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New version of pairing algorithm (alpha)

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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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77
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" */ /* Format and print the time, "ddd yyyy-mm-dd hh:mm:ss zzz" */
ts = localtime(&now); ts = localtime(&now);
strftime(buf, sizeof(buf), "%a %Y-%m-%d %H:%M:%S %Z", ts); 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() void printcurrenttimeinmilli()
@ -90,6 +90,9 @@ void printcurrenttimeinmilli()
} }
/*TR: Added*/ /*TR: Added*/
#ifdef MASKEDCODE
void printpairs (pairscount_t pairs, poptions_t options, int32_t rankdbstats, uint32_t seqdbsize) void printpairs (pairscount_t pairs, poptions_t options, int32_t rankdbstats, uint32_t seqdbsize)
{ {
uint32_t i; uint32_t i;
@ -98,9 +101,9 @@ void printpairs (pairscount_t pairs, poptions_t options, int32_t rankdbstats, ui
double sens; double sens;
double speci; double speci;
float avg; float avg;
quorumseqs = seqdbsize * 70 / 100; quorumseqs = seqdbsize * 70 / 100;
printf("primer_1\tseq_1\tPrimer_2\tseq_2\tamplifia_count\t%s_snes\t%s_spe\tmin_l\tmax_l\tavr_l\n", options->taxonrank, options->taxonrank); printf("primer_1\tseq_1\tPrimer_2\tseq_2\tamplifia_count\t%s_snes\t%s_spe\tmin_l\tmax_l\tavr_l\n", options->taxonrank, options->taxonrank);
for (i=0; i < pairs.paircount; i++) for (i=0; i < pairs.paircount; i++)
@ -121,9 +124,12 @@ void printpairs (pairscount_t pairs, poptions_t options, int32_t rankdbstats, ui
} }
} }
#endif /* MASKEDCODE */
/*updateseqparams: This function counts the insample and outsample sequences /*updateseqparams: This function counts the insample and outsample sequences
* and with each sequences adds a tag of the taxon to which the sequence beongs*/ * 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,
void updateseqparams (pecodnadb_t seqdb, uint32_t seqdbsize, ecotaxonomy_t *taxonomy,
poptions_t options, int32_t *insamples, int32_t *outsamples) poptions_t options, int32_t *insamples, int32_t *outsamples)
{ {
uint32_t i; uint32_t i;
@ -131,7 +137,7 @@ void updateseqparams (pecodnadb_t seqdb, uint32_t seqdbsize, ecotaxonomy_t *taxo
ecotx_t *tmptaxon; ecotx_t *tmptaxon;
for (i=0;i<seqdbsize;i++) for (i=0;i<seqdbsize;i++)
{ {
seqdb[i]->isexample=isGoodTaxon(taxonomy,seqdb[i]->taxid,options); seqdb[i]->isexample=isGoodTaxon(taxonomy,seqdb[i]->taxid,options);
if (seqdb[i]->isexample) if (seqdb[i]->isexample)
(*insamples)++; (*insamples)++;
@ -139,7 +145,7 @@ void updateseqparams (pecodnadb_t seqdb, uint32_t seqdbsize, ecotaxonomy_t *taxo
(*outsamples)++; (*outsamples)++;
taxid = taxonomy->taxons->taxon[seqdb[i]->taxid].taxid; taxid = taxonomy->taxons->taxon[seqdb[i]->taxid].taxid;
tmptaxon = eco_findtaxonbytaxid(taxonomy, taxid); tmptaxon = eco_findtaxonbytaxid(taxonomy, taxid);
if (tmptaxon) if (tmptaxon)
tmptaxon = eco_findtaxonatrank(tmptaxon, options->taxonrankidx); tmptaxon = eco_findtaxonatrank(tmptaxon, options->taxonrankidx);
if (tmptaxon) if (tmptaxon)
@ -154,7 +160,7 @@ void setresulttaxonrank (ecotaxonomy_t *taxonomy, poptions_t options)
/*set taxon rank for which result is to be given*/ /*set taxon rank for which result is to be given*/
