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ecoprimers
Commit e3d922e1 authored by Eric Coissac's avatar Eric Coissac
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Merge of eric-test branche to the trunk 

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@200 60f365c0-8329-0410-b2a4-ec073aeeaa1d
parent b8af5dd6
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src/ecoPrimer 0 → 100755
View file @ e3d922e1
File added
src/ecoprimer.c
View file @ e3d922e1
......@@ -25,9 +25,59 @@
static void PrintHelp()
{
PP "------------------------------------------\n");
PP " ecoPrimer Version %s\n", VERSION);
PP "------------------------------------------\n");
PP "------------------------------------------\n");
PP " ecoPrimer Version %s\n", VERSION);
PP "------------------------------------------\n");
PP "synopsis : finding primers and measureing the quality of primers and barcode region\n");
PP "usage: ./ecoPrimer [options] \n");
PP "------------------------------------------\n");
PP "options:\n");
PP "-d : [D]atabase : to match the expected format, the database\n");
PP " has to be formated first by the ecoPCRFormat.py program located.\n");
PP " in the ecoPCR/tools directory.\n");
PP " ecoPCRFormat.py creates three file types :\n");
PP " .sdx : contains the sequences\n");
PP " .tdx : contains information concerning the taxonomy\n");
PP " .rdx : contains the taxonomy rank\n\n");
PP " ecoPrimer needs all the file type. As a result, you have to write the\n");
PP " database radical without any extension. For example /ecoPrimerDB/fstvert\n\n");
PP "-e : [E]rror : max error allowed by oligonucleotide (0 by default)\n\n");
PP "-h : [H]elp - print <this> help\n\n");
PP "-i : [I]gnore the given taxonomy id.\n\n");
PP "-l : minimum [L]ength : define the minimum amplication length. \n\n");
PP "-L : maximum [L]ength : define the maximum amplicationlength. \n\n");
PP "-r : [R]estricts the search to the given taxonomic id.\n\n");
PP "-c : Consider that the database sequences are [c]ircular\n\n");
PP "-3 : Three prime strict match\n\n");
PP "-q : Strict matching [q]uorum, percentage of the sequences in which strict primers are found. By default it is 70\n\n");
PP "-s : [S]ensitivity quorum\n\n");
PP "-t : required [t]axon level for results, by default the results are computed at species level\n\n");
PP "-x : false positive quorum\n\n");
PP "-D : set in [d]ouble strand mode\n\n");
PP "-S : Set in [s]ingle strand mode\n\n");
PP "-U : No multi match\n\n");
PP "\n");
PP "------------------------------------------\n");
PP "Table result description : \n");
PP "column 1 : serial number\n");
PP "column 2 : primer1\n");
PP "column 3 : primer2\n");
PP "column 4 : good/bad\n");
PP "column 5 : in sequence count\n");
PP "column 6 : out sequence count\n");
PP "column 7 : yule\n");
PP "column 8 : in taxa count\n");
PP "column 9 : out taxa count\n");
PP "column 10 : coverage\n");
PP "column 11 : specificity\n");
PP "column 12 : minimum amplified length\n");
PP "column 13 : maximum amplified length\n");
PP "column 14 : average amplified length\n");
PP "------------------------------------------\n");
PP " http://www.grenoble.prabi.fr/trac/ecoPrimer/\n");
PP "------------------------------------------\n\n");
PP "\n");
}
static void ExitUsage(int stat)
......@@ -56,7 +106,7 @@ void initoptions(poptions_t options)
options->strict_exclude_quorum=0.1;
options->sensitivity_quorum=0.9;
options->false_positive_quorum=0.1;
