Initial commit.

Makefile

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+# MAKEFILE SOURCE:
+# Author: yanick.rochon@gmail.com
+# Date  : 2011-08-10
+
+# project name (generate executable with this name)
+TARGET   = pollux
+
+CC       = gcc
+# compiling flags here
+CFLAGS   = -std=c99 -I.
+
+LINKER   = gcc -o
+# linking flags here
+LFLAGS   = -Wall -I. -lm
+
+# change these to set the proper directories where each files should be
+SRCDIR   = source
+OBJDIR   = source
+BINDIR   = .
+
+SOURCES  := $(wildcard $(SRCDIR)/*.c)
+INCLUDES := $(wildcard $(SRCDIR)/*.h)
+OBJECTS  := $(SOURCES:$(SRCDIR)/%.c=$(OBJDIR)/%.o)
+rm       = rm -f
+
+
+$(BINDIR)/$(TARGET): $(OBJECTS)
+	@$(LINKER) $@ $(LFLAGS) $(OBJECTS)
+	@echo "Linking complete!"
+
+$(OBJECTS): $(OBJDIR)/%.o : $(SRCDIR)/%.c
+	@$(CC) $(CFLAGS) -c $< -o $@
+	@echo "Compiled "$<" successfully!"
+
+.PHONEY: clean
+clean:
+	@$(rm) $(OBJECTS)
+	@echo "Cleanup complete!"
+
+.PHONEY: remove
+remove: clean
+	@$(rm) $(BINDIR)/$(TARGET)
+	@echo "Executable removed!"
+
+

README

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+======================================================================
+Pollux
+Copyright (C) 2014 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
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+======================================================================
+
+-- Description --
+
+Pollux is a platform independent error corrector which targets errors 
+produced by second-generation sequencing technologies.
+
+-- Release --
+
+Pollux 1.00
+4 November 2014
+
+This is the initial release of Pollux.
+
+-- Requirements --
+
+Pollux requires a 64 bit Unix-based operating system.
+
+-- Installation --
+
+make
+
+-- Running Pollux --
+
+Pollux's command line arguments can be found by running:
+./pollux
+
+Simple correction:
+./pollux -i <fastq_reads>
+
+-- Contact --
+
+Brendan McConkey: mcconkey@uwaterloo.ca
+Eric Marinier: eric.marinier@uwaterloo.ca
+
+-- Credits --
+
+The Makefile is derived from yanick.rochon@gmail.com (2010-11-05).
+(http://stackoverflow.com/users/320700/yanick-rochon)
+
+The source makes use of data structures provided by Simon Howard.
+(http://c-algorithms.sourceforge.net/)
+
+

source/Correction.c

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+/*
+
+Pollux
+Copyright (C) 2014  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
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+*/
+
+#include <stdlib.h>
+#include "Correction.h"
+
+Correction* createCorrection(Reads** reads, unsigned int numReadSets,
+        KMerHashTable* kmers, unsigned int kmerSize, unsigned int lowKMerThreshold,
+        char* outputDirectory, CorrectionFunction correctionFunction)
+{
+    Correction* correction = (Correction*)malloc(sizeof(Correction));
+
+    correction->reads = reads;
+    correction->numReadSets = numReadSets;
+
+    correction->kmers = kmers;
+    correction->kmerSize = kmerSize;
+    correction->lowKMerThreshold = lowKMerThreshold;
+
+    correction->substitutions = true;
+    correction->insertions = true;
+    correction->deletions = true;
+    correction->homopolymers = true;
+
+    correction->outputDirectory = outputDirectory;
+
+    correction->correctionFunction = correctionFunction;
+
+    return correction;
+}
+
+Reads** correctionGetReads(Correction* correction)
+{
+    return correction->reads;
+}
+
+unsigned int correctionGetNumReadSets(Correction* correction)
+{
+    return correction->numReadSets;
+}
+
+KMerHashTable* correctionGetKMers(Correction* correction)
+{
+    return correction->kmers;
+}
+
+unsigned int correctionGetKMerSize(Correction* correction)
+{
+    return correction->kmerSize;
+}
+
+unsigned int correctionGetLowThreshold(Correction* correction)
+{
+    return correction->lowKMerThreshold;
+}
+
+CorrectionFunction correctionGetFunction(Correction* correction)
+{
+    return correction->correctionFunction;
+}
+
+char* correctionGetOutputDirectory(Correction* correction)
+{
+    return correction->outputDirectory;
+}