for (i = 0; i < taxonomy->ranks->count; i++) for (i = 0; i < taxonomy->ranks->count; i++)
{ {
if (strcmp(taxonomy->ranks->label[i], options->taxonrank) == 0) if (strcmp(taxonomy->ranks->label[i], options->taxonrank) == 0)
{ {
options->taxonrankidx = i; options->taxonrankidx = i;
break; break;
@ -168,7 +174,7 @@ void setresulttaxonrank (ecotaxonomy_t *taxonomy, poptions_t options)
} }
} }
/* to get db stats, totals of species, genus etc....*/ /* to get db stats, totals of species, genus etc....*/
int32_t getrankdbstats(pecodnadb_t seqdb, uint32_t seqdbsize, ecotaxonomy_t *taxonomy, int32_t getrankdbstats(pecodnadb_t seqdb, uint32_t seqdbsize, ecotaxonomy_t *taxonomy,
poptions_t options) poptions_t options)
{ {
uint32_t i; uint32_t i;
@ -177,7 +183,7 @@ int32_t getrankdbstats(pecodnadb_t seqdb, uint32_t seqdbsize, ecotaxonomy_t *tax
uint32_t namesindex = 0; uint32_t namesindex = 0;
int32_t *ranktaxonids = ECOMALLOC(nameslots * sizeof(int32_t), "Error in taxon rank allocation"); int32_t *ranktaxonids = ECOMALLOC(nameslots * sizeof(int32_t), "Error in taxon rank allocation");
int32_t taxid; int32_t taxid;
ecotx_t *tmptaxon; ecotx_t *tmptaxon;
for (i=0;i<seqdbsize;i++) for (i=0;i<seqdbsize;i++)
@ -193,7 +199,7 @@ int32_t getrankdbstats(pecodnadb_t seqdb, uint32_t seqdbsize, ecotaxonomy_t *tax
if (tmptaxon->taxid == ranktaxonids[j]) break; if (tmptaxon->taxid == ranktaxonids[j]) break;
} }
if (j < namesindex) continue; /* name is already in list, so no need to add it*/ if (j < namesindex) continue; /* name is already in list, so no need to add it*/
if (namesindex == nameslots) if (namesindex == nameslots)
{ {
nameslots += 500; nameslots += 500;
@ -204,11 +210,13 @@ int32_t getrankdbstats(pecodnadb_t seqdb, uint32_t seqdbsize, ecotaxonomy_t *tax
} }
} }
ECOFREE(ranktaxonids, "free rank taxon table"); ECOFREE(ranktaxonids, "free rank taxon table");
return namesindex; return namesindex;
} }
void setoktaxforspecificity (ppairscount_t pairs) #ifdef MASKEDCODE
void setoktaxforspecificity (ppairtree_t pairs)
{ {
uint32_t i; uint32_t i;
uint32_t j; uint32_t j;
@ -216,7 +224,7 @@ void setoktaxforspecificity (ppairscount_t pairs)
uint32_t l; uint32_t l;
int taxcount; int taxcount;
int32_t taxid; int32_t taxid;
for (i = 0; i < pairs->paircount; i++) for (i = 0; i < pairs->paircount; i++)
{ {
for (j = 0; j < pairs->pairs[i].taxsetindex; j++) for (j = 0; j < pairs->pairs[i].taxsetindex; j++)
@ -235,13 +243,13 @@ void setoktaxforspecificity (ppairscount_t pairs)
taxcount += pairs->pairs[i].ampset[l].seqidindex; taxcount += pairs->pairs[i].ampset[l].seqidindex;
break; break;
} }
if (taxid != pairs->pairs[i].ampset[l].taxonids[0]) if (taxid != pairs->pairs[i].ampset[l].taxonids[0])
{ {
if (!taxid) taxid = pairs->pairs[i].ampset[l].taxonids[0]; if (!taxid) taxid = pairs->pairs[i].ampset[l].taxonids[0];
taxcount++; taxcount++;
} }
if (taxcount > 1) break; if (taxcount > 1) break;
} }
} }
@ -251,6 +259,8 @@ void setoktaxforspecificity (ppairscount_t pairs)
} }
} }
#endif
int main(int argc, char **argv) int main(int argc, char **argv)
{ {
pecodnadb_t seqdb; /* of type ecoseq_t */ pecodnadb_t seqdb; /* of type ecoseq_t */
@ -264,11 +274,11 @@ int main(int argc, char **argv)
