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Speed up reading the reference. #5

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Speed up reading the reference. #5

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2 changes: 1 addition & 1 deletion Makefile
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@

#CC=gcc -Wall
CC=gcc -D_GNU_SOURCE
CFLAGS=-c -Wall
CFLAGS=-c -Wall -lz
SAMTOOLS=parsebam/samtools-0.1.18

all:
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34 changes: 18 additions & 16 deletions parsebam/readfasta.c
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Original file line number Diff line number Diff line change
Expand Up @@ -3,9 +3,14 @@
#include<stdlib.h>
#include<string.h>
#include<ctype.h>
#include<time.h>
#include<zlib.h>
#include "readfasta.h"
#define MAX_BUF_SIZE 4096

#include "kseq.h"
KSEQ_INIT(gzFile, gzread)

// initialize the reflist datastructure
REFLIST* init_reflist(char* fastafile,REFLIST* reflist)
{
Expand Down Expand Up @@ -202,25 +207,21 @@ int read_next_chromosome(REFLIST* reflist,int chrom,FILE* fp)
}
int read_fasta(char* seqfile, REFLIST* reflist)
{
FILE* fp = fopen(seqfile,"r");
if (fp == NULL) { fprintf(stderr,"file %s not found \n",seqfile); return -1; }
clock_t t;
kseq_t *seq;
gzFile fp = gzopen(seqfile, "r");
seq = kseq_init(fp);
fprintf(stderr,"reading reference sequence file %s with %d sequences\n",seqfile,reflist->ns);
int i=-1,j=0; char c;
while (c != EOF)
{
c = fgetc(fp);
if (c == '>')
{
while (c != '\n') c = fgetc(fp);
//if (i >= 0)printf("%c %d %d",c,i,j);
i++; j=0;
}
else if (c != '\n' && c != '\t' && c != ' ')
{
reflist->sequences[i][j] = toupper(c); j++;
t = clock();
int i=0, j=0; char c;
while (kseq_read(seq) >= 0) {
memcpy(reflist->sequences[i], seq->seq.s, seq->seq.l);
for (j = 0; j < seq->seq.l; j++) {
reflist->sequences[i][j] = toupper(reflist->sequences[i][j]);
}
i++;
}
fclose(fp);
gzclose(fp); fp=NULL;
for (i=0;i<reflist->ns;i++)
{
reflist->sequences[i][reflist->lengths[i]] = '\0';
Expand All @@ -231,6 +232,7 @@ int read_fasta(char* seqfile, REFLIST* reflist)
fprintf(stderr,"\n");
}
}
fprintf(stderr, "read FASTA in %.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC);
return 1;
}

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