.gitignore

@@ -6,6 +6,7 @@ auxprogs/utrrnaseq/Debug/src/*.o
 auxprogs/utrrnaseq/Debug/utrrnaseq
 auxprogs/utrrnaseq/*.gff
 src/*.o
+src/googletest/*.o
 auxprogs/bam2hints/bam2hints
 auxprogs/bam2hints/bam2hints.o
 auxprogs/bam2wig/bam2wig

.travis.yml

 language: generic
+
+matrix:
+  include:
+  - os: linux
+    dist: xenial
+    sudo: required
+  - os: linux
+    dist: trusty
+    sudo: required
+
 sudo: required
 
+addons:
+  apt:
+    packages:
+      - doxygen
+      - doxygen-doc
+      - doxygen-latex
+      - doxygen-gui
+      - graphviz
+
 services:
   - docker
 
@@ -8,4 +27,16 @@ before_install:
   - printenv | grep -E '^TRAVIS_' > .env
   
 script:
-  - docker build -t augustus .
+  - docker build -f Dockerfile -t augustus .
+  - docker build -f Dockerfile-cgp-file -t augustus-cgp-file .
+  - docker build -f Dockerfile-cgp-mysql -t augustus-cgp-mysql .
+  - docker build -f Dockerfile-cgp-sqlite -t augustus-cgp-sqlite .
+  - doxygen doxygen.conf
+
+deploy:
+  provider: pages
+  skip-cleanup: true
+  local-dir: $TRAVIS_BUILD_DIR/doxygen/html
+  github-token: $GITHUB_API_KEY
+  on:
+    branch: master

Dockerfile

@@ -18,10 +18,7 @@ RUN apt-get install -y libncurses5-dev
 # Install additional dependencies for bam2wig
 RUN apt-get install -y libssl-dev libcurl3-dev
 
-# Clone AUGUSTUS repository
-RUN git clone --recursive https://github.com/Gaius-Augustus/Augustus /root/augustus
-
-# Build bam2wig dependencies (htslib, bfctools, tabix, samtools)
+# Build bam2wig dependencies (htslib, bfctools, samtools)
 RUN git clone https://github.com/samtools/htslib.git /root/htslib
 WORKDIR "/root/htslib"
 RUN autoheader
@@ -36,9 +33,6 @@ RUN autoconf
 RUN ./configure
 RUN make
 RUN make install
-RUN git clone https://github.com/samtools/tabix.git /root/tabix
-WORKDIR "/root/tabix"
-RUN make
 RUN git clone https://github.com/samtools/samtools.git /root/samtools
 WORKDIR "/root/samtools"
 RUN autoheader
@@ -48,8 +42,11 @@ RUN make
 RUN make install
 ENV TOOLDIR="/root"
 
+# Clone AUGUSTUS repository
+ADD / /root/augustus
+
 # Build bam2wig
-RUN mkdir /root/augustus/bin
+RUN mkdir -p /root/augustus/bin
 WORKDIR "/root/augustus/auxprogs/bam2wig"
 RUN make
 
@@ -57,6 +54,7 @@ RUN make
 WORKDIR "/root/augustus"
 RUN make
 RUN make install
+ENV PATH="/root/augustus/bin:${PATH}"
 
