/usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
/usr/include/sys/resource.h /usr/include/machine/endian.h \
/usr/include/i386/endian.h /usr/include/sys/_endian.h \
/usr/include/libkern/_OSByteOrder.h \
/usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
/usr/include/machine/types.h /usr/include/i386/types.h

15
src/libecoPCR/ecoIOUtils.P Normal file
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@ -0,0 +1,15 @@
ecoIOUtils.o ecoIOUtils.P : ecoIOUtils.c ecoPCR.h /usr/include/stdio.h \
/usr/include/_types.h /usr/include/sys/_types.h \
/usr/include/sys/cdefs.h /usr/include/machine/_types.h \
/usr/include/i386/_types.h /usr/include/inttypes.h \
/usr/lib/gcc/i686-apple-darwin9/4.0.1/include/stdint.h \
/usr/include/stdlib.h /usr/include/available.h /usr/include/sys/wait.h \
/usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
/usr/include/machine/signal.h /usr/include/i386/signal.h \
/usr/include/i386/_structs.h /usr/include/sys/_structs.h \
/usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
/usr/include/sys/resource.h /usr/include/machine/endian.h \
/usr/include/i386/endian.h /usr/include/sys/_endian.h \
/usr/include/libkern/_OSByteOrder.h \
/usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
/usr/include/machine/types.h /usr/include/i386/types.h

15
src/libecoPCR/ecoMalloc.P Normal file
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@ -0,0 +1,15 @@
ecoMalloc.o ecoMalloc.P : ecoMalloc.c ecoPCR.h /usr/include/stdio.h \
/usr/include/_types.h /usr/include/sys/_types.h \
/usr/include/sys/cdefs.h /usr/include/machine/_types.h \
/usr/include/i386/_types.h /usr/include/inttypes.h \
/usr/lib/gcc/i686-apple-darwin9/4.0.1/include/stdint.h \
/usr/include/stdlib.h /usr/include/available.h /usr/include/sys/wait.h \
/usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
/usr/include/machine/signal.h /usr/include/i386/signal.h \
/usr/include/i386/_structs.h /usr/include/sys/_structs.h \
/usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
/usr/include/sys/resource.h /usr/include/machine/endian.h \
/usr/include/i386/endian.h /usr/include/sys/_endian.h \
/usr/include/libkern/_OSByteOrder.h \
/usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
/usr/include/machine/types.h /usr/include/i386/types.h

5
src/libecoPCR/ecodna.P Normal file
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@ -0,0 +1,5 @@
ecodna.o ecodna.P : ecodna.c /usr/include/string.h /usr/include/_types.h \
/usr/include/sys/_types.h /usr/include/sys/cdefs.h \
/usr/include/machine/_types.h /usr/include/i386/_types.h ecoPCR.h \
/usr/include/stdio.h /usr/include/inttypes.h \
/usr/lib/gcc/i686-apple-darwin9/4.0.1/include/stdint.h

5
src/libecoPCR/ecofilter.P Normal file
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@ -0,0 +1,5 @@
ecofilter.o ecofilter.P : ecofilter.c ecoPCR.h /usr/include/stdio.h \
/usr/include/_types.h /usr/include/sys/_types.h \
/usr/include/sys/cdefs.h /usr/include/machine/_types.h \
/usr/include/i386/_types.h /usr/include/inttypes.h \
/usr/lib/gcc/i686-apple-darwin9/4.0.1/include/stdint.h

15
src/libecoPCR/econame.P Normal file
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@ -0,0 +1,15 @@
econame.o econame.P : econame.c ecoPCR.h /usr/include/stdio.h /usr/include/_types.h \
/usr/include/sys/_types.h /usr/include/sys/cdefs.h \
/usr/include/machine/_types.h /usr/include/i386/_types.h \
/usr/include/inttypes.h \
/usr/lib/gcc/i686-apple-darwin9/4.0.1/include/stdint.h \
/usr/include/string.h /usr/include/stdlib.h /usr/include/available.h \
/usr/include/sys/wait.h /usr/include/sys/signal.h \
/usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
/usr/include/i386/signal.h /usr/include/i386/_structs.h \
/usr/include/sys/_structs.h /usr/include/machine/_structs.h \
/usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
/usr/include/machine/endian.h /usr/include/i386/endian.h \
/usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
/usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
/usr/include/machine/types.h /usr/include/i386/types.h

15
src/libecoPCR/ecorank.P Normal file
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@ -0,0 +1,15 @@
ecorank.o ecorank.P : ecorank.c ecoPCR.h /usr/include/stdio.h /usr/include/_types.h \
/usr/include/sys/_types.h /usr/include/sys/cdefs.h \
/usr/include/machine/_types.h /usr/include/i386/_types.h \
/usr/include/inttypes.h \
/usr/lib/gcc/i686-apple-darwin9/4.0.1/include/stdint.h \
/usr/include/string.h /usr/include/stdlib.h /usr/include/available.h \
/usr/include/sys/wait.h /usr/include/sys/signal.h \
/usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
/usr/include/i386/signal.h /usr/include/i386/_structs.h \
/usr/include/sys/_structs.h /usr/include/machine/_structs.h \
/usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
/usr/include/machine/endian.h /usr/include/i386/endian.h \
/usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
/usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
/usr/include/machine/types.h /usr/include/i386/types.h

19
src/libecoPCR/ecoseq.P Normal file
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@ -0,0 +1,19 @@
ecoseq.o ecoseq.P : ecoseq.c ecoPCR.h /usr/include/stdio.h /usr/include/_types.h \
/usr/include/sys/_types.h /usr/include/sys/cdefs.h \
/usr/include/machine/_types.h /usr/include/i386/_types.h \
/usr/include/inttypes.h \
/usr/lib/gcc/i686-apple-darwin9/4.0.1/include/stdint.h \
/usr/include/stdlib.h /usr/include/available.h /usr/include/sys/wait.h \
/usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
/usr/include/machine/signal.h /usr/include/i386/signal.h \
/usr/include/i386/_structs.h /usr/include/sys/_structs.h \
/usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
/usr/include/sys/resource.h /usr/include/machine/endian.h \
/usr/include/i386/endian.h /usr/include/sys/_endian.h \
/usr/include/libkern/_OSByteOrder.h \
/usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
/usr/include/machine/types.h /usr/include/i386/types.h \
/usr/include/string.h /usr/include/zlib.h /usr/include/zconf.h \
/usr/include/sys/types.h /usr/include/unistd.h \
/usr/include/sys/unistd.h /usr/include/sys/select.h \
/usr/include/sys/_select.h

