Input reads

Assembly.cpp

@@ -0,0 +1,32 @@
+#include "Assembly.h"
+#include <stdio.h>
+#include <stdlib.h>
+#include "Process_Read.h"
+
+void Counting()
+{
+    Read r;
+    init_Read(&r);
+
+    long long read_number = 0;
+
+    while (inputRead(&r))
+    {
+        
+        fprintf(stderr,"%s\n",r.name);
+        
+        fprintf(stderr,"%s\n",r.seq);
+        fprintf(stderr,"+\n");
+        fprintf(stderr,"%s\n",r.qual);
+        
+
+        read_number++;
+
+        clear_read(&r);
+    }
+    
+    fprintf(stdout, "read_number: %lld\n",read_number);
+
+
+
+}

Assembly.h

@@ -0,0 +1,8 @@
+#ifndef __ASSEMBLY__
+#define __ASSEMBLY__
+
+
+
+void Counting();
+
+#endif

CommandLines.cpp

@@ -0,0 +1,63 @@
+#include "CommandLines.h"
+#include <stdlib.h>
+#include <getopt.h>
+#include <stdio.h>
+
+char* read_file_name = NULL;
+char* output_file_name = NULL;
+int thread_num = 1;
+
+void Print_H()
+{
+    fprintf(stderr, "Incorrect options.\n");
+}
+
+
+
+
+int CommandLine_process (int argc, char *argv[])
+{
+    int o; 
+    int index;
+
+    static struct option longOptions[] =
+    {
+        {"seq",		required_argument, 0, 'q'},
+        {"threads",	required_argument, 0, 't'},
+        {"threads",	required_argument, 0, 'o'},
+        {0,  0,  0, 0},
+    };
+
+
+    while ( (o = getopt_long ( argc, argv, "q:t:o:", longOptions, &index)) != -1 )
+    {
+        switch (o)
+        {
+            case 'q':
+                read_file_name = optarg;
+                break;
+            case 'o':
+                output_file_name = optarg;
+                break;
+            case 't':
+                thread_num = atoi(optarg);
+                break;
+            case '?':
+                fprintf(stderr, "Unrecognized option!\n" );
+                return 0;   
+                break;
+            default:
+                Print_H();
+                return 0;   
+        }
+    }
+
+    if (argc == 1)
+    {
+        Print_H();
+        return 0;
+    }
+
+
+    return 1;
+}

CommandLines.h

@@ -0,0 +1,10 @@
+#ifndef __COMMAND_LINE_PARSER__
+#define __COMMAND_LINE_PARSER__
+
+extern char* read_file_name;
+extern char* output_file_name;
+extern int thread_num;
+
+int CommandLine_process (int argc, char *argv[]);
+
+#endif

Makefile

@@ -0,0 +1,18 @@
+CC=g++
+
+CFLAGS = -w -c -msse4.2 -mpopcnt -fomit-frame-pointer -Winline -O3 -lz
+LDFLAGS = -lm -lz -lpthread -O3 -mpopcnt -msse4.2 -lz -w
+
+SOURCES = main.cpp CommandLines.cpp Process_Read.cpp Assembly.cpp
+OBJECTS = $(SOURCES:.c=.o)
+EXECUTABLE = ccs_assembly
+
+
+all: $(SOURCES) $(EXECUTABLE)
+$(EXECUTABLE): $(OBJECTS)
+	$(CC) $(OBJECTS) -o $@ $(LDFLAGS) 
+
+.c.o:
+	$(CC) $(CFLAGS) $< -o $@ 
+clean:
+	rm -f *.o *~ \#* ccs_assembly

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;
+
+}

Process_Read.h

@@ -0,0 +1,76 @@
+#ifndef __READ__
+#define __READ__
+
+#include<stdint.h>
+#include <string.h>
+#include <stdlib.h>
+
+
+#define FASTQ 1
+#define FASTQGZ 2
+
+#define NAME_SZIE 25
+#define SEQ_SZIE 20000
+
+
+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

main.cpp

@@ -0,0 +1,28 @@
+#include <stdio.h>
+#include <stdlib.h>
+#include "CommandLines.h"
+#include "Process_Read.h"
+#include "Assembly.h"
+
+
+int main(int argc, char *argv[])
+{
+
+    if (!CommandLine_process(argc, argv))
+        return 1;
+
+
+    if (!initiReadAllReads(read_file_name))
+    {
+        fprintf(stdout, "Cannot open read files. \n");
+        return 1;
+    }
+
+
+    Counting();
+
+    
+
+
+    return 1;
+}