C语言计算fastq文件GC含量2

改进了一下，利用zlib可以读取gz格式的压缩文件，也可以直接计算非压缩格式

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <zlib.h>

#define buff 1024

typedef unsigned long long int u_llong;

static void usage(int num,const char *str)
{
	if(num !=2)
	{
		fprintf(stderr,"usage: %s fqFile\n",str);
		exit(0);
	}
}

static u_llong* gcN(char base[buff])
{
	base[strlen(base)-1]='\0'; 
	
	int i;
	static u_llong gactn[]={0,0,0,0,0};
	for(i=0; i<strlen(base); i++)
	{
		if(base[i]=='G')
			gactn[0]++; 
		if(base[i]=='A')
			gactn[1]++; 
		if(base[i]=='C')
			gactn[2]++;
		if(base[i]=='T')
			gactn[3]++; 
		if(base[i]=='N')
			gactn[4]++;
	}
	return gactn;
}

static void calc(const char *fqfile)
{
	//FILE *fq;
	gzFile fq;
	if((fq=gzopen(fqfile,"r")) == NULL)
	{
		perror("fopen");
		exit(1);
	}
	//fprintf(stderr,"fq file <%s> open suceed!\n",fqfile);
	
	char base[buff];
	char qual=0;
	u_llong *p=NULL;
	while((gzgets(fq,base,buff))!= NULL)  //  这里用 gzgets 替代 fgets
	{
		if(base[0]=='@')
		{
			continue;
		}
		if(base[0]=='+')
		{
			qual=1;
			continue;
		}
		if(qual==1)
		{
			qual=0;
			continue;
		}
		
		p=gcN(base); // G A C T N
	}

	float GClevel; 
	u_llong sum=0;
	for(int i=0; i<5; i++)
	{
		sum+=*(p+i);
	}
	GClevel=(float)(*p+*(p+2)) / sum * 100;
	
	fprintf(stdout,"G:%lld\tA:%lld\nC:%lld\tT:%lld\nN:%lld\tsum:%lld\n",*p,*(p+1),*(p+2),*(p+3),*(p+4),sum);
	fprintf(stdout,"GC:%.2f%%\n",GClevel);
}

int main(int argc,const char *argv[])
{		
	usage(argc,argv[0]);
	calc(argv[1]);

	exit(0);
}

　备注： gcc编译记得添加参数 -lz