obitools/ecoprimers
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fixed segmentation fault reported by Pierre.

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git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@289 60f365c0-8329-0410-b2a4-ec073aeeaa1d
This commit is contained in:
Eric Coissac
2010-12-16 20:56:57 +00:00
parent 5d8103f4b4
commit 4c9c8382fe
2 changed files with 81 additions and 2 deletions
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32
src/libecoprimer/strictprimers.c
View File

@ -132,7 +132,7 @@ pwordcount_t lookforStrictPrimer(pecodnadb_t database, uint32_t seqdbsize,
double seconde;
char *logfilename;
FILE *logfile;
uint32_t i;
uint32_t i, j;
bool_t first=TRUE;
pwordcount_t strictprimers=NULL;
uint64_t totallength=0;
@ -232,6 +232,36 @@ pwordcount_t lookforStrictPrimer(pecodnadb_t database, uint32_t seqdbsize,
if (neededWords)
ECOFREE(neededWords,"Clean needed word table");
//TR: Somehow for some primers strictcount value is extremely large hence invalid
//we need to remove these primers from the list
j = strictprimers->size+1;
for (i=0; i<strictprimers->size; i++)
{
if (strictprimers->strictcount[i] > seqdbsize)
{
if (j == (strictprimers->size+1))
j = i;
}
if (j < i && strictprimers->strictcount[i] <= seqdbsize)
{
strictprimers->words[j] = strictprimers->words[i];
strictprimers->strictcount[j] = strictprimers->strictcount[i];
j++;
}
}
if (j < strictprimers->size)
{
strictprimers->size = j;
strictprimers->strictcount = ECOREALLOC(strictprimers->strictcount,
sizeof(uint32_t)*strictprimers->size,
"Cannot reallocate strict primer count table");
strictprimers->words = ECOREALLOC(strictprimers->words,
sizeof(word_t)*strictprimers->size,
"Cannot reallocate strict primer table");
}
return strictprimers;
}

51
src/libecoprimer/taxstats.c
View File

@ -126,7 +126,7 @@ float taxonomycoverage(ppair_t pair, poptions_t options)
return pair->bc;
}
/*
static int cmpamp(const void *ampf1, const void* ampf2)
{
int i;
@ -170,6 +170,55 @@ static int cmpamp(const void *ampf1, const void* ampf2)
if (pampf1->length > pampf2->length) return chd ? -1: 1;
if (pampf2->length > pampf1->length) return chd ? 1: -1;
return 0;
}*/
static int cmpamp(const void *ampf1, const void* ampf2)
{
int i;
char cd1;
char cd2;
int len = 0;
char *ch1;
char *ch2;
int incr1;
int incr2;
pamptotaxon_t pampf1 = (pamptotaxon_t) ampf1;
pamptotaxon_t pampf2 = (pamptotaxon_t) ampf2;
ch1 = pampf1->amplifia;
ch2 = pampf2->amplifia;
incr1 = 1;
incr2 = 1;
if (!pampf1->strand)
incr1 = -1;
if (!pampf2->strand)
incr2 = -1;
len = (pampf1->length <= pampf2->length)? pampf1->length: pampf2->length;
for (i = 0; i < len; i++)
{
cd1 = *ch1;
if (incr1 == -1)
cd1 = ecoComplementChar(*ch1);
cd2 = *ch2;
if (incr2 == -1)
cd2 = ecoComplementChar(*ch2);
if (cd1 < cd2) return -1;
if (cd2 < cd1) return 1;
ch1 += incr1;
ch2 += incr2;
}
if (pampf1->length > pampf2->length) return 1;
if (pampf2->length > pampf1->length) return -1;
return 0;
}