options->strict_three_prime=2;
options->strict_three_prime=0;
options->r=0;
options->g=0;
options->no_multi_match=FALSE;
......@@ -75,7 +125,7 @@ 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()
......@@ -90,7 +140,125 @@ void printcurrenttimeinmilli()
}
/*TR: Added*/
void printapair(int32_t index,ppair_t pair, poptions_t options)
{
uint32_t wellidentifiedtaxa;
printf("%6d\t",index);
if (pair->asdirect1)
printf("%s\t",ecoUnhashWord(pair->p1->word,options->primer_length));
else
printf("%s\t",ecoUnhashWord(ecoComplementWord(pair->p1->word,
options->primer_length),options->primer_length));
if (pair->asdirect2)
printf("%s",ecoUnhashWord(pair->p2->word,options->primer_length));
else
printf("%s",ecoUnhashWord(ecoComplementWord(pair->p2->word,
options->primer_length),options->primer_length));
printf("\t%c%c", "bG"[(int)pair->p1->good],"bG"[(int)pair->p2->good]);
printf("\t%d", pair->inexample);
printf("\t%d", pair->outexample);
printf("\t%4.3f", pair->yule);
printf("\t%d", pair->intaxa);
printf("\t%d", pair->outtaxa);
printf("\t%4.3f", (float)pair->intaxa/options->intaxa);
wellidentifiedtaxa = (pair->intaxa + pair->outtaxa) - pair->notwellidentifiedtaxa;
//printf("\t%d", pair->notwellidentifiedtaxa);
//printf("\t%d", (pair->intaxa + pair->outtaxa));
printf("\t%4.3f", (float)wellidentifiedtaxa/(options->intaxa + options->outtaxa));
printf("\t%d", pair->mind);
printf("\t%d", pair->maxd);
printf("\t%3.2f\n", (float)pair->sumd/pair->inexample);
}
uint32_t filterandsortpairs(ppair_t* sortedpairs,uint32_t count, poptions_t options)
{
uint32_t i,j;
float q,qfp;
for (i=0,j=0;i < count;i++)
{
if (options->insamples)
q = (float)sortedpairs[i]->inexample/options->insamples;
else q=1.0;
if (options->outsamples)
qfp = (float)sortedpairs[i]->outexample/options->outsamples;
else qfp=0.0;
sortedpairs[i]->quorumin = q;
sortedpairs[i]->quorumout = qfp;
sortedpairs[i]->yule = q -qfp;
sortedpairs[j]=sortedpairs[i];
if (q > options->sensitivity_quorum &&
qfp < options->false_positive_quorum)
{
(void)taxonomycoverage(sortedpairs[j],options);
taxonomyspecificity(sortedpairs[j]);
j++;
}
}
return j;
}
void printpairs (ppairtree_t pairs, poptions_t options)
{
ppair_t* sortedpairs;
ppair_t* index;
ppairlist_t pl;
size_t i,j;
int32_t count;
//printf("Index\tPrimer1\tPrimer2\tGB\tInexampleCount\tOutexampleCount\tYule\tIntaxaCount\tOuttaxaCount\tCoverage\tSpecificity\tMinAmplifiedLength\tMaxAmplifiedLength\tAvgAmplifiedLength\n");
fprintf(stderr,"Total pair count : %d\n",pairs->count);
sortedpairs = ECOMALLOC(pairs->count*sizeof(ppair_t),"Cannot Allocate ordered pairs");
index=sortedpairs;
pl=pairs->first;
j=0;
while(pl->next)
{
for (i=0;i<pl->paircount;i++,j++)
sortedpairs[j]=pl->pairs+i;
pl=pl->next;
}
for (i=0;i<pl->paircount;i++,j++)
sortedpairs[j]=pl->pairs+i;
count=filterandsortpairs(sortedpairs,pairs->count,options);
for (i=0;i < count;i++)
printapair(i,sortedpairs[i],options);
}
#ifdef MASKEDCODE
void printpairs (pairscount_t pairs, poptions_t options, int32_t rankdbstats, uint32_t seqdbsize)
{
uint32_t i;
uint32_t wordsize = options->primer_length;
......@@ -98,9 +266,9 @@ void printpairs (pairscount_t pairs, poptions_t options, int32_t rankdbstats, ui
double sens;
double speci;
float avg;
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);
for (i=0; i < pairs.paircount; i++)
......@@ -121,9 +289,12 @@ 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,
void updateseqparams (pecodnadb_t seqdb, uint32_t seqdbsize, ecotaxonomy_t *taxonomy,