int32_t insamples=0; int32_t insamples=0;
int32_t outsamples=0; int32_t outsamples=0;
uint32_t i; uint32_t i;
pwordcount_t words; pwordcount_t words;
pprimercount_t primers; pprimercount_t primers;
pairscount_t pairs; ppairtree_t pairs;
int32_t rankdbstats = 0; int32_t rankdbstats = 0;
//printcurrenttime(); //printcurrenttime();
@ -337,7 +347,7 @@ int main(int argc, char **argv)
strncpy(options.taxonrank, optarg, 19); strncpy(options.taxonrank, optarg, 19);
options.taxonrank[19] = 0; options.taxonrank[19] = 0;
break; break;
/* -------------------- */ /* -------------------- */
case 'x': /* strict matching quorum */ case 'x': /* strict matching quorum */
/* -------------------- */ /* -------------------- */
@ -396,16 +406,16 @@ int main(int argc, char **argv)
fprintf(stderr,"Reading taxonomy database ..."); fprintf(stderr,"Reading taxonomy database ...");
taxonomy = read_taxonomy(options.prefix,0); taxonomy = read_taxonomy(options.prefix,0);
fprintf(stderr,"Ok\n"); fprintf(stderr,"Ok\n");
setresulttaxonrank(taxonomy, &options); /*TR: set rank level for statistics*/ setresulttaxonrank(taxonomy, &options); /*TR: set rank level for statistics*/
fprintf(stderr,"Reading sequence database ...\n"); fprintf(stderr,"Reading sequence database ...\n");
seqdb = readdnadb(options.prefix,&seqdbsize); seqdb = readdnadb(options.prefix,&seqdbsize);
fprintf(stderr,"Ok\n"); fprintf(stderr,"Ok\n");
fprintf(stderr,"Sequence read : %d\n",(int32_t)seqdbsize); fprintf(stderr,"Sequence read : %d\n",(int32_t)seqdbsize);
updateseqparams(seqdb, seqdbsize, taxonomy, &options, &insamples , &outsamples); updateseqparams(seqdb, seqdbsize, taxonomy, &options, &insamples , &outsamples);
rankdbstats = getrankdbstats(seqdb, seqdbsize, taxonomy, &options); rankdbstats = getrankdbstats(seqdb, seqdbsize, taxonomy, &options);
@ -419,7 +429,7 @@ int main(int argc, char **argv)
printcurrenttimeinmilli(); printcurrenttimeinmilli();
words = lookforStrictPrimer(seqdb,seqdbsize,insamples,&options); words = lookforStrictPrimer(seqdb,seqdbsize,insamples,&options);
printcurrenttimeinmilli(); printcurrenttimeinmilli();
fprintf(stderr,"\n Strict primer count : %d\n",words->size); fprintf(stderr,"\n Strict primer count : %d\n",words->size);
if (options.no_multi_match) if (options.no_multi_match)
@ -460,13 +470,14 @@ int main(int argc, char **argv)
/*TR: Added*/ /*TR: Added*/
pairs = buildPrimerPairs(seqdb, seqdbsize, primers, &options); pairs = buildPrimerPairs(seqdb, seqdbsize, primers, &options);
setoktaxforspecificity (&pairs);
// setoktaxforspecificity (&pairs);
printpairs (pairs, &options, rankdbstats, seqdbsize);
// printpairs (pairs, &options, rankdbstats, seqdbsize);
ECOFREE(pairs.pairs,"Free pairs table");
//ECOFREE(pairs.pairs,"Free pairs table");
return 0; 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 $< MAKEDEPEND = gcc -D$(MACHINE) -M $(CPPFLAGS) -o $*.d $<
CC=gcc 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 -O0 -m64 -g
#CFLAGS= -W -Wall -O5 -fast -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 \ queue.c \
libstki.c \ libstki.c \
sortmatch.c \ sortmatch.c \
pairtree.c \
pairs.c \ pairs.c \
apat_search.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
View File