 # Test AUGUSTUS
 RUN make test

Dockerfile-cgp-file

+FROM ubuntu:18.04
+
+
+# Install required packages
+RUN apt-get update
+RUN apt-get install -y build-essential wget git autoconf
+
+# Install dependencies for AUGUSTUS
+RUN apt-get install -y libboost-iostreams-dev zlib1g-dev
+RUN apt-get install -y libgsl-dev libboost-graph-dev libsuitesparse-dev liblpsolve55-dev libsqlite3-dev libmysql++-dev
+RUN apt-get install -y libbamtools-dev
+RUN apt-get install -y libboost-all-dev
+
+# Install additional dependencies for htslib and samtools
+RUN apt-get install -y libbz2-dev liblzma-dev
+RUN apt-get install -y libncurses5-dev
+
+# Install additional dependencies for bam2wig
+RUN apt-get install -y libssl-dev libcurl3-dev
+
+# Build bam2wig dependencies (htslib, bfctools, samtools)
+RUN git clone https://github.com/samtools/htslib.git /root/htslib
+WORKDIR "/root/htslib"
+RUN autoheader
+RUN autoconf
+RUN ./configure
+RUN make
+RUN make install
+RUN git clone https://github.com/samtools/bcftools.git /root/bcftools
+WORKDIR "/root/bcftools"
+RUN autoheader
+RUN autoconf
+RUN ./configure
+RUN make
+RUN make install
+RUN git clone https://github.com/samtools/samtools.git /root/samtools
+WORKDIR "/root/samtools"
+RUN autoheader
+RUN autoconf -Wno-syntax
+RUN ./configure
+RUN make
+RUN make install
+ENV TOOLDIR="/root"
+
+# Clone AUGUSTUS repository
+ADD / /root/augustus
+
+WORKDIR "/root/augustus"
+
+RUN sed -i "s/# COMPGENEPRED = true/COMPGENEPRED = true/g" /root/augustus/common.mk
+
+# Build bam2wig
+RUN mkdir -p /root/augustus/bin
+WORKDIR "/root/augustus/auxprogs/bam2wig"
+RUN make
+
+# Build AUGUSTUS
+WORKDIR "/root/augustus"
+RUN make
+RUN make install
+
+# Test AUGUSTUS
+RUN make test
+

Dockerfile-cgp-mysql

+FROM ubuntu:18.04
+
+
+# Install required packages
+RUN apt-get update
+RUN apt-get install -y build-essential wget git autoconf
+
+# Install dependencies for AUGUSTUS
+RUN apt-get install -y libboost-iostreams-dev zlib1g-dev
+RUN apt-get install -y libgsl-dev libboost-graph-dev libsuitesparse-dev liblpsolve55-dev libsqlite3-dev libmysql++-dev
+RUN apt-get install -y libbamtools-dev
+RUN apt-get install -y libboost-all-dev
+
+# Install additional dependencies for htslib and samtools
+RUN apt-get install -y libbz2-dev liblzma-dev
+RUN apt-get install -y libncurses5-dev
+
+# Install additional dependencies for bam2wig
+RUN apt-get install -y libssl-dev libcurl3-dev
+
+# Build bam2wig dependencies (htslib, bfctools, samtools)
+RUN git clone https://github.com/samtools/htslib.git /root/htslib
+WORKDIR "/root/htslib"
+RUN autoheader
+RUN autoconf
+RUN ./configure
+RUN make
+RUN make install
+RUN git clone https://github.com/samtools/bcftools.git /root/bcftools
+WORKDIR "/root/bcftools"
+RUN autoheader
+RUN autoconf
+RUN ./configure
+RUN make
+RUN make install
+RUN git clone https://github.com/samtools/samtools.git /root/samtools
+WORKDIR "/root/samtools"
+RUN autoheader
+RUN autoconf -Wno-syntax
+RUN ./configure
+RUN make
+RUN make install
+ENV TOOLDIR="/root"
+
+# Clone AUGUSTUS repository
+ADD / /root/augustus
+
+RUN sed -i "s/#.*MYSQL = true/MYSQL = true/g" /root/augustus/common.mk
+RUN sed -i "s/# COMPGENEPRED = true/COMPGENEPRED = true/g" /root/augustus/common.mk
+
+# Build bam2wig
+RUN mkdir -p /root/augustus/bin
+WORKDIR "/root/augustus/auxprogs/bam2wig"
+RUN make
+
+# Build AUGUSTUS
+WORKDIR "/root/augustus"
+RUN make
+RUN make install
+
+# Test AUGUSTUS
+RUN make test
+
+