15
src/libecoPCR/ecotax.P Normal file
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@ -0,0 +1,15 @@
ecotax.o ecotax.P : ecotax.c ecoPCR.h /usr/include/stdio.h /usr/include/_types.h \
/usr/include/sys/_types.h /usr/include/sys/cdefs.h \
/usr/include/machine/_types.h /usr/include/i386/_types.h \
/usr/include/inttypes.h \
/usr/lib/gcc/i686-apple-darwin9/4.0.1/include/stdint.h \
/usr/include/string.h /usr/include/stdlib.h /usr/include/available.h \
/usr/include/sys/wait.h /usr/include/sys/signal.h \
/usr/include/sys/appleapiopts.h /usr/include/machine/signal.h \
/usr/include/i386/signal.h /usr/include/i386/_structs.h \
/usr/include/sys/_structs.h /usr/include/machine/_structs.h \
/usr/include/mach/i386/_structs.h /usr/include/sys/resource.h \
/usr/include/machine/endian.h /usr/include/i386/endian.h \
/usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
/usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
/usr/include/machine/types.h /usr/include/i386/types.h

1
src/libecoprimer/Makefile
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@ -10,6 +10,7 @@ SOURCES = goodtaxon.c \
queue.c \
libstki.c \
sortmatch.c \
pairtree.c \
pairs.c \
apat_search.c

131
src/libecoprimer/amplifiatree.c Normal file
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@ -0,0 +1,131 @@
/*
* amplifiatree.c
*
* Created on: 7 mars 2009
* Author: coissac
*/
#include "ecoprimer.h"
#include <search.h>
static void cleanamplifia(pamplifia_t amplifia);
static void deleteamplifialist(pamplifialist_t list);
static int cmpamplifia(const void* p1,const void*p2);
static void cleanamplifiatlist(pamplifiacount_t list)
{
if (list->amplifias)
ECOFREE(list->amplifias,
"Free amplifia list");
}
static void cleanamplifia(pamplifia_t amplifia)
{
cleanamplifiatlist(&(amplifia->pcr));
}
static pamplifialist_t newamplifialist(pamplifialist_t parent, size_t size)
{
pamplifialist_t tmp;
tmp=ECOMALLOC(sizeof(amplifialist_t)+sizeof(amplifia_t)*(size-1),
"Cannot allocate new amplifia list");
tmp->amplifiaslots=size;
tmp->amplifiacount=0;
tmp->next=NULL;
if (parent)
parent->next=(void*)tmp;
return tmp;
}
static void deleteamplifialist(pamplifialist_t list)
{
size_t i;
if (list)
{
if (list->next)
{
deleteamplifialist(list->next);
list->next=NULL;
}
for (i=0; i < list->amplifiacount; i++)
cleanamplifia((list->amplifias)+i);
ECOFREE(list,"Delete amplifia list");
}
}
static int cmpamplifia(const void* p1,const void*p2)
{
pamplifia_t pr1,pr2;
pr1=(pamplifia_t)p1;
pr2=(pamplifia_t)p2;
if (pr1->p1 < pr2->p1) return -1;
if (pr1->p1 > pr2->p1) return 1;
if (pr1->asdirect1 < pr2->asdirect1) return -1;
if (pr1->asdirect1 > pr2->asdirect1) return 1;
if (pr1->p2 < pr2->p2) return -1;
if (pr1->p2 > pr2->p2) return 1;
if (pr1->asdirect2 < pr2->asdirect2) return -1;
if (pr1->asdirect2 > pr2->asdirect2) return 1;
return 0;
}
pamplifia_t amplifiaintree (amplifia_t key,
pamplifiatree_t amplifialist)
{
if (!amplifialist->tree)
return NULL;
return *((pamplifia_t*)tsearch((const void *)(&key),
&(amplifialist->tree),
cmpamplifia
));
}
pamplifia_t insertamplifia(amplifia_t key,
pamplifiatree_t list)
{
pamplifia_t current;
pamplifia_t found;
if (list->last->amplifiacount==list->last->amplifiaslots)
{
list->last->next=newamplifialist(list,100);
list->last=list->last->next;
}
current = list->last->amplifias + list->last->amplifiacount;
*current=key;
found = *((pamplifia_t*)tsearch((const void *)current,
&(list->tree),
cmpamplifia));
if (found==current)
list->last->amplifiacount++;
return found;
}
pamplifiatree_t initamplifiatree(pamplifiatree_t tree)
{
if (!tree)
tree = ECOMALLOC(sizeof(amplifiatree_t),"Cannot allocate amplifia tree");
tree->first=newamplifialist(NULL,500);
tree->last=tree->first;
tree->tree=NULL;
}

17
src/libecoprimer/apat_search.P Normal file
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@ -0,0 +1,17 @@
apat_search.o apat_search.P : apat_search.c /usr/include/stdio.h /usr/include/_types.h \
/usr/include/sys/_types.h /usr/include/sys/cdefs.h \
/usr/include/machine/_types.h /usr/include/i386/_types.h \
/usr/include/stdlib.h /usr/include/available.h /usr/include/sys/wait.h \
/usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
/usr/include/machine/signal.h /usr/include/i386/signal.h \
/usr/include/i386/_structs.h /usr/include/sys/_structs.h \
/usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
/usr/include/sys/resource.h /usr/include/machine/endian.h \
/usr/include/i386/endian.h /usr/include/sys/_endian.h \
/usr/include/libkern/_OSByteOrder.h \
/usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
/usr/include/machine/types.h /usr/include/i386/types.h \
/usr/include/string.h libstki.h ecotype.h apat.h \
/usr/include/inttypes.h \
/usr/lib/gcc/i686-apple-darwin9/4.0.1/include/stdint.h \
../libecoPCR/ecoPCR.h