source/Correction.h

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+/*
+
+Pollux
+Copyright (C) 2014  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
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+*/
+
+#include "Reads.h"
+#include "KMerHashTable.h"
+#include "Utility.h"
+
+#ifndef CORRECTION_H
+#define	CORRECTION_H
+
+#ifdef	__cplusplus
+extern "C" {
+#endif
+
+typedef struct Correction Correction;
+typedef bool (*CorrectionFunction)(struct read* read, Correction* correction);
+
+struct Correction
+{
+    Reads** reads;
+    unsigned int numReadSets;
+
+    KMerHashTable* kmers;
+    unsigned int kmerSize;   
+    unsigned int lowKMerThreshold;
+
+    // Enabled Corrections:
+    bool substitutions;
+    bool insertions;
+    bool deletions;
+    bool homopolymers;
+
+    bool filtering;
+    bool qualityUpdating;
+
+    char* outputDirectory;
+
+    CorrectionFunction correctionFunction;    // Correction function pointer.
+
+};
+
+Correction* createCorrection(Reads** reads, unsigned int numReadSets,
+        KMerHashTable* kmers, unsigned int kmerSize, unsigned int lowKMerThreshold,
+        char* outputDirectory, CorrectionFunction correctionFunction);
+
+Reads** correctionGetReads(Correction* correction);
+unsigned int correctionGetNumReadSets(Correction* correction);
+KMerHashTable* correctionGetKMers(Correction* correction);
+unsigned int correctionGetKMerSize(Correction* correction);
+unsigned int correctionGetLowThreshold(Correction* correction);
+CorrectionFunction correctionGetFunction(Correction* correction);
+char* correctionGetOutputDirectory(Correction* correction);
+
+#ifdef	__cplusplus
+}
+#endif
+
+#endif	/* CORRECTION_H */
+

source/Counting.c

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+/*
+
+Pollux
+Copyright (C) 2014  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
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+*/
+
+#include "Counting.h"
+#include "Utility.h"
+
+void getKMerCounts(unsigned long long int* sequence, unsigned int length, 
+        KMerHashTable* kmers,  unsigned int kmerSize, unsigned int* counts)
+{
+    // Variables:
+    unsigned long long int kmer;
+    int total = length - kmerSize + 1;
+
+    // Iterate over all k-mers within the read:
+    for(int i = 0; i < total; i++)
+    {
+        // Get the next k-mer:
+        kmer = getKMer(sequence, i, i + kmerSize);
+
+        // Get the count:     
+        counts[i] = KMerTableLookup(kmers, kmer);
+    }
+}
+
+unsigned int areCountsBelowThreshold(unsigned int* counts, unsigned int start, 
+        unsigned int end, const unsigned int THRESHOLD)
+{
+    for(int i = start; i < end; i++)
+    {        
+        if(counts[i] > THRESHOLD)
+        {
+            return 0;
+        }
+    }
+
+    return 1;
+}

source/Counting.h

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+/*
+
+Pollux
+Copyright (C) 2014  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
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+*/
+
+#include "KMerHashTable.h"
+
+#ifndef COUNTING_H
+#define	COUNTING_H
+
+#ifdef	__cplusplus
+extern "C" {
+#endif
+
+/**
+ * This function fills the passed array with the number of the occurances of a 
+ * given k-mer over the entire length of the sequence.
+ * 
+ * @param sequence The sequence to get the k-mer counts for.
+ * @param length The length of the sequence.
+ * @param kmers The k-mer hash table data structure.
+ * @param kmerSize The length of the kmers.
+ * @param counts The counts array to fill. There will be (length - kmerSize + 1) 
+ *      entries expected to be filled.
+ */    
+void getKMerCounts(unsigned long long int* sequence, unsigned int length, 
+        KMerHashTable* kmers,  unsigned int kmerSize, unsigned int* counts);
+
+/**
+ * This function determines whether or not all the entries between the specified 
+ * range in the passed array are below the given threshold.
+ * 
+ * @param counts The array to examine.
+ * @param start The starting index.
+ * @param end The ending index.
+ * @param THRESHOLD The threshold. Less than or equal to the threshold!
+ * 
+ * @return Whether or not the values are less than or equal to the threshold.
+ */
+unsigned int areCountsBelowThreshold(unsigned int* counts, unsigned int start, 
+        unsigned int end, const unsigned int THRESHOLD);
+
+
+#ifdef	__cplusplus
+}
+#endif
+
+#endif	/* COUNTING_H */
+