Dockerfile-cgp-sqlite

+FROM ubuntu:18.04
+
+# Install required packages
+RUN apt-get update
+RUN apt-get install -y build-essential wget git autoconf
+
+# Install dependencies for AUGUSTUS
+RUN apt-get install -y libboost-iostreams-dev zlib1g-dev
+RUN apt-get install -y libgsl-dev libboost-graph-dev libsuitesparse-dev liblpsolve55-dev libsqlite3-dev libmysql++-dev
+RUN apt-get install -y libbamtools-dev
+RUN apt-get install -y libboost-all-dev
+
+# Install additional dependencies for htslib and samtools
+RUN apt-get install -y libbz2-dev liblzma-dev
+RUN apt-get install -y libncurses5-dev
+
+# Install additional dependencies for bam2wig
+RUN apt-get install -y libssl-dev libcurl3-dev
+
+# Build bam2wig dependencies (htslib, bfctools, samtools)
+RUN git clone https://github.com/samtools/htslib.git /root/htslib
+WORKDIR "/root/htslib"
+RUN autoheader
+RUN autoconf
+RUN ./configure
+RUN make
+RUN make install
+RUN git clone https://github.com/samtools/bcftools.git /root/bcftools
+WORKDIR "/root/bcftools"
+RUN autoheader
+RUN autoconf
+RUN ./configure
+RUN make
+RUN make install
+RUN git clone https://github.com/samtools/samtools.git /root/samtools
+WORKDIR "/root/samtools"
+RUN autoheader
+RUN autoconf -Wno-syntax
+RUN ./configure
+RUN make
+RUN make install
+ENV TOOLDIR="/root"
+
+# Clone AUGUSTUS repository
+ADD / /root/augustus
+
+RUN sed -i "s/# SQLITE = true/SQLITE = true/g" /root/augustus/common.mk
+RUN sed -i "s/# COMPGENEPRED = true/COMPGENEPRED = true/g" /root/augustus/common.mk
+
+# Build bam2wig
+RUN mkdir -p /root/augustus/bin
+WORKDIR "/root/augustus/auxprogs/bam2wig"
+RUN make
+
+# Build AUGUSTUS
+WORKDIR "/root/augustus"
+RUN make
+RUN make install
+
+# Test AUGUSTUS
+RUN make test
+

HISTORY.TXT

+List of changes from version 3.3.2 to 3.3.3 (until Sep 13th, 2019)
+     - docker container
+     - new script tfix_in_frame_stop_codon_genes.py that replaces genes where spliced in-frame stop codons were predicted
+     - new scripts: compare_masking.pl, merge_masking.pl
+     - new program bamToWig.py as alternarive to bam2wig C++ binary
+     - fix warnings on new GCC compiler (8.3)
+     - introduced unit tests of C++ code (make test)
+     - bugfixes (lex.cc, autoAug.pl)
+     - DIAMOND as alternative to BLAST in aa2nonred.pl
 List of changes from version 3.3.1 to 3.3.2 (until Oct 5th, 2018)
      - bugfixes in comparative augustus, utrrnaseq
      - new species Chiloscyllium punctatum (bamboo shark), Scyliorhinus torazame (cat shark), Rhincodon typus (whale shark)
@@ -42,7 +51,7 @@ List of changes from version 3.2 to 3.2.1 (until October 23rd, 2015)
      - comparative gene prediction (CGP): make the parameters from the GCB proceedings paper match again
      - new CGP default parameters (tested on 5 clades)
      - CGP version penalizes very long introns equivalently to a geometric distribution
-     - code now under artistic licence only
+     - code now under artistic license only
 List of changes from version 3.1 to 3.2 (until September 25th, 2015)
      - comparative gene prediction (CGP option) has sensible default parameters of the logistic regression model
      - new tool hal2maf_split.pl for splitting an alignment for parallel comparative prediction
@@ -85,10 +94,10 @@ List of changes from version 3.0.2 to 3.0.3 (until August 28th, 2014)
      - other bugfixes in comparative mode
      - removal of mysql++ code from package: this is available as Debian/Ubuntu package
 List of changes from version 3.0 to 3.0.2 (until February 22nd, 2014)
-     - inclusion of scanner and parser code for Newick tree format (GPL licence), easier installation of 
+     - inclusion of scanner and parser code for Newick tree format (GPL license), easier installation of 
        comparative augustus functionality
-     - therefore release under more restrictive GPL licence (the plan is to replace this later
-       and switch back to the more permissive and non-viral artistic open source licence)
+     - therefore release under more restrictive GPL license (the plan is to replace this later
+       and switch back to the more permissive and non-viral artistic open source license)
      - drop requirement to set environment variable AUGUSTUS_CONFIG_PATH
      - bugfixes (etraining: "not Genbank format", gtf2gff.pl, compilation warning)
 List of changes from version 2.7 to 3.0 (until January 8th, 2014)
@@ -153,7 +162,7 @@ List of changes from version 2.4 to 2.5 (until Nov 13th, 2010)
      - new species pneumocystis (fungus), user contributed by Marco Pagni
 List of changes from version 2.3.1 to 2.4 (until July 27, 2010)
      - improved human parameter set: roughly 13 percent points better on CDS exon level
-     - improved fly paramter set
+     - improved fly parameter set
      - added new species 'lamprey', contributed by Falk Hildebrand and Shigehiro Kuraku
      - added new species Leishmania tarentolae, Trichinella spiralis
      - added maize5 parameter set, better than 'maize' and with UTR model
@@ -274,7 +283,7 @@ List of changes from version 1.6 to version 1.7 (until October 5th, 2005):
 