17
src/libecoprimer/aproxpattern.P Normal file
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@ -0,0 +1,17 @@
aproxpattern.o aproxpattern.P : aproxpattern.c ecoprimer.h /usr/include/inttypes.h \
/usr/include/sys/cdefs.h /usr/include/_types.h \
/usr/include/sys/_types.h /usr/include/machine/_types.h \
/usr/include/i386/_types.h \
/usr/lib/gcc/i686-apple-darwin9/4.0.1/include/stdint.h \
/usr/include/stdlib.h /usr/include/available.h /usr/include/sys/wait.h \
/usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
/usr/include/machine/signal.h /usr/include/i386/signal.h \
/usr/include/i386/_structs.h /usr/include/sys/_structs.h \
/usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
/usr/include/sys/resource.h /usr/include/machine/endian.h \
/usr/include/i386/endian.h /usr/include/sys/_endian.h \
/usr/include/libkern/_OSByteOrder.h \
/usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
/usr/include/machine/types.h /usr/include/i386/types.h \
/usr/include/stdio.h ecotype.h ../libecoPCR/ecoPCR.h apat.h libstki.h \
debug.h /usr/include/math.h /usr/include/architecture/i386/math.h

108
src/libecoprimer/ecoprimer.h
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@ -79,28 +79,39 @@ typedef union {
uint32_t value;
} poslist_t, *ppostlist_t;
typedef struct {
word_t word;
uint32_t *directCount;
ppostlist_t directPos;
/**
* primer_t structure store fuzzy match positions for a primer
* on all sequences
*/
uint32_t *reverseCount;
ppostlist_t reversePos;
bool_t good;
uint32_t inexample;
uint32_t outexample;
typedef struct {
word_t word; //< code for the primer
uint32_t *directCount; //< Occurrence count on direct strand
ppostlist_t directPos; //< list of position list on direct strand
uint32_t *reverseCount; //< Occurrence count on reverse strand
ppostlist_t reversePos; //< list of position list on reverse strand
bool_t good; //< primer match more than quorum example and no
// more counterexample quorum.
uint32_t inexample; //< count of example sequences matching primer
uint32_t outexample; //< count of counterexample sequences matching primer
} primer_t, *pprimer_t;
/**
* primercount_t structure store fuzzy match positions for all primers
* on all sequences as a list of primer_t
*/
typedef struct {
pprimer_t primers;
uint32_t size;
} primercount_t, *pprimercount_t;
typedef struct {
word_t word;
pprimer_t primer;
uint32_t position;
bool_t strand;
bool_t good; /*TR: Added*/
} primermatch_t, *pprimermatch_t;
/*TR: Added*/
@ -109,6 +120,19 @@ typedef struct {
uint32_t matchcount;
} primermatchcount_t, *pprimermatchcount_t;
typedef struct {
pecoseq_t sequence;
bool_t strand;
const char *amplifia;
int32_t length;
} amplifia_t, *pamplifia_t;
typedef struct {
pamplifia_t amplifias;
uint32_t ampcount;
uint32_t ampslot;
} amplifiacount_t, *pamplifiacount_t;
typedef struct {
char *amplifia;
int32_t *taxonids;
@ -124,30 +148,51 @@ typedef struct {
} taxampset_t, *ptaxampset_t;
typedef struct {
word_t w1;
word_t w2;
uint32_t inexample; /*inexample count*/
uint32_t outexample; /*outexample count*/
pprimer_t p1;
bool_t asdirect1;
pprimer_t p2;
bool_t asdirect2;
uint32_t mind;
uint32_t maxd;
amplifiacount_t pcr;
uint32_t ampsetcount;
uint32_t ampsetindex;
pampseqset_t ampset;
uint32_t inexample; //< example sequence count
uint32_t outexample; //< counterexample sequence count
uint32_t taxsetcount;
uint32_t taxsetindex;
ptaxampset_t taxset;
uint32_t oktaxoncount;
} pairs_t, *ppairs_t;
// these statistics are relative to inexample sequences
uint32_t mind; //< minimum distance between primers
uint32_t maxd; //< maximum distance between primers
uint32_t sumd; //< distance sum
//
// uint32_t ampsetcount;
// uint32_t ampsetindex;
// pampseqset_t ampset;
//
// uint32_t taxsetcount;
// uint32_t taxsetindex;
// ptaxampset_t taxset;
//
// uint32_t oktaxoncount;
} pair_t, *ppair_t;
/*TR: Added*/
typedef struct {
ppairs_t pairs;
uint32_t paircount;
}pairscount_t, *ppairscount_t;
size_t paircount;
size_t pairslots;
void* next;
pair_t pairs[1];
} pairlist_t, *ppairlist_t;
typedef struct {
ppairlist_t first;
ppairlist_t last;
void *tree;
} pairtree_t, *ppairtree_t;
typedef struct {
pword_t words;
@ -232,7 +277,12 @@ pprimercount_t lookforAproxPrimer(pecodnadb_t database, uint32_t seqdbsize,uint3
void sortmatch(pprimermatch_t table,uint32_t N);
ppairtree_t initpairtree(ppairtree_t tree);
ppair_t pairintree (pair_t key,ppairtree_t pairlist);
ppair_t insertpair(pair_t key,ppairtree_t list);
/*TR: Added*/
pairscount_t buildPrimerPairs(pecodnadb_t seqdb,uint32_t seqdbsize,pprimercount_t primers,poptions_t options);
ppairtree_t buildPrimerPairs(pecodnadb_t seqdb,uint32_t seqdbsize,pprimercount_t primers,poptions_t options);
#endif /* EPSORT_H_ */

17
src/libecoprimer/goodtaxon.P Normal file
View File

@ -0,0 +1,17 @@
goodtaxon.o goodtaxon.P : goodtaxon.c ecoprimer.h /usr/include/inttypes.h \
/usr/include/sys/cdefs.h /usr/include/_types.h \
/usr/include/sys/_types.h /usr/include/machine/_types.h \
/usr/include/i386/_types.h \
/usr/lib/gcc/i686-apple-darwin9/4.0.1/include/stdint.h \
/usr/include/stdlib.h /usr/include/available.h /usr/include/sys/wait.h \
/usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
/usr/include/machine/signal.h /usr/include/i386/signal.h \
/usr/include/i386/_structs.h /usr/include/sys/_structs.h \
/usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
/usr/include/sys/resource.h /usr/include/machine/endian.h \
/usr/include/i386/endian.h /usr/include/sys/_endian.h \
/usr/include/libkern/_OSByteOrder.h \
/usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
/usr/include/machine/types.h /usr/include/i386/types.h \
/usr/include/stdio.h ecotype.h ../libecoPCR/ecoPCR.h apat.h libstki.h \
debug.h

