Using klib

Process_Read.h

@@ -4,73 +4,15 @@
 #include<stdint.h>
 #include <string.h>
 #include <stdlib.h>
+#include <zlib.h>
+#include "kseq.h"
 
 
-#define FASTQ 1
-#define FASTQGZ 2
+KSEQ_INIT(gzFile, gzread)
 
-#define NAME_SZIE 25
-#define SEQ_SZIE 20000
+void init_kseq(char* file);
+void destory_kseq();
+int get_read(kseq_t *s);
 
 
-typedef struct
-{
-	char* centext;
-	uint32_t length;
-	uint32_t size;
-
-}str_v;
-
-
-inline void init_str_v(str_v* buf, uint32_t length)
-{
-	buf->size = length + 1;
-	buf->length = 0;
-	buf->centext = (char*)malloc(sizeof(char)*buf->size);
-}
-
-
-inline void append_str(str_v* buf, char* input)
-{
-	int length = strlen(input);
-	buf->length = buf->length + length;
-	if (buf->length > buf->size)
-	{
-		buf->centext = (char*)realloc(buf->centext, buf->length + 1);
-	}
-	memcpy(buf->centext + buf->length - length, input, length);
-	buf->centext[buf->length] = '\0';
-}
-
-inline void clear_str(str_v* buf)
-{
-	buf->length = 0;
-}
-
-typedef struct
-{
-	str_v name;
-	str_v seq;
-	str_v qual;
-
-} Read;
-
-inline void init_Read(Read* r)
-{
-	init_str_v(&r->name, NAME_SZIE);
-	init_str_v(&r->seq, SEQ_SZIE);
-	init_str_v(&r->qual, SEQ_SZIE);
-}
-
-inline void clear_read(Read* r)
-{
-	clear_str(&r->name);
-	clear_str(&r->seq);
-	clear_str(&r->qual);
-}
-
-
-int initiReadAllReads(char *fileName);
-int inputRead(Read *read);
-
 #endif