 List of changes from version 1.5 to version 1.6 (until August 3rd, 2005):
 
-     - The source code is now freely available (Artistic Licence).
+     - The source code is now freely available (Artistic License).
      - New species: Tribolium castaneum, Aedes aegypti, Coprinus cinereus
      - Bugfix: Wrong interpretation of reading frame for reverse strand exon hints.
      - Training of hints possible with nested genes.

Makefile

@@ -29,7 +29,6 @@ install:
 release:
 	find . -name "*~" | xargs rm -f
 	rm -f src/makedepend.pl
-	rm -r augustus-training
 	cd docs/tutorial2015/results; ls | grep -v do.sh | grep -v README | xargs rm; cd -
 	rm -r auxprogs/utrrnaseq/input/human-chr19
 	rm -r docs/tutorial-cgp/results/cactusout
@@ -39,6 +38,8 @@ release:
 	cd ..; tar -czf augustus-$(AUGVERSION).tar.gz augustus-$(AUGVERSION)
 
 test:
+	cd src && ${MAKE} unittest
+	cd src/unittests && ./unittests
 	./bin/augustus --species=human --UTR=on examples/example.fa
 
 # remove -static from src/Makefile for MAC users

README-cgp.md

+[![Build Status](https://travis-ci.org/Gaius-Augustus/Augustus.svg?branch=master)](https://travis-ci.org/Gaius-Augustus/Augustus)
+
+# Gene Prediction with AUGUSTUS in comparative gene prediction (cgp) mode
+  genes are predicted simultaneously in several aligned genomes
+
+[INTRODUCTION](#introduction)  
+[INSTALLATION](#installation)  
+[RUNNING AUGUSTUS IN CGP MODE](docs/RUNNING-AUGUSTUS-IN-CGP-MODE.md)  
+[BUILDING THE NEWICK PARSER FROM SCRATCH](docs/CHANGE-TREE-PARSER.md)  
+   (not needed unless you run into compiler errors related to 'parse.cc' or 'lex.cc')  
+[AUTHORS AND CONTACT](docs/CONTACT.md)  
+[REFERENCES](README.md#references)  
+[LICENSES](README.md#licenses)  
+
+# INTRODUCTION
+
+   The cgp mode is an extension to AUGUSTUS that takes an alignment of two or more genomes
+   and simultaneously predicts genes in all of them.
+   Beside the genomes and the alignment, a phylogenetic tree of the species is required input.
+   AUGUSTUS-cgp can either be used
+
+   - de novo, or
+   - with extrinsic evidence for any subset of species  
+     Such evidence includes for example already existing and trusted gene structures 
+     or hints from RNA-Seq alignments.
+
+   Both genomes and extrinsic evidence can either be read in from a flat file or 
+   alternatively retrieved from a MySQL or SQLite database.  
+   All three approaches are described below in more detail.
+
+   This manual assumes that you are already familiar with AUGUSTUS
+   and that you know how to use AUGUSTUS for gene prediction in a single genome.
+
+# INSTALLATION
+
+## Install dependencies
+
+   See [these instructions](README.md#install-dependencies) for a complete overview.
+
+## Enable cgp mode
+
+   Open the file [common.mk](./common.mk) with a text editor and uncomment the 
+   following lines to enable comparative gene prediction.
+   
+    COMPGENEPRED = true
+
+   To support a SQLite database uncomment this line
+
+     SQLite = true
+
+   or for MySQL this
+
+     MYSQL = true
+   
+## Compile from sources
+
+   Once all dependencies are available, you can compile AUGUSTUS using make.
+
+    make
+
+   In case you had previously compiled AUGUSTUS with disabled cgp mode first you 
+   have to call
+
+    make clean
+
+   After compilation has finished, the command bin/augustus should be executable 
+   and print a usage message.