17
src/libecoprimer/hashsequence.P Normal file
View File

@ -0,0 +1,17 @@
hashsequence.o hashsequence.P : hashsequence.c ecoprimer.h /usr/include/inttypes.h \
/usr/include/sys/cdefs.h /usr/include/_types.h \
/usr/include/sys/_types.h /usr/include/machine/_types.h \
/usr/include/i386/_types.h \
/usr/lib/gcc/i686-apple-darwin9/4.0.1/include/stdint.h \
/usr/include/stdlib.h /usr/include/available.h /usr/include/sys/wait.h \
/usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
/usr/include/machine/signal.h /usr/include/i386/signal.h \
/usr/include/i386/_structs.h /usr/include/sys/_structs.h \
/usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
/usr/include/sys/resource.h /usr/include/machine/endian.h \
/usr/include/i386/endian.h /usr/include/sys/_endian.h \
/usr/include/libkern/_OSByteOrder.h \
/usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
/usr/include/machine/types.h /usr/include/i386/types.h \
/usr/include/stdio.h ecotype.h ../libecoPCR/ecoPCR.h apat.h libstki.h \
debug.h

17
src/libecoprimer/libstki.P Normal file
View File

@ -0,0 +1,17 @@
libstki.o libstki.P : libstki.c /usr/include/stdio.h /usr/include/_types.h \
/usr/include/sys/_types.h /usr/include/sys/cdefs.h \
/usr/include/machine/_types.h /usr/include/i386/_types.h \
/usr/include/stdlib.h /usr/include/available.h /usr/include/sys/wait.h \
/usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
/usr/include/machine/signal.h /usr/include/i386/signal.h \
/usr/include/i386/_structs.h /usr/include/sys/_structs.h \
/usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
/usr/include/sys/resource.h /usr/include/machine/endian.h \
/usr/include/i386/endian.h /usr/include/sys/_endian.h \
/usr/include/libkern/_OSByteOrder.h \
/usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
/usr/include/machine/types.h /usr/include/i386/types.h \
/usr/include/string.h libstki.h ecotype.h ecoprimer.h \
/usr/include/inttypes.h \
/usr/lib/gcc/i686-apple-darwin9/4.0.1/include/stdint.h \
../libecoPCR/ecoPCR.h apat.h debug.h

17
src/libecoprimer/merge.P Normal file
View File

@ -0,0 +1,17 @@
merge.o merge.P : merge.c ecoprimer.h /usr/include/inttypes.h \
/usr/include/sys/cdefs.h /usr/include/_types.h \
/usr/include/sys/_types.h /usr/include/machine/_types.h \
/usr/include/i386/_types.h \
/usr/lib/gcc/i686-apple-darwin9/4.0.1/include/stdint.h \
/usr/include/stdlib.h /usr/include/available.h /usr/include/sys/wait.h \
/usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
/usr/include/machine/signal.h /usr/include/i386/signal.h \
/usr/include/i386/_structs.h /usr/include/sys/_structs.h \
/usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
/usr/include/sys/resource.h /usr/include/machine/endian.h \
/usr/include/i386/endian.h /usr/include/sys/_endian.h \
/usr/include/libkern/_OSByteOrder.h \
/usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
/usr/include/machine/types.h /usr/include/i386/types.h \
/usr/include/stdio.h ecotype.h ../libecoPCR/ecoPCR.h apat.h libstki.h \
debug.h

17
src/libecoprimer/pairs.P Normal file
View File

@ -0,0 +1,17 @@
pairs.o pairs.P : pairs.c ecoprimer.h /usr/include/inttypes.h \
/usr/include/sys/cdefs.h /usr/include/_types.h \
/usr/include/sys/_types.h /usr/include/machine/_types.h \
/usr/include/i386/_types.h \
/usr/lib/gcc/i686-apple-darwin9/4.0.1/include/stdint.h \
/usr/include/stdlib.h /usr/include/available.h /usr/include/sys/wait.h \
/usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
/usr/include/machine/signal.h /usr/include/i386/signal.h \
/usr/include/i386/_structs.h /usr/include/sys/_structs.h \
/usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
/usr/include/sys/resource.h /usr/include/machine/endian.h \
/usr/include/i386/endian.h /usr/include/sys/_endian.h \
/usr/include/libkern/_OSByteOrder.h \
/usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
/usr/include/machine/types.h /usr/include/i386/types.h \
/usr/include/stdio.h ecotype.h ../libecoPCR/ecoPCR.h apat.h libstki.h \
debug.h /usr/include/string.h

