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

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#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