@ -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

116
src/libecoprimer/ecoprimer.h
View File

@ -79,28 +79,39 @@ typedef union {
uint32_t value; uint32_t value;
} poslist_t, *ppostlist_t; } poslist_t, *ppostlist_t;
typedef struct { /**
word_t word; * primer_t structure store fuzzy match positions for a primer
uint32_t *directCount; * on all sequences
ppostlist_t directPos; */
uint32_t *reverseCount; typedef struct {
ppostlist_t reversePos; word_t word; //< code for the primer
bool_t good; uint32_t *directCount; //< Occurrence count on direct strand
uint32_t inexample; ppostlist_t directPos; //< list of position list on direct strand
uint32_t outexample;
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; } 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 { typedef struct {
pprimer_t primers; pprimer_t primers;
uint32_t size; uint32_t size;
} primercount_t, *pprimercount_t; } primercount_t, *pprimercount_t;
typedef struct { typedef struct {
word_t word; pprimer_t primer;
uint32_t position; uint32_t position;
bool_t strand; bool_t strand;
bool_t good; /*TR: Added*/
} primermatch_t, *pprimermatch_t; } primermatch_t, *pprimermatch_t;
/*TR: Added*/ /*TR: Added*/
@ -109,6 +120,19 @@ typedef struct {
uint32_t matchcount; uint32_t matchcount;
} primermatchcount_t, *pprimermatchcount_t; } 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 { typedef struct {
char *amplifia; char *amplifia;
int32_t *taxonids; int32_t *taxonids;
@ -124,30 +148,51 @@ typedef struct {
} taxampset_t, *ptaxampset_t; } taxampset_t, *ptaxampset_t;
typedef struct { typedef struct {
word_t w1; pprimer_t p1;
word_t w2; bool_t asdirect1;
uint32_t inexample; /*inexample count*/ pprimer_t p2;
uint32_t outexample; /*outexample count*/ bool_t asdirect2;
uint32_t mind; amplifiacount_t pcr;
uint32_t maxd;
uint32_t inexample; //< example sequence count
uint32_t ampsetcount; uint32_t outexample; //< counterexample sequence count
uint32_t ampsetindex;
pampseqset_t ampset;
uint32_t taxsetcount; // these statistics are relative to inexample sequences
uint32_t taxsetindex;
ptaxampset_t taxset; uint32_t mind; //< minimum distance between primers
uint32_t maxd; //< maximum distance between primers
uint32_t oktaxoncount; uint32_t sumd; //< distance sum
} pairs_t, *ppairs_t;
//
// 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*/ /*TR: Added*/
typedef struct { typedef struct {
ppairs_t pairs; size_t paircount;
uint32_t paircount; size_t pairslots;
}pairscount_t, *ppairscount_t; 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 { typedef struct {
pword_t words; 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); 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*/ /*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_ */ #endif /* EPSORT_H_ */

17
src/libecoprimer/goodtaxon.P Normal file
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@ -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