369
src/libecoprimer/pairs.c
View File

@ -7,22 +7,28 @@
#include "ecoprimer.h"
#include <string.h>
#include <stdlib.h>
primermatchcount_t buildPrimerPairsForOneSeq(uint32_t seqid,pprimercount_t primers,poptions_t options);
static void buildPrimerPairsForOneSeq(uint32_t seqid,
pecodnadb_t seqdb,
pprimercount_t primers,
ppairtree_t pairs,
poptions_t options);
int32_t pairinlist (ppairs_t pairlist, word_t w1, word_t w2, uint32_t size)
{
uint32_t i;
for (i = 0; i < size; i++)
{
if (w1 == pairlist[i].w1 && w2 == pairlist[i].w2) return i;
if (w1 == pairlist[i].w2 && w2 == pairlist[i].w1) return i;
}
return -1;
}
char *addamplifiasetelem (ppairs_t pair, char* amplifia, int32_t taxid)
/*************************************
*
* pair collection management
*
*************************************/
#ifdef MASKEDCODE
char *addamplifiasetelem (ppair_t pair, char* amplifia, int32_t taxid)
{
uint32_t i;
uint32_t j;
@ -79,7 +85,7 @@ char *addamplifiasetelem (ppairs_t pair, char* amplifia, int32_t taxid)
return ampused;
}
void addtaxampsetelem (ppairs_t pair, int32_t taxid, char *amplifia)
void addtaxampsetelem (ppair_t pair, int32_t taxid, char *amplifia)
{
uint32_t i;
uint32_t j;
@ -135,6 +141,7 @@ void addtaxampsetelem (ppairs_t pair, int32_t taxid, char *amplifia)
char *getamplifia (pecoseq_t seq, uint32_t start, uint32_t len)
{
fprintf(stderr,"start : %d length : %d\n",start,len);
char *amplifia = ECOMALLOC((len + 1) * sizeof(char),"Cannot allocate amplifia");
char *seqc = &seq->SQ[start];
@ -142,9 +149,10 @@ char *getamplifia (pecoseq_t seq, uint32_t start, uint32_t len)
return amplifia;
}
#endif
/*TR: Added*/
pairscount_t buildPrimerPairs(pecodnadb_t seqdb,uint32_t seqdbsize,pprimercount_t primers,poptions_t options)
ppairtree_t buildPrimerPairs(pecodnadb_t seqdb,uint32_t seqdbsize,pprimercount_t primers,poptions_t options)
{
uint32_t i;
uint32_t j;
@ -152,11 +160,7 @@ pairscount_t buildPrimerPairs(pecodnadb_t seqdb,uint32_t seqdbsize,pprimercount_
uint32_t d;
uint32_t strt;
uint32_t end;
uint32_t paircount = 0;
uint32_t pairslots = 500;
int32_t foundindex;
ppairs_t pairs;
pairscount_t primerpairs;
ppairtree_t primerpairs;
primermatchcount_t seqmatchcount;
word_t w1;
word_t w2;
@ -164,103 +168,113 @@ pairscount_t buildPrimerPairs(pecodnadb_t seqdb,uint32_t seqdbsize,pprimercount_
char *oldamp;
pairs = ECOMALLOC(pairslots * sizeof(pairs_t),"Cannot allocate pairs table");
primerpairs = initpairtree(NULL);
for (i=0; i < seqdbsize; i++)
{
seqmatchcount = buildPrimerPairsForOneSeq(i, primers, options);
if (seqmatchcount.matchcount == 0) continue;
buildPrimerPairsForOneSeq(i, seqdb, primers, primerpairs, options);
}
// if (seqmatchcount.matchcount == 0) continue;
//
// for (j=0; j < seqmatchcount.matchcount; j++)
// {
// strt = 0;
// w1 = seqmatchcount.matches[j].word;
// /*first word should b on direct strand*/
// if (!seqmatchcount.matches[j].strand)
// w1 = ecoComplementWord(w1, options->primer_length);
// else
// strt = options->primer_length;
//
// for (k=j+1; k < seqmatchcount.matchcount; k++)
// {
// end = 0;
// w2 = seqmatchcount.matches[k].word;
// /*second word should be on reverse strand*/
// if (seqmatchcount.matches[k].strand)
// w2 = ecoComplementWord(w2, options->primer_length);
// else
// end = options->primer_length;
//
// if (!(seqmatchcount.matches[j].good || seqmatchcount.matches[k].good)) continue;
// if (w1 == w2) continue;
//
// d = seqmatchcount.matches[k].position - seqmatchcount.matches[j].position;
// if (d >= options->lmin && d <= options->lmax)
// {
// /*get amplified string*/
// amplifia = getamplifia (seqdb[i], seqmatchcount.matches[j].position + strt, d - strt - end);
//
// foundindex = pairinlist(pairs, w1, w2, paircount);
// if (foundindex != -1) /*pair is found*/
// {
// if (seqdb[i]->isexample)
// pairs[foundindex].inexample++;
// else
// pairs[foundindex].outexample++;
//
// if (pairs[foundindex].mind > d) pairs[foundindex].mind = d;
// else if (pairs[foundindex].maxd < d) pairs[foundindex].maxd = d;
//
// oldamp = addamplifiasetelem (&pairs[foundindex], amplifia, seqdb[i]->ranktaxonid);
// /*if exact same string is already in amplifia set then use that for taxon set, it will help for
// * calculating the fully identified taxons i.e specificity, we will compare pointrs instead of strings
// * because same string means same pointer*/
// if (oldamp)
// {
// ECOFREE (amplifia, "free amplifia");
// amplifia = oldamp;
// }
// addtaxampsetelem (&pairs[foundindex], seqdb[i]->ranktaxonid, amplifia);
//
// continue;
// }
//
// if (paircount == pairslots)
// {
// pairslots += 500;
// pairs = ECOREALLOC(pairs, pairslots * sizeof(pairs_t), "Cannot allocate pairs table");
// }
// pairs[paircount].w1 = w1;
// pairs[paircount].w2 = w2;
// if (seqdb[i]->isexample) pairs[paircount].inexample = 1;
// else pairs[paircount].outexample = 1;
// pairs[paircount].mind = d;
// pairs[paircount].maxd = d;
// oldamp = addamplifiasetelem (&pairs[paircount], amplifia, seqdb[i]->ranktaxonid);
// addtaxampsetelem (&pairs[paircount], seqdb[i]->ranktaxonid, amplifia);
//
// paircount++;
// }
// else if (d > options->lmax)
// break; /*once if the distance is greater than lmax then it will keep on increasing*/
// }
// }
// ECOFREE(seqmatchcount.matches, "Cannot free matches table");
// }
// primerpairs.pairs = ECOREALLOC(pairs, paircount * sizeof(pairs_t), "Cannot allocate pairs table");
// primerpairs.paircount = paircount;
// return primerpairs;
}
for (j=0; j < seqmatchcount.matchcount; j++)
{
strt = 0;
w1 = seqmatchcount.matches[j].word;
/*first word should b on direct strand*/
if (!seqmatchcount.matches[j].strand)
w1 = ecoComplementWord(w1, options->primer_length);
else
strt = options->primer_length;
for (k=j+1; k < seqmatchcount.matchcount; k++)
{
end = 0;
w2 = seqmatchcount.matches[k].word;
/*second word should be on reverse strand*/
if (seqmatchcount.matches[k].strand)
w2 = ecoComplementWord(w2, options->primer_length);
else
end = options->primer_length;
if (!(seqmatchcount.matches[j].good || seqmatchcount.matches[k].good)) continue;
if (w1 == w2) continue;
d = seqmatchcount.matches[k].position - seqmatchcount.matches[j].position;
if (d >= options->lmin && d <= options->lmax)
{
/*get amplified string*/
amplifia = getamplifia (seqdb[i], seqmatchcount.matches[j].position + strt, d - strt - end);
foundindex = pairinlist(pairs, w1, w2, paircount);
if (foundindex != -1) /*pair is found*/
{
if (seqdb[i]->isexample)
pairs[foundindex].inexample++;
else
pairs[foundindex].outexample++;
if (pairs[foundindex].mind > d) pairs[foundindex].mind = d;
