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Some linux patch

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git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@212 60f365c0-8329-0410-b2a4-ec073aeeaa1d
This commit is contained in:
Eric Coissac
2009-05-12 15:48:59 +00:00
parent 04ee4e531c
commit 5dc55c7f53
1 changed files with 9 additions and 2 deletions
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11
src/libecoprimer/strictprimers.c
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@ -5,14 +5,18 @@
* Author: coissac * Author: coissac
*/ */
#define _GNU_SOURCE
#include "ecoprimer.h" #include "ecoprimer.h"
#include <string.h> #include <string.h>
#include <math.h> #include <math.h>
#include <sys/resource.h> #include <sys/resource.h>
#include <unistd.h> #include <unistd.h>
#include <stdio.h>
#ifndef RUSAGE_SELF
#define RUSAGE_SELF 0 #define RUSAGE_SELF 0
#define RUSAGE_CHILDREN -1 #define RUSAGE_CHILDREN -1
#endif
static double timeval_subtract (struct timeval *x, struct timeval *y); static double timeval_subtract (struct timeval *x, struct timeval *y);
@ -187,7 +191,8 @@ pwordcount_t lookforStrictPrimer(pecodnadb_t database, uint32_t seqdbsize,
seconde = timeval_subtract(&(usage.ru_utime),&(start.ru_utime)) + seconde = timeval_subtract(&(usage.ru_utime),&(start.ru_utime)) +
timeval_subtract(&(usage.ru_stime),&(start.ru_stime)); timeval_subtract(&(usage.ru_stime),&(start.ru_stime));
fprintf(logfile,"%d\t%llu\t%lu\t%8.3f\t%8.3e\n",i, fprintf(logfile,"%d\t%llu\t%lu\t%8.3f\t%8.3e\n",i,
totallength,strictprimers->size*sizeof(int64_t), (long long unsigned)totallength,
strictprimers->size*sizeof(int64_t),
seconde,seconde/(double)totallength); seconde,seconde/(double)totallength);
fclose(logfile); fclose(logfile);
} }
@ -195,7 +200,9 @@ pwordcount_t lookforStrictPrimer(pecodnadb_t database, uint32_t seqdbsize,
else else
strictprimers->outseqcount++; strictprimers->outseqcount++;
fprintf(stderr," Indexed sequences %5d/%5d : considered words %-10d \r",(int32_t)i+1,(int32_t)seqdbsize,strictprimers->size); fprintf(stderr," Indexed sequences %5d/%5d : considered words %-10llu \r",
(int32_t)i+1,(int32_t)seqdbsize,
(long long unsigned)strictprimers->size);
// DEBUG_LOG("First word : %s ==> %d",ecoUnhashWord(strictprimers->words[0],18),strictprimers->incount[0]) // DEBUG_LOG("First word : %s ==> %d",ecoUnhashWord(strictprimers->words[0],18),strictprimers->incount[0])
// DEBUG_LOG("Second word : %s ==> %d",ecoUnhashWord(strictprimers->words[1],18),strictprimers->incount[1]) // DEBUG_LOG("Second word : %s ==> %d",ecoUnhashWord(strictprimers->words[1],18),strictprimers->incount[1])