poptions_t options, int32_t *insamples, int32_t *outsamples)
{
uint32_t i;
......@@ -131,7 +302,7 @@ void updateseqparams (pecodnadb_t seqdb, uint32_t seqdbsize, ecotaxonomy_t *taxo
ecotx_t *tmptaxon;
for (i=0;i<seqdbsize;i++)
{
{
seqdb[i]->isexample=isGoodTaxon(taxonomy,seqdb[i]->taxid,options);
if (seqdb[i]->isexample)
(*insamples)++;
......@@ -139,7 +310,7 @@ void updateseqparams (pecodnadb_t seqdb, uint32_t seqdbsize, ecotaxonomy_t *taxo
(*outsamples)++;
taxid = taxonomy->taxons->taxon[seqdb[i]->taxid].taxid;
tmptaxon = eco_findtaxonbytaxid(taxonomy, taxid);
tmptaxon = eco_findtaxonbytaxid(taxonomy, taxid);
if (tmptaxon)
tmptaxon = eco_findtaxonatrank(tmptaxon, options->taxonrankidx);
if (tmptaxon)
......@@ -154,7 +325,7 @@ void setresulttaxonrank (ecotaxonomy_t *taxonomy, poptions_t options)
/*set taxon rank for which result is to be given*/
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;
break;
......@@ -168,47 +339,10 @@ void setresulttaxonrank (ecotaxonomy_t *taxonomy, poptions_t options)
}
}
/* to get db stats, totals of species, genus etc....*/
int32_t getrankdbstats(pecodnadb_t seqdb, uint32_t seqdbsize, ecotaxonomy_t *taxonomy,
poptions_t options)
{
uint32_t i;
uint32_t j;
uint32_t nameslots = 500;
uint32_t namesindex = 0;
int32_t *ranktaxonids = ECOMALLOC(nameslots * sizeof(int32_t), "Error in taxon rank allocation");
int32_t taxid;
ecotx_t *tmptaxon;
for (i=0;i<seqdbsize;i++)
{
taxid = taxonomy->taxons->taxon[seqdb[i]->taxid].taxid;
tmptaxon = eco_findtaxonbytaxid(taxonomy, taxid);
if (tmptaxon)
tmptaxon = eco_findtaxonatrank(tmptaxon, options->taxonrankidx);
if (tmptaxon)
{
for (j = 0; j < namesindex; j++)
{
if (tmptaxon->taxid == ranktaxonids[j]) break;
}
if (j < namesindex) continue; /* name is already in list, so no need to add it*/
if (namesindex == nameslots)
{
nameslots += 500;
ranktaxonids = ECOREALLOC(ranktaxonids, nameslots * sizeof(int32_t), "Cannot allocate pair rank taxon table");
}
ranktaxonids[namesindex] = tmptaxon->taxid;
namesindex++;
}
}
ECOFREE(ranktaxonids, "free rank taxon table");
return namesindex;
}
#ifdef MASKEDCODE
void setoktaxforspecificity (ppairscount_t pairs)
void setoktaxforspecificity (ppairtree_t pairs)
{
uint32_t i;
uint32_t j;
......@@ -216,7 +350,7 @@ void setoktaxforspecificity (ppairscount_t pairs)
uint32_t l;
int taxcount;
int32_t taxid;
for (i = 0; i < pairs->paircount; i++)
{
for (j = 0; j < pairs->pairs[i].taxsetindex; j++)
......@@ -235,13 +369,13 @@ void setoktaxforspecificity (ppairscount_t pairs)
taxcount += pairs->pairs[i].ampset[l].seqidindex;
break;
}
if (taxid != pairs->pairs[i].ampset[l].taxonids[0])
{
if (!taxid) taxid = pairs->pairs[i].ampset[l].taxonids[0];
taxcount++;
taxcount++;
}
if (taxcount > 1) break;
}
}
......@@ -251,6 +385,8 @@ void setoktaxforspecificity (ppairscount_t pairs)
}
}
#endif
int main(int argc, char **argv)
{
pecodnadb_t seqdb; /* of type ecoseq_t */
......@@ -264,11 +400,11 @@ int main(int argc, char **argv)
int32_t insamples=0;
int32_t outsamples=0;
uint32_t i;
pwordcount_t words;
pprimercount_t primers;
pairscount_t pairs;
pwordcount_t words;
pprimercount_t primers;
ppairtree_t pairs;
int32_t rankdbstats = 0;
//printcurrenttime();
......@@ -290,9 +426,9 @@ int main(int argc, char **argv)
/* -------------------- */
case 'h': /* help */
/* -------------------- */
PrintHelp();
exit(0);
break;
PrintHelp();
exit(0);
break;
/* ------------------------- */
case 'l': /* min amplification lenght */