else if (pairs[foundindex].maxd < d) pairs[foundindex].maxd = d;
oldamp = addamplifiasetelem (&pairs[foundindex], amplifia, seqdb[i]->ranktaxonid);
/*if exact same string is already in amplifia set then use that for taxon set, it will help for
* calculating the fully identified taxons i.e specificity, we will compare pointrs instead of strings
* because same string means same pointer*/
if (oldamp)
{
ECOFREE (amplifia, "free amplifia");
amplifia = oldamp;
}
addtaxampsetelem (&pairs[foundindex], seqdb[i]->ranktaxonid, amplifia);
continue;
}
if (paircount == pairslots)
{
pairslots += 500;
pairs = ECOREALLOC(pairs, pairslots * sizeof(pairs_t), "Cannot allocate pairs table");
}
pairs[paircount].w1 = w1;
pairs[paircount].w2 = w2;
if (seqdb[i]->isexample) pairs[paircount].inexample = 1;
else pairs[paircount].outexample = 1;
pairs[paircount].mind = d;
pairs[paircount].maxd = d;
oldamp = addamplifiasetelem (&pairs[paircount], amplifia, seqdb[i]->ranktaxonid);
addtaxampsetelem (&pairs[paircount], seqdb[i]->ranktaxonid, amplifia);
paircount++;
}
else if (d > options->lmax)
break; /*once if the distance is greater than lmax then it will keep on increasing*/
}
}
ECOFREE(seqmatchcount.matches, "Cannot free matches table");
}
primerpairs.pairs = ECOREALLOC(pairs, paircount * sizeof(pairs_t), "Cannot allocate pairs table");
primerpairs.paircount = paircount;
return primerpairs;
}
primermatchcount_t buildPrimerPairsForOneSeq(uint32_t seqid,pprimercount_t primers,poptions_t options)
#define DMAX (2000000000)
static void buildPrimerPairsForOneSeq(uint32_t seqid,
pecodnadb_t seqdb,
pprimercount_t primers,
ppairtree_t pairs,
poptions_t options)
{
static uint32_t paircount=0;
uint32_t i,j,k;
uint32_t matchcount=0;
pprimermatch_t matches = NULL;
primermatchcount_t seqmatchcount;
seqmatchcount.matchcount = 0;
seqmatchcount.matches = NULL;
ppair_t pcurrent;
pair_t current;
pprimer_t wswp;
bool_t bswp;
size_t distance;
for (i=0;i < primers->size; i++)
{
@ -268,7 +282,9 @@ primermatchcount_t buildPrimerPairsForOneSeq(uint32_t seqid,pprimercount_t prime
matchcount+=primers->primers[i].reverseCount[seqid];
}
if (matchcount <= 0) return seqmatchcount;
if (matchcount <= 0)
return;
matches = ECOMALLOC(matchcount * sizeof(primermatch_t),"Cannot allocate primers match table");
for (i=0,j=0;i < primers->size; i++)
@ -277,17 +293,15 @@ primermatchcount_t buildPrimerPairsForOneSeq(uint32_t seqid,pprimercount_t prime
{
if (primers->primers[i].directCount[seqid]==1)
{
matches[j].word = primers->primers[i].word;
matches[j].primer = primers->primers+i;
matches[j].strand=TRUE;
matches[j].good=primers->primers[i].good;/*TR: Added*/
matches[j].position=primers->primers[i].directPos[seqid].value;
j++;
}
else for (k=0; k < primers->primers[i].directCount[seqid]; k++,j++)
{
matches[j].word = primers->primers[i].word;
matches[j].primer = primers->primers+i;
matches[j].strand=TRUE;
matches[j].good=primers->primers[i].good;/*TR: Added*/
matches[j].position=primers->primers[i].directPos[seqid].pointer[k];
}
}
@ -296,26 +310,139 @@ primermatchcount_t buildPrimerPairsForOneSeq(uint32_t seqid,pprimercount_t prime
{
if (primers->primers[i].reverseCount[seqid]==1)
{
matches[j].word = primers->primers[i].word;
matches[j].primer = primers->primers+i;
matches[j].strand=FALSE;
matches[j].good=primers->primers[i].good;/*TR: Added*/
matches[j].position=primers->primers[i].reversePos[seqid].value;
j++;
}
else for (k=0; k < primers->primers[i].reverseCount[seqid]; k++,j++)
{
matches[j].word = primers->primers[i].word;
matches[j].primer = primers->primers+i;
matches[j].strand=FALSE;
matches[j].good=primers->primers[i].good;/*TR: Added*/
matches[j].position=primers->primers[i].reversePos[seqid].pointer[k];
}
}
}
sortmatch(matches,matchcount); // sort in asscending order by position
if (matchcount>1)
{
fprintf(stderr,"\n====================================\n");
sortmatch(matches,matchcount); // sort in ascending order by position
for (i=0; i < matchcount;i++)
{
// For all primers matching the sequence
for(j=i+1;
(j<matchcount)
&& ((distance=matches[j].position - matches[i].position - options->primer_length) < options->lmax);
j++
)
// For all not too far primers
if ( (matches[i].primer->good || matches[j].primer->good)
&& (distance > options->lmin)
)
{
// If possible primer pair
current.p1 = matches[i].primer;
current.asdirect1=matches[i].strand;
current.p2 = matches[j].primer;
current.asdirect2= !matches[j].strand;
current.maxd=DMAX;
current.mind=DMAX;
current.sumd=0;
current.inexample=0;
current.outexample=0;
// Standardize the pair
if (current.p2->word < current.p1->word)
{
wswp = current.p1;
current.p1=current.p2;
current.p2=wswp;
bswp = current.asdirect1;
current.asdirect1=current.asdirect2;
current.asdirect2=bswp;
}
// Look for the new pair in already seen pairs
pcurrent = insertpair(current,pairs);
if (seqdb[seqid]->isexample)
{
pcurrent->inexample++;
pcurrent->sumd+=distance;
if (pcurrent->maxd=DMAX || distance > pcurrent->maxd)
pcurrent->maxd = distance;
if (distance < pcurrent->mind)
pcurrent->mind = distance;
}
else
pcurrent->outexample++;
if ((pcurrent->outexample+pcurrent->inexample)==1)
{
paircount++;
pcurrent->pcr.ampslot=200;
pcurrent->pcr.ampcount=0;
pcurrent->pcr.amplifias = ECOMALLOC(sizeof(amplifia_t)*pcurrent->pcr.ampslot,
"Cannot allocate amplifia table");
}
else
{
if (pcurrent->pcr.ampslot==pcurrent->pcr.ampcount)
{
pcurrent->pcr.ampslot+=200;
pcurrent->pcr.amplifias = ECOREALLOC(pcurrent->pcr.amplifias,
sizeof(amplifia_t)*pcurrent->pcr.ampslot,
"Cannot allocate amplifia table");
}
}
pcurrent->pcr.amplifias[pcr.ampcount].length=distance;
pcurrent->pcr.amplifias[pcr.ampcount].sequence=*(seqdb[seqid]);
// pcurrent->pcr.amplifias[pcr.ampcount].strand= ;
// pcurrent->pcr.amplifias[pcr.ampcount].amplifia= ;
pcurrent->pcr.ampcount++;
fprintf(stderr,"%c%c W1 : %s direct : %c",
"bG"[(int)pcurrent->p1->good],
"bG"[(int)pcurrent->p2->good],
ecoUnhashWord(pcurrent->p1->word, options->primer_length),
"><"[(int)pcurrent->asdirect1]
);
fprintf(stderr," W2 : %s direct : %c distance : %d (min/max/avg : %d/%d/%f) in/out: %d/%d %c (%d pairs)\n",
ecoUnhashWord(pcurrent->p2->word, options->primer_length),
"><"[(int)pcurrent->asdirect2],
distance,
pcurrent->mind,pcurrent->maxd,
(pcurrent->inexample) ? (float)pcurrent->sumd/pcurrent->inexample:0.0,
pcurrent->inexample,pcurrent->outexample,
" N"[(pcurrent->outexample+pcurrent->inexample)==1],
paircount
);
}
}
}
/*TR: Added*/
seqmatchcount.matches = matches;
seqmatchcount.matchcount = matchcount;
return seqmatchcount;
}