415
src/libecoprimer/pairs.c
View File

@ -7,34 +7,40 @@
#include "ecoprimer.h" #include "ecoprimer.h"
#include <string.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 i;
uint32_t j; uint32_t j;
char *ampused = NULL; char *ampused = NULL;
if(pair->ampsetcount == 0) if(pair->ampsetcount == 0)
{ {
pair->ampsetcount = 500; pair->ampsetcount = 500;
pair->ampsetindex = 0; pair->ampsetindex = 0;
pair->ampset = ECOMALLOC(pair->ampsetcount * sizeof(ampseqset_t),"Cannot allocate amplifia set"); pair->ampset = ECOMALLOC(pair->ampsetcount * sizeof(ampseqset_t),"Cannot allocate amplifia set");
} }
for (i = 0; i < pair->ampsetindex; i++) for (i = 0; i < pair->ampsetindex; i++)
{ {
if (strcmp (pair->ampset[i].amplifia, amplifia) == 0) if (strcmp (pair->ampset[i].amplifia, amplifia) == 0)
@ -43,43 +49,43 @@ char *addamplifiasetelem (ppairs_t pair, char* amplifia, int32_t taxid)
break; break;
} }
} }
if (i == 0) if (i == 0)
{ {
pair->ampset[i].seqidcount = 100; pair->ampset[i].seqidcount = 100;
pair->ampset[i].seqidindex = 0; pair->ampset[i].seqidindex = 0;
pair->ampset[i].taxonids = ECOMALLOC(pair->ampset[i].seqidcount * sizeof(uint32_t),"Cannot allocate amplifia sequence table"); pair->ampset[i].taxonids = ECOMALLOC(pair->ampset[i].seqidcount * sizeof(uint32_t),"Cannot allocate amplifia sequence table");
} }
if (pair->ampsetindex == pair->ampsetcount) if (pair->ampsetindex == pair->ampsetcount)
{ {
pair->ampsetcount += 500; pair->ampsetcount += 500;
pair->ampset = ECOREALLOC(pair->ampset, pair->ampsetcount * sizeof(ampseqset_t), "Cannot allocate amplifia set"); pair->ampset = ECOREALLOC(pair->ampset, pair->ampsetcount * sizeof(ampseqset_t), "Cannot allocate amplifia set");
} }
if (pair->ampset[i].seqidindex == pair->ampset[i].seqidcount) if (pair->ampset[i].seqidindex == pair->ampset[i].seqidcount)
{ {
pair->ampset[i].seqidcount += 100; pair->ampset[i].seqidcount += 100;
pair->ampset[i].taxonids = ECOREALLOC(pair->ampset[i].taxonids, pair->ampset[i].seqidcount * sizeof(int32_t), "Cannot allocate amplifia sequence table"); pair->ampset[i].taxonids = ECOREALLOC(pair->ampset[i].taxonids, pair->ampset[i].seqidcount * sizeof(int32_t), "Cannot allocate amplifia sequence table");
} }
if (pair->ampset[i].amplifia == NULL) if (pair->ampset[i].amplifia == NULL)
{ {
pair->ampset[i].amplifia = amplifia; pair->ampset[i].amplifia = amplifia;
pair->ampsetindex++; pair->ampsetindex++;
} }
for (j = 0; j < pair->ampset[i].seqidindex; j++) for (j = 0; j < pair->ampset[i].seqidindex; j++)
{ {
if (pair->ampset[i].taxonids[j] == taxid) break; if (pair->ampset[i].taxonids[j] == taxid) break;
} }
if (j == pair->ampset[i].seqidindex) if (j == pair->ampset[i].seqidindex)
pair->ampset[i].taxonids[pair->ampset[i].seqidindex++] = taxid; pair->ampset[i].taxonids[pair->ampset[i].seqidindex++] = taxid;
return ampused; 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 i;
uint32_t j; uint32_t j;
@ -90,42 +96,42 @@ void addtaxampsetelem (ppairs_t pair, int32_t taxid, char *amplifia)
pair->taxsetindex = 0; pair->taxsetindex = 0;
pair->taxset = ECOMALLOC(pair->taxsetcount * sizeof(taxampset_t),"Cannot allocate taxon set"); pair->taxset = ECOMALLOC(pair->taxsetcount * sizeof(taxampset_t),"Cannot allocate taxon set");
} }
for (i = 0; i < pair->taxsetindex; i++) for (i = 0; i < pair->taxsetindex; i++)
{ {
if (pair->taxset[i].taxonid == taxid) break; if (pair->taxset[i].taxonid == taxid) break;
} }
if (i == 0) if (i == 0)
{ {
pair->taxset[i].amplifiacount = 100; pair->taxset[i].amplifiacount = 100;
pair->taxset[i].amplifiaindex = 0; pair->taxset[i].amplifiaindex = 0;
pair->taxset[i].amplifia = ECOMALLOC(pair->taxset[i].amplifiacount * sizeof(char *),"Cannot allocate amplifia table"); pair->taxset[i].amplifia = ECOMALLOC(pair->taxset[i].amplifiacount * sizeof(char *),"Cannot allocate amplifia table");
} }
if (pair->taxsetindex == pair->taxsetcount) if (pair->taxsetindex == pair->taxsetcount)
{ {
pair->taxsetcount += 500; pair->taxsetcount += 500;
pair->taxset = ECOREALLOC(pair->taxset, pair->taxsetcount * sizeof(taxampset_t), "Cannot allocate taxon set"); pair->taxset = ECOREALLOC(pair->taxset, pair->taxsetcount * sizeof(taxampset_t), "Cannot allocate taxon set");
} }
if (pair->taxset[i].amplifiaindex == pair->taxset[i].amplifiacount) if (pair->taxset[i].amplifiaindex == pair->taxset[i].amplifiacount)
{ {
pair->taxset[i].amplifiacount += 100; pair->taxset[i].amplifiacount += 100;
pair->taxset[i].amplifia = ECOREALLOC(pair->taxset[i].amplifia, pair->taxset[i].amplifiacount * sizeof(char *), "Cannot allocate amplifia table"); pair->taxset[i].amplifia = ECOREALLOC(pair->taxset[i].amplifia, pair->taxset[i].amplifiacount * sizeof(char *), "Cannot allocate amplifia table");
} }
if (pair->taxset[i].taxonid == 0) if (pair->taxset[i].taxonid == 0)
{ {
pair->taxset[i].taxonid = taxid; pair->taxset[i].taxonid = taxid;
pair->taxsetindex++; pair->taxsetindex++;
} }
for (j = 0; j < pair->taxset[i].amplifiaindex; j++) for (j = 0; j < pair->taxset[i].amplifiaindex; j++)
{ {
