Input reads

Process_Read.cpp

@@ -0,0 +1,164 @@
+#include "Process_Read.h"
+#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;
+
+
+int check_file_format(char *fileName)
+{
+	int i = 0;
+
+	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);
+}
+
+
+int initiReadAllReads(char *fileName)
+{
+
+	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);
+    }
+    
+}
+
+#define BUFFER_SIZE 20000
+char Read_Buffer[BUFFER_SIZE];
+char true_flag[2];
+
+
+inline char *Input_line_from_file(char *seq)
+{
+	if (format == FASTQ)
+	{
+		return fgets(Read_Buffer, BUFFER_SIZE, _r_fp);
+	}
+	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;
+
+}