17
src/libecoprimer/pairtree.P Normal file
View File

@ -0,0 +1,17 @@
pairtree.o pairtree.P : pairtree.c ecoprimer.h /usr/include/inttypes.h \
/usr/include/sys/cdefs.h /usr/include/_types.h \
/usr/include/sys/_types.h /usr/include/machine/_types.h \
/usr/include/i386/_types.h \
/usr/lib/gcc/i686-apple-darwin9/4.0.1/include/stdint.h \
/usr/include/stdlib.h /usr/include/available.h /usr/include/sys/wait.h \
/usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
/usr/include/machine/signal.h /usr/include/i386/signal.h \
/usr/include/i386/_structs.h /usr/include/sys/_structs.h \
/usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
/usr/include/sys/resource.h /usr/include/machine/endian.h \
/usr/include/i386/endian.h /usr/include/sys/_endian.h \
/usr/include/libkern/_OSByteOrder.h \
/usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
/usr/include/machine/types.h /usr/include/i386/types.h \
/usr/include/stdio.h ecotype.h ../libecoPCR/ecoPCR.h apat.h libstki.h \
debug.h /usr/include/search.h

133
src/libecoprimer/pairtree.c Normal file
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@ -0,0 +1,133 @@
/*
* pairtree.c
*
* Created on: 7 mars 2009
* Author: coissac
*/
#include "ecoprimer.h"
#include <search.h>
static void cleanpair(ppair_t pair);
static void deletepairlist(ppairlist_t list);
static int cmppair(const void* p1,const void*p2);
static void cleanamplifiatlist(pamplifiacount_t list)
{
if (list->amplifias)
ECOFREE(list->amplifias,
"Free amplifia list");
}
static void cleanpair(ppair_t pair)
{
cleanamplifiatlist(&(pair->pcr));
}
static ppairlist_t newpairlist(ppairlist_t parent, size_t size)
{
ppairlist_t tmp;
tmp=ECOMALLOC(sizeof(pairlist_t)+sizeof(pair_t)*(size-1),
"Cannot allocate new pair list");
tmp->pairslots=size;
tmp->paircount=0;
tmp->next=NULL;
if (parent)
parent->next=(void*)tmp;
return tmp;
}
static void deletepairlist(ppairlist_t list)
{
size_t i;
if (list)
{
if (list->next)
{
deletepairlist(list->next);
list->next=NULL;
}
for (i=0; i < list->paircount; i++)
cleanpair((list->pairs)+i);
ECOFREE(list,"Delete pair list");
}
}
static int cmppair(const void* p1,const void*p2)
{
ppair_t pr1,pr2;
pr1=(ppair_t)p1;
pr2=(ppair_t)p2;
if (pr1->p1 < pr2->p1) return -1;
if (pr1->p1 > pr2->p1) return 1;
if (pr1->asdirect1 < pr2->asdirect1) return -1;
if (pr1->asdirect1 > pr2->asdirect1) return 1;
if (pr1->p2 < pr2->p2) return -1;
if (pr1->p2 > pr2->p2) return 1;
if (pr1->asdirect2 < pr2->asdirect2) return -1;
if (pr1->asdirect2 > pr2->asdirect2) return 1;
return 0;
}
ppair_t pairintree (pair_t key,
ppairtree_t pairlist)
{
if (!pairlist->tree)
return NULL;
return *((ppair_t*)tsearch((const void *)(&key),
&(pairlist->tree),
cmppair
));
}
ppair_t insertpair(pair_t key,
ppairtree_t list)
{
ppair_t current;
ppair_t found;
if (list->last->paircount==list->last->pairslots)
{
list->last->next=newpairlist(list,100);
list->last=list->last->next;
}
current = list->last->pairs + list->last->paircount;
*current=key;
found = *((ppair_t*)tsearch((const void *)current,
&(list->tree),
cmppair));
if (found==current)
list->last->paircount++;
return found;
}
ppairtree_t initpairtree(ppairtree_t tree)
{
fprintf(stderr,"coucou from initpairtree\n");
if (!tree)
tree = ECOMALLOC(sizeof(pairtree_t),"Cannot allocate pair tree");
tree->first=newpairlist(NULL,500);
tree->last=tree->first;
tree->tree=NULL;
}

