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‎LISCENCE‎

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‎Makefile‎

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

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

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

‎source/Correction.h‎

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

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

‎source/Counting.h‎

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