if (strcmp(pair->taxset[i].amplifia[j], amplifia) == 0) break; if (strcmp(pair->taxset[i].amplifia[j], amplifia) == 0) break;
} }
if (j == pair->taxset[i].amplifiaindex) if (j == pair->taxset[i].amplifiaindex)
{ {
pair->taxset[i].amplifia[j] = amplifia; pair->taxset[i].amplifia[j] = amplifia;
@ -135,16 +141,18 @@ void addtaxampsetelem (ppairs_t pair, int32_t taxid, char *amplifia)
char *getamplifia (pecoseq_t seq, uint32_t start, uint32_t len) 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 *amplifia = ECOMALLOC((len + 1) * sizeof(char),"Cannot allocate amplifia");
char *seqc = &seq->SQ[start]; char *seqc = &seq->SQ[start];
strncpy(amplifia, seqc, len); strncpy(amplifia, seqc, len);
return amplifia; return amplifia;
} }
#endif
/*TR: Added*/ /*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 i;
uint32_t j; uint32_t j;
@ -152,123 +160,131 @@ pairscount_t buildPrimerPairs(pecodnadb_t seqdb,uint32_t seqdbsize,pprimercount_
uint32_t d; uint32_t d;
uint32_t strt; uint32_t strt;
uint32_t end; uint32_t end;
uint32_t paircount = 0; ppairtree_t primerpairs;
uint32_t pairslots = 500;
int32_t foundindex;
ppairs_t pairs;
pairscount_t primerpairs;
primermatchcount_t seqmatchcount; primermatchcount_t seqmatchcount;
word_t w1; word_t w1;
word_t w2; word_t w2;
char *amplifia; char *amplifia;
char *oldamp; char *oldamp;
pairs = ECOMALLOC(pairslots * sizeof(pairs_t),"Cannot allocate pairs table");
primerpairs = initpairtree(NULL);
for (i=0; i < seqdbsize; i++) for (i=0; i < seqdbsize; i++)
{ {
seqmatchcount = buildPrimerPairsForOneSeq(i, primers, options); 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"); // if (seqmatchcount.matchcount == 0) continue;
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)
{
uint32_t i,j,k; static void buildPrimerPairsForOneSeq(uint32_t seqid,
uint32_t matchcount=0; pecodnadb_t seqdb,
pprimermatch_t matches = NULL; pprimercount_t primers,
primermatchcount_t seqmatchcount; 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;
ppair_t pcurrent;
pair_t current;
pprimer_t wswp;
bool_t bswp;
size_t distance;
seqmatchcount.matchcount = 0;
seqmatchcount.matches = NULL;
for (i=0;i < primers->size; i++) for (i=0;i < primers->size; i++)
{ {
matchcount+=primers->primers[i].directCount[seqid]; matchcount+=primers->primers[i].directCount[seqid];
matchcount+=primers->primers[i].reverseCount[seqid]; 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"); matches = ECOMALLOC(matchcount * sizeof(primermatch_t),"Cannot allocate primers match table");
for (i=0,j=0;i < primers->size; i++) 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) 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].strand=TRUE;
matches[j].good=primers->primers[i].good;/*TR: Added*/
matches[j].position=primers->primers[i].directPos[seqid].value; matches[j].position=primers->primers[i].directPos[seqid].value;
j++; j++;
} }
else for (k=0; k < primers->primers[i].directCount[seqid]; k++,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].strand=TRUE;
matches[j].good=primers->primers[i].good;/*TR: Added*/
matches[j].position=primers->primers[i].directPos[seqid].pointer[k]; 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) 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].strand=FALSE;
matches[j].good=primers->primers[i].good;/*TR: Added*/
matches[j].position=primers->primers[i].reversePos[seqid].value; matches[j].position=primers->primers[i].reversePos[seqid].value;
j++; j++;
} }
else for (k=0; k < primers->primers[i].reverseCount[seqid]; k++,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].strand=FALSE;
matches[j].good=primers->primers[i].good;/*TR: Added*/
matches[j].position=primers->primers[i].reversePos[seqid].pointer[k]; matches[j].position=primers->primers[i].reversePos[seqid].pointer[k];
} }
} }
} }
sortmatch(matches,matchcount); // sort in asscending order by position if (matchcount>1)
{
/*TR: Added*/ fprintf(stderr,"\n====================================\n");
seqmatchcount.matches = matches;
seqmatchcount.matchcount = matchcount; sortmatch(matches,matchcount); // sort in ascending order by position
return seqmatchcount;
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
);
}
}
}
} }

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;
}

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

@ -0,0 +1,17 @@
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

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

@ -0,0 +1,17 @@
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

10
src/libecoprimer/smothsort.P Normal file
View File

@ -0,0 +1,10 @@
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

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

@ -0,0 +1,17 @@
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

17
src/libecoprimer/sortword.P Normal file
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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

18
src/libecoprimer/strictprimers.P Normal file
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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