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queue.o queue.P : queue.c ecoprimer.h /usr/include/inttypes.h \
/usr/include/sys/cdefs.h /usr/include/_types.h \
/usr/include/sys/_types.h /usr/include/machine/_types.h \
/usr/include/i386/_types.h \
/usr/lib/gcc/i686-apple-darwin9/4.0.1/include/stdint.h \
/usr/include/stdlib.h /usr/include/available.h /usr/include/sys/wait.h \
/usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
/usr/include/machine/signal.h /usr/include/i386/signal.h \
/usr/include/i386/_structs.h /usr/include/sys/_structs.h \
/usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
/usr/include/sys/resource.h /usr/include/machine/endian.h \
/usr/include/i386/endian.h /usr/include/sys/_endian.h \
/usr/include/libkern/_OSByteOrder.h \
/usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
/usr/include/machine/types.h /usr/include/i386/types.h \
/usr/include/stdio.h ecotype.h ../libecoPCR/ecoPCR.h apat.h libstki.h \
debug.h

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readdnadb.o readdnadb.P : readdnadb.c ecoprimer.h /usr/include/inttypes.h \
/usr/include/sys/cdefs.h /usr/include/_types.h \
/usr/include/sys/_types.h /usr/include/machine/_types.h \
/usr/include/i386/_types.h \
/usr/lib/gcc/i686-apple-darwin9/4.0.1/include/stdint.h \
/usr/include/stdlib.h /usr/include/available.h /usr/include/sys/wait.h \
/usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
/usr/include/machine/signal.h /usr/include/i386/signal.h \
/usr/include/i386/_structs.h /usr/include/sys/_structs.h \
/usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
/usr/include/sys/resource.h /usr/include/machine/endian.h \
/usr/include/i386/endian.h /usr/include/sys/_endian.h \
/usr/include/libkern/_OSByteOrder.h \
/usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
/usr/include/machine/types.h /usr/include/i386/types.h \
/usr/include/stdio.h ecotype.h ../libecoPCR/ecoPCR.h apat.h libstki.h \
debug.h

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smothsort.o smothsort.P : smothsort.c /usr/include/assert.h /usr/include/sys/cdefs.h \
/usr/include/stdio.h /usr/include/_types.h /usr/include/sys/_types.h \
/usr/include/machine/_types.h /usr/include/i386/_types.h \
/usr/include/sys/types.h /usr/include/sys/appleapiopts.h \
/usr/include/machine/types.h /usr/include/i386/types.h \
/usr/include/machine/endian.h /usr/include/i386/endian.h \
/usr/include/sys/_endian.h /usr/include/libkern/_OSByteOrder.h \
/usr/include/libkern/i386/_OSByteOrder.h /usr/include/sys/_structs.h \
/usr/include/inttypes.h \
/usr/lib/gcc/i686-apple-darwin9/4.0.1/include/stdint.h

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sortmatch.o sortmatch.P : sortmatch.c ecoprimer.h /usr/include/inttypes.h \
/usr/include/sys/cdefs.h /usr/include/_types.h \
/usr/include/sys/_types.h /usr/include/machine/_types.h \
/usr/include/i386/_types.h \
/usr/lib/gcc/i686-apple-darwin9/4.0.1/include/stdint.h \
/usr/include/stdlib.h /usr/include/available.h /usr/include/sys/wait.h \
/usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
/usr/include/machine/signal.h /usr/include/i386/signal.h \
/usr/include/i386/_structs.h /usr/include/sys/_structs.h \
/usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
/usr/include/sys/resource.h /usr/include/machine/endian.h \
/usr/include/i386/endian.h /usr/include/sys/_endian.h \
/usr/include/libkern/_OSByteOrder.h \
/usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
/usr/include/machine/types.h /usr/include/i386/types.h \
/usr/include/stdio.h ecotype.h ../libecoPCR/ecoPCR.h apat.h libstki.h \
debug.h /usr/include/math.h /usr/include/architecture/i386/math.h

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sortword.o sortword.P : sortword.c ecoprimer.h /usr/include/inttypes.h \
/usr/include/sys/cdefs.h /usr/include/_types.h \
/usr/include/sys/_types.h /usr/include/machine/_types.h \
/usr/include/i386/_types.h \
/usr/lib/gcc/i686-apple-darwin9/4.0.1/include/stdint.h \
/usr/include/stdlib.h /usr/include/available.h /usr/include/sys/wait.h \
/usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
/usr/include/machine/signal.h /usr/include/i386/signal.h \
/usr/include/i386/_structs.h /usr/include/sys/_structs.h \
/usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
/usr/include/sys/resource.h /usr/include/machine/endian.h \
/usr/include/i386/endian.h /usr/include/sys/_endian.h \
/usr/include/libkern/_OSByteOrder.h \
/usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
/usr/include/machine/types.h /usr/include/i386/types.h \
/usr/include/stdio.h ecotype.h ../libecoPCR/ecoPCR.h apat.h libstki.h \
debug.h /usr/include/math.h /usr/include/architecture/i386/math.h

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strictprimers.o strictprimers.P : strictprimers.c ecoprimer.h /usr/include/inttypes.h \
/usr/include/sys/cdefs.h /usr/include/_types.h \
/usr/include/sys/_types.h /usr/include/machine/_types.h \
/usr/include/i386/_types.h \
/usr/lib/gcc/i686-apple-darwin9/4.0.1/include/stdint.h \
/usr/include/stdlib.h /usr/include/available.h /usr/include/sys/wait.h \
/usr/include/sys/signal.h /usr/include/sys/appleapiopts.h \
/usr/include/machine/signal.h /usr/include/i386/signal.h \
/usr/include/i386/_structs.h /usr/include/sys/_structs.h \
/usr/include/machine/_structs.h /usr/include/mach/i386/_structs.h \
/usr/include/sys/resource.h /usr/include/machine/endian.h \
/usr/include/i386/endian.h /usr/include/sys/_endian.h \
/usr/include/libkern/_OSByteOrder.h \
/usr/include/libkern/i386/_OSByteOrder.h /usr/include/alloca.h \
/usr/include/machine/types.h /usr/include/i386/types.h \
/usr/include/stdio.h ecotype.h ../libecoPCR/ecoPCR.h apat.h libstki.h \
debug.h /usr/include/string.h /usr/include/math.h \
/usr/include/architecture/i386/math.h