Fixed a crash when the output directory was missing.

Author: emarinier

README

@@ -1,6 +1,6 @@
 ======================================================================
 Pollux
-Copyright (C) 2014 Eric Marinier
+Copyright (C) 2014-2015 Eric Marinier
 
 This program is free software: you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by
@@ -24,10 +24,10 @@ produced by second-generation sequencing technologies.
 
 -- Release --
 
-Pollux 1.01
-11 February 2015
+Pollux 1.0.2
+6 June 2015
 
-Added compability with older versions of the GCC compiler.
+Fixed a crash when the output directory was missing.
 
 -- Requirements --
 
@@ -45,6 +45,9 @@ Pollux's command line arguments can be found by running:
 Simple correction:
 ./pollux -i <fastq_reads>
 
+Paired correction:
+./pollux -p -i <fastq_reads_1> <fastq_reads_2> -o ouput
+
 -- Contact --
 
 Brendan McConkey: [email protected]

ReleaseNotes

@@ -1,13 +1,20 @@
 ======================================================================
 
-Pollux 1.01
+Pollux 1.0.2
+6 June 2015
+
+Fixed a crash when the output directory was missing.
+
+======================================================================
+
+Pollux 1.0.1
 11 February 2015
 
 Added compability with older versions of the GCC compiler.
 
 ======================================================================
 
-Pollux 1.00
+Pollux 1.0.0
 4 November 2014
 
 This is the initial release of Pollux.

source/ErrorProcessing.c

@@ -18,9 +18,6 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 */
 
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
 #include "Globals.h"
 #include "Utility.h"
 #include "ErrorProcessing.h"
@@ -29,7 +26,14 @@ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #include "ErrorCorrection.h"
 #include "Reads.h"
 #include "Correction.h"
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
 #include <libgen.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <unistd.h>
 
 unsigned int KMER_SIZE = 31;
 
@@ -107,6 +111,19 @@ void hashReads(Correction* correction)
     }
 }
 
+void checkDirectoryExistsAndCreate(char* directory)
+{
+	const int MISSING = -1;
+
+	struct stat st = {0};
+
+	if (stat(directory, &st) == MISSING) 
+	{
+		printf("Creating directory: %s\n", directory);
+		mkdir(directory, 0700);
+	}
+}
+
 void executePairedCorrection(Correction* correction,
         FILE* leftCorrectedFile, FILE* rightCorrectedFile, 
         FILE* leftGarbageFile, FILE* rightGarbageFile, FILE* extraFile)
@@ -402,14 +419,17 @@ Correction* preprocessing(int numInputFiles, char* inputFileNames, char* outputD
 {
     unsigned int LOW_COVERAGE_THRESHOLD_DEFAULT = 3;
 
-    // Data Structures:
-    KMerHashTable* kmers = newKMerHashTable();
-    Reads** reads = (Reads**)malloc(sizeof(Reads*) * numInputFiles);
-    Correction* correction = (Correction*)malloc(sizeof(Correction));
-    
-    // CREATE READS:      
-    printf("Creating read objects...\n");    
-    for(int i = 0; i < numInputFiles; i++)
+	// DATA STRUCTURES:
+	KMerHashTable* kmers = newKMerHashTable();
+	Reads** reads = (Reads**)malloc(sizeof(Reads*) * numInputFiles);
+	Correction* correction = (Correction*)malloc(sizeof(Correction));
+
+	// OUTPUT DIRECTORY:
+	checkDirectoryExistsAndCreate(outputDirectory);
+
+	// CREATE READS:      
+	printf("Creating read objects...\n");    
+	for(int i = 0; i < numInputFiles; i++)
     {
         char* inputFileName = &(inputFileNames[i * 200]);
         printf("Reading file: %s\n", inputFileName);

source/main.c

@@ -128,7 +128,7 @@ int main(int argc, char**argv)
     bool filtering = true;
 
     printf("\n");
-    printf("Pollux 1.00\n");
+    printf("Pollux 1.0.2\n");
     printf("Source compiled on %s at %s.\n", __DATE__, __TIME__);
     printf("\n");