Using klib

Process_Read.cpp

@@ -2,163 +2,58 @@
 #include <stdlib.h>
 #include <stdio.h>
 #include <string.h>
-#include <zlib.h>
 #include <fcntl.h>
 
 
-int format = -1;
-FILE *_r_fp = NULL;
-gzFile g_r_fp;
+gzFile fp;
+kseq_t *seq;
 
-
-int check_file_format(char *fileName)
+void init_kseq(char* file)
 {
-	int i = 0;
+	fp = gzopen(file, "r");
+  	seq = kseq_init(fp);
+}
 
-	char* file_extention;
-	i = strlen(fileName) - 1;
-	while (i >= 0 && fileName[i] != '.')
-	{
-		i--;
-	}
-
-	if (i < 0)
-	{
-		fprintf(stderr, 
-			"ERROR: the input read files must be FASTQ format (file extension: .fq or .fastq) or compressed FASTQ format (file extension: .fq.gz or .fastq.gz)!\n");
-		exit(0);
-	}
-
-	if ((strcmp(".fq", fileName+i) == 0)
-		||
-		strcmp(".fastq", fileName + i) == 0)
-	{
-		return FASTQ;
-	}
-	else if (strcmp(".gz", fileName + i) == 0)
-	{
-		i--;
-		while (i >= 0 && fileName[i] != '.')
-		{
-			i--;
-		}
-
-
-		if (i < 0)
-		{
-			fprintf(stderr,
-				"ERROR: the input read files must be FASTQ format (file extension: .fq or .fastq) or compressed FASTQ format (file extension: .fq.gz or .fastq.gz)!\n");
-			exit(0);
-		}
-
-		if ((strcmp(".fq.gz", fileName + i) == 0)
-			||
-			strcmp(".fastq.gz", fileName + i) == 0)
-		{
-			return FASTQGZ;
-		}
-		else
-		{
-			fprintf(stderr,
-				"ERROR: the input read files must be FASTQ format (file extension: .fq or .fastq) or compressed FASTQ format (file extension: .fq.gz or .fastq.gz)!\n");
-			exit(0);
-		}
-
-	}
-
-
-	fprintf(stderr,
-		"ERROR: the input read files must be FASTQ format (file extension: .fq or .fastq) or compressed FASTQ format (file extension: .fq.gz or .fastq.gz)!\n");
-	exit(0);
+void destory_kseq()
+{
+	kseq_destroy(seq);
+  	gzclose(fp);
 }
 
 
-int initiReadAllReads(char *fileName)
+inline void exchage_kstring_t(kstring_t* a, kstring_t* b)
 {
-
-	format = check_file_format(fileName);
-
-    if (format == FASTQ)
-	{
-		_r_fp = fopen(fileName, "r");
-
-		if (_r_fp == NULL)
-		{
-			return 0;
-		}
-
-        fprintf(stdout,
-				" Read files are in FASTQ format...\n");
-	}
-	else if (format == FASTQGZ)
-	{
-		int fd = open(fileName, O_CREAT | O_RDONLY, 0666);
-		g_r_fp = gzdopen(fd, "rb");
-
-        fprintf(stdout,
-				" Read files are in compressed FASTQ format...\n");
-	}
-    else
-    {
-        fprintf(stderr,
-			"ERROR: the input read files must be FASTQ format (file extension: .fq or .fastq) or compressed FASTQ format (file extension: .fq.gz or .fastq.gz)!\n");
-		exit(0);
-    }
-    
+	kstring_t tmp;
+	tmp = *a;
+	*a = *b;
+	*b = tmp;
 }
 
-#define BUFFER_SIZE 20000
-char Read_Buffer[BUFFER_SIZE];
-char true_flag[2];
-
-
-inline char *Input_line_from_file(char *seq)
+int get_read(kseq_t *s)
 {
-	if (format == FASTQ)
+	int l;
+
+	if ((l = kseq_read(seq)) >= 0)
 	{
-		return fgets(Read_Buffer, BUFFER_SIZE, _r_fp);
+		
+		exchage_kstring_t(&seq->comment, &s->comment);
+		exchage_kstring_t(&seq->name, &s->name);
+		exchage_kstring_t(&seq->qual, &s->qual);
+		exchage_kstring_t(&seq->seq, &s->seq);
+		
+		return 1;
 	}
 	else
 	{
-		seq = gzgets(g_r_fp, seq, BUFFER_SIZE);
-
-		return (!gzeof(g_r_fp)) ? true_flag : NULL;
-
-	}
-  
-}
-
-inline int get_whole_line(str_v* line)
-{
-	while(Input_line_from_file(Read_Buffer))
-	{
-		append_str(line, Read_Buffer);
-
-		if (line->centext[line->length - 1] == '\n')
-		{
-			line->length--;
-			line->centext[line->length] = '\0';
-			return 1;
-		}
-		
-	}
-
-	return 0;
-}
-
-
-int inputRead(Read *read)
-{
-	int buffer_length;
-
-	if (get_whole_line(&read->name))
-	{
-		get_whole_line(&read->seq);
-		Input_line_from_file(Read_Buffer);
-		get_whole_line(&read->qual);
-		return 1;
+		return 0;
 	}
 	
-	return 0;
+	
+}
+
+
+
+
+
+
 
-}