......@@ -337,7 +473,7 @@ int main(int argc, char **argv)
strncpy(options.taxonrank, optarg, 19);
options.taxonrank[19] = 0;
break;
/* -------------------- */
case 'x': /* strict matching quorum */
/* -------------------- */
......@@ -396,22 +532,27 @@ int main(int argc, char **argv)
fprintf(stderr,"Reading taxonomy database ...");
taxonomy = read_taxonomy(options.prefix,0);
fprintf(stderr,"Ok\n");
setresulttaxonrank(taxonomy, &options); /*TR: set rank level for statistics*/
fprintf(stderr,"Reading sequence database ...\n");
seqdb = readdnadb(options.prefix,&seqdbsize);
fprintf(stderr,"Ok\n");
fprintf(stderr,"Sequence read : %d\n",(int32_t)seqdbsize);
updateseqparams(seqdb, seqdbsize, taxonomy, &options, &insamples , &outsamples);
options.dbsize=seqdbsize;
options.insamples=insamples;
options.outsamples=outsamples;
rankdbstats = getrankdbstats(seqdb, seqdbsize, taxonomy, &options);
fprintf(stderr,"Database is constituted of %5d examples\n",insamples);
fprintf(stderr," and %5d counterexamples\n",outsamples);
fprintf(stderr,"Database is constituted of %5d examples corresponding to %5d %s\n",insamples,
options.intaxa,options.taxonrank);
fprintf(stderr," and %5d counterexamples corresponding to %5d %s\n",outsamples,
options.outtaxa,options.taxonrank);
fprintf(stderr,"Total distinct %s count %d\n",options.taxonrank, rankdbstats);
fprintf(stderr,"\nIndexing words in sequences\n");
......@@ -419,7 +560,7 @@ int main(int argc, char **argv)
printcurrenttimeinmilli();
words = lookforStrictPrimer(seqdb,seqdbsize,insamples,&options);
printcurrenttimeinmilli();
fprintf(stderr,"\n Strict primer count : %d\n",words->size);
if (options.no_multi_match)
......@@ -460,13 +601,15 @@ int main(int argc, char **argv)
/*TR: Added*/
pairs = buildPrimerPairs(seqdb, seqdbsize, primers, &options);
setoktaxforspecificity (&pairs);
printpairs (pairs, &options, rankdbstats, seqdbsize);
ECOFREE(pairs.pairs,"Free pairs table");
// setoktaxforspecificity (&pairs);
printpairs (pairs, &options);
//ECOFREE(pairs.pairs,"Free pairs table");
return 0;
}
src/libecoPCR/ecoError.P 0 → 100644
View file @ e3d922e1
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
src/libecoPCR/ecoIOUtils.P 0 → 100644
View file @ e3d922e1
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
src/libecoPCR/ecoMalloc.P 0 → 100644
View file @ e3d922e1
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
src/libecoPCR/ecodna.P 0 → 100644
View file @ e3d922e1
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
src/libecoPCR/ecofilter.P 0 → 100644
View file @ e3d922e1
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
src/libecoPCR/econame.P 0 → 100644
View file @ e3d922e1
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
src/libecoPCR/ecorank.P 0 → 100644
View file @ e3d922e1
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
src/libecoPCR/ecoseq.P 0 → 100644
View file @ e3d922e1
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
src/libecoPCR/ecotax.P 0 → 100644
View file @ e3d922e1
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
src/libecoprimer/Makefile
View file @ e3d922e1
......@@ -10,7 +10,9 @@ SOURCES = goodtaxon.c \
queue.c \
libstki.c \
sortmatch.c \
pairtree.c \
pairs.c \
taxstats.c \
apat_search.c
SRCS=$(SOURCES)
......
src/libecoprimer/aproxpattern.c
View file @ e3d922e1
......@@ -61,7 +61,7 @@ void encodeSequence(ecoseq_t *seq)
for (i=0;i<seq->SQ_length;i++,data++,cseq++)
{
*data = encoder[(IS_UPPER(*cseq) ? *cseq - 'A' : 'Z')];