add user configuration

config.c

@@ -0,0 +1,171 @@
+//
+//  config.c
+//  PASSFinder
+//
+//  Created by Georgi Tushev on 07/09/16.
+//  Copyright © 2016 Scientific Computing. All rights reserved.
+//
+
+#include "config.h"
+
+const char VERSION[] = "v0.01";
+const char PROGRAM_NAME[] = "FastPASSFinder";
+
+int parseSettings(int argc, char *argv[], Settings *config)
+{
+    // initialize default values
+    config->input = NULL;
+    config->maskpoly = NULL;
+    config->output = NULL;
+    config->window = DEFAULT_WINDOW;
+    config->depth = DEFAULT_DEPTH;
+    config->sizepoly = DEFAULT_SIZEPOLY;
+
+    if(argc < 5)
+    {
+        fprintf(stderr,"Error:: provide input and output streams!\n");
+        return EXIT_FAILURE;
+    }
+
+    // do some parsing
+    for(int i = 1; i < argc; i++)
+    {
+        // current paramter length
+        uint64_t parameterLength = strlen(argv[i]);
+
+        // check each parameter and its value
+        if((PARAMETER_CHECK("-h", 2, parameterLength)) ||
+           (PARAMETER_CHECK("--help", 6, parameterLength)))
+        {
+            help();
+        }
+        else if((PARAMETER_CHECK("-v", 2, parameterLength)) ||
+                (PARAMETER_CHECK("--version", 9, parameterLength)))
+        {
+            version();
+        }
+        else if((PARAMETER_CHECK("-w", 2, parameterLength)) || (PARAMETER_CHECK("--window", 8, parameterLength)))
+        {
+            i += 1;
+            config->window = strtol(argv[i], NULL, 10);
+
+            if (config->window <= 0)
+            {
+                fprintf(stderr, "Error:: window size should be >0!\n");
+                return EXIT_FAILURE;
+            }
+        }
+        else if((PARAMETER_CHECK("-d", 2, parameterLength)) ||
+                (PARAMETER_CHECK("--depth", 7, parameterLength)))
+        {
+            i += 1;
+            config->depth = strtol(argv[i], NULL, 10);
+
+            if(config->depth <= 0)
+            {
+                fprintf(stderr,"Error:: base depth should be >0!\n");
+                return EXIT_FAILURE;
+            }
+
+        }
+        else if((PARAMETER_CHECK("-p", 2, parameterLength)) ||
+                (PARAMETER_CHECK("--polysize", 10, parameterLength)))
+        {
+            i += 1;
+            config->sizepoly = strtol(argv[i], NULL, 10);
+
+            if(config->sizepoly <= 0)
+            {
+                fprintf(stderr,"Error:: read poly tail/head size should be >0!\n");
+                return EXIT_FAILURE;
+            }
+
+        }
+        else if((PARAMETER_CHECK("-i", 2, parameterLength)) ||
+                (PARAMETER_CHECK("--input", 7, parameterLength)))
+        {
+            i += 1;
+
+            config->input = argv[i];
+
+            if (config->input == NULL)
+            {
+                fprintf(stderr,"Error:: could not open input stream!\n");
+                return EXIT_FAILURE;
+            }
+        }
+        else if((PARAMETER_CHECK("-m", 2, parameterLength)) ||
+                (PARAMETER_CHECK("--maskpoly", 10, parameterLength)))
+        {
+            i += 1;
+
+            config->maskpoly = argv[i];
+
+            if (config->maskpoly == NULL)
+            {
+                fprintf(stderr, "Error:: could not open genome poly mask file!\n");
+                return EXIT_FAILURE;
+            }
+
+        }
+        else if((PARAMETER_CHECK("-o", 2, parameterLength)) ||
+                (PARAMETER_CHECK("--output", 8, parameterLength)))
+        {
+            i += 1;
+
+            config->output = argv[i];
+
+            if (config->output == NULL)
+            {
+                fprintf(stderr, "Error:: could not open file output stream!\n");
+                return EXIT_FAILURE;
+            }
+
+        }
+        else
+        {
+            fprintf(stderr, "Error:: Unknown parameter %s\n", argv[i]);
+            return EXIT_FAILURE;
+        }
+
+
+    }
+
+    return 0;
+}
+
+int version(void)
+{
+    fprintf(stderr, "FastPASSFinder %s\n", VERSION);
+    return 0;
+}
+
+int help(void)
+{
+
+    fprintf(stderr, "\nTool: FastPASSFinder\n");
+    fprintf(stderr, "Version: %s\n", VERSION);
+    fprintf(stderr, "Summary:\n");
+    fprintf(stderr, "\tCluster PolyA supported sites from 3'End sequencing.\n");
+    fprintf(stderr, "\nUsage:\t%s [OPTIONS] -i/--input <bam/stdin> -m/--maskpoly <bed> -o/--output <bed/stdout>\n", PROGRAM_NAME);
+    fprintf(stderr, "Options:\n");
+    fprintf(stderr, "\t-i/--input BAM/stdin file\n");
+    fprintf(stderr, "\t-o/--output BED/stdout file\n");
+    fprintf(stderr, "\t-m/--maskpoly BED/stdin file with genomic poly regions\n");
+    fprintf(stderr, "\t-w/--window\tsliding window size\n");
+    fprintf(stderr, "\t-d/--depth\tminimum number of polyA reads to define PASS\n");
+    fprintf(stderr, "\t-p/--polysize\tminimum number of As for tail and Ts for head to define poly stretch\n");
+    fprintf(stderr, "\t-h/--help\tprint help message\n");
+    fprintf(stderr, "\t-v/--version\tprint current version\n");
+    return 1;
+}
+
+int chompNewLine(char *line_buf)
+{
+    size_t  line_length;
+    line_length = strlen(line_buf) - 1;
+    if(line_buf[line_length] == '\n')
+        line_buf[line_length] = '\0';
+
+    return 0;
+}

config.h

@@ -0,0 +1,47 @@
+//
+//  config.h
+//  PASSFinder
+//
+//  Created by Georgi Tushev on 07/09/16.
+//  Copyright © 2016 Scientific Computing. All rights reserved.
+//
+
+#ifndef config_h
+#define config_h
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+// define some constants
+#define MAX_LENGTH 1024
+#define DEFAULT_WINDOW 200
+#define DEFAULT_DEPTH 5
+#define DEFAULT_SIZEPOLY 3
+
+// define MIN & MAX macros
+#define MIN(a,b) (((a)<(b))?(a):(b))
+#define MAX(a,b) (((a)>(b))?(a):(b))
+
+// define our parameter checking macro
+#define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, MIN(actualLen, paramLen))== 0) && (actualLen == paramLen)
+
+
+// define parameters
+typedef struct _Settings
+{
+    char *input;
+    char *maskpoly;
+    char *output;
+    int64_t window;
+    int64_t depth;
+    int64_t sizepoly;
+} Settings;
+
+// function declarations
+int chompNewLine(char *);
+int parseSettings(int, char **, Settings *);
+int help(void);
+int version(void);
+
+#endif /* config_h */