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Optimize memory allocation of the apat algorithms

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Former-commit-id: 5010c5a666b322715b3b81c1078d325e1f647ede
This commit is contained in:
Eric Coissac
2023-03-28 19:37:05 +07:00
parent 21819cd41e
commit 988ae79989
19 changed files with 117 additions and 180 deletions
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103
pkg/obiapat/obiapat.c
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@@ -6,7 +6,7 @@
#include "obiapat.h"
static void EncodeSequence(SeqPtr seq);
static void EncodeSequence(SeqPtr seq, const char *in);
static void UpperSequence(char *seq);
/*
@@ -142,64 +142,6 @@ char *ecoComplementPattern(char *nucAcSeq)
return reverseSequence(LXBioSeqComplement(nucAcSeq),1);
}
char *ecoComplementSequence(char *nucAcSeq)
{
return reverseSequence(LXBioSeqComplement(nucAcSeq),0);
}
char *getSubSequence(char* nucAcSeq,int32_t begin,int32_t end,
int *errno, char **errmsg)
/*
extract subsequence from nucAcSeq [begin,end[
*/
{
static char *buffer = NULL;
static int32_t buffSize= 0;
int32_t length;
if (begin < end)
{
length = end - begin;
if (length >= buffSize)
{
buffSize = length+1;
if (buffer)
buffer=ECOREALLOC(buffer,buffSize,
"Error in reallocating sub sequence buffer",errno,errmsg);
else
buffer=ECOMALLOC(buffSize,
"Error in allocating sub sequence buffer",errno,errmsg);
}
strncpy(buffer,nucAcSeq + begin,length);
buffer[length]=0;
}
else
{
length = end + strlen(nucAcSeq) - begin;
if (length >= buffSize)
{
buffSize = length+1;
if (buffer)
buffer=ECOREALLOC(buffer,buffSize,
"Error in reallocating sub sequence buffer",errno,errmsg);
else
buffer=ECOMALLOC(buffSize,
"Error in allocating sub sequence buffer",errno,errmsg);
}
strncpy(buffer,nucAcSeq+begin,length - end);
strncpy(buffer+(length-end),nucAcSeq ,end);
buffer[length]=0;
}
return buffer;
}
/* -------------------------------------------- */
/* uppercase sequence */
@@ -229,29 +171,27 @@ void UpperSequence(char *seq)
/* -------------------------------------------- */
#define IS_UPPER(c) (((c) >= 'A') && ((c) <= 'Z'))
#define IS_LOWER(c) (((c) >= 'a') && ((c) <= 'z'))
void EncodeSequence(SeqPtr seq)
void EncodeSequence(SeqPtr seq, const char *in)
{
int i;
uint8_t *data;
char *cseq;
const char *cseq;
char nuc;
data = seq->data;
cseq = seq->cseq;
while (*cseq) {
nuc = *cseq & (~32);
*data = (IS_UPPER(nuc) ? nuc - 'A' : 0x0);
data++;
cseq++;
for (i=0,cseq=in; i < seq->seqlen; i++,cseq++,data++) {
nuc = *cseq;
*data = (IS_LOWER(nuc) ? nuc - 'a' : 0x0);
}
for (i=0,cseq=seq->cseq;i < seq->circular; i++,cseq++,data++) {
nuc = *cseq & (~32);
*data = (IS_UPPER(nuc) ? nuc - 'A' : 0x0);
for (i=0,cseq=in; i < seq->circular; i++,cseq++,data++) {
nuc = *cseq;
*data = (IS_LOWER(nuc) ? nuc - 'a' : 0x0);
}
for (i = 0 ; i < MAX_PATTERN ; i++)
@@ -266,6 +206,7 @@ SeqPtr new_apatseq(const char *in,int32_t circular, int32_t seqlen,
SeqPtr out,
int *errno, char **errmsg)
{
// fprintf(stderr,">>>>>>>> new_apatseq\n");
int i;
if (circular != 0) circular=MAX_PAT_LEN;
@@ -287,28 +228,26 @@ SeqPtr new_apatseq(const char *in,int32_t circular, int32_t seqlen,
}
out->seqsiz = out->seqlen = seqlen;
out->circular = circular;
if (!out->data)
{
out->data = ECOMALLOC((out->seqlen+circular) *sizeof(uint8_t),
out->data = ECOMALLOC((seqlen+circular) *sizeof(uint8_t),
"Error in Allocation of a new Seq data member",
errno,errmsg);
out->datsiz= out->seqlen+circular;
out->datsiz= seqlen+circular;
}
else if ((out->seqlen +circular) >= out->datsiz)
else if ((seqlen +circular) >= out->datsiz)
{
out->data = ECOREALLOC(out->data,(out->seqlen+circular) *sizeof(uint8_t),
out->data = ECOREALLOC(out->data,(seqlen+circular) *sizeof(uint8_t),
"Error during Seq data buffer realloc",
errno,errmsg);
out->datsiz= out->seqlen+circular;
out->datsiz= seqlen+circular;
}
out->cseq = (char *)in;
EncodeSequence(out);
out->circular = circular;
out->seqlen = seqlen;
EncodeSequence(out,in);
// fprintf(stderr,">>>>>>>> Encodage ok\n");
return out;
}