auxprogs/bam2hints/Makefile

@@ -21,6 +21,7 @@ LINK.cc = g++
 # $<: .c file of target. 
 bam2hints : $(OBJECTS) 
 	$(LINK.cc) $(CXXFLAGS) $(LDFLAGS) -o $@ $(OBJECTS) $(LIBS)
+	mkdir -p ../../bin
 	cp bam2hints ../../bin
 
 all:$(OBJECTS) # Compiles each foo.cc into foo.o

auxprogs/bam2hints/bam2hints.cc

@@ -541,7 +541,7 @@ int main(int argc, char* argv[])
          << "                          CACW21662.g1    3       C2      5TNS       Unknown\n"
          << "                          CACW25491.g1    3       F21     5TNS       3TNS-NP\n"
       */
-         << "  --maxgenelen=n     -G   alignments of the same clone are considered to be of the same gene if not separeted by more than this (set to " << MaxGeneLen << ")\n"
+         << "  --maxgenelen=n     -G   alignments of the same clone are considered to be of the same gene if not separated by more than this (set to " << MaxGeneLen << ")\n"
          << "                          Alignments that span more than this are ignored, but better filter long introns through an alignment program.\n"
          << "  --help             -h   show this help text\n"
          << "\n";
@@ -560,7 +560,7 @@ int main(int argc, char* argv[])
 
   // Estimating the right value of the arrays:  PSLb;  PSLq;  PSLt; BlockBegins; BlockEnds and FolOK;
   // This is done by sweeping through all the alignments and calculating the maxBlock size.
-  cout << "Wait a moment, calculating maximum block size that needs to be allocated... ";
+  // cout << "Wait a moment, calculating maximum block size that needs to be allocated... ";
   int alignmentBlock, maxBlock=0;
   while (BAM.GetNextAlignment(*pal)) 
 	{ 	
@@ -576,7 +576,7 @@ int main(int argc, char* argv[])
 
 	  if (alignmentBlock >= maxBlock) maxBlock = alignmentBlock;
 	} // end while
-  cout << ".. done" << endl;
+  // cout << ".. done" << endl;
 
   // closing and opening handle of BAM file
   BAM.Close();
@@ -587,7 +587,7 @@ int main(int argc, char* argv[])
   SamHeader header = BAM.GetHeader();
   if(header.HasSortOrder() && header.SortOrder == "unsorted" && IntOnly && Mult)
   {
-    cout << "\nBAM file MUST be sorted by target sequence names when 'intronsonly' and 'mult' options are active\n";
+    cout << "\nBAM file MUST be sorted by read names (samtools sort -n) when 'intronsonly' and 'mult' options are active\n";
     return -1;
   }
 
@@ -820,13 +820,13 @@ int main(int argc, char* argv[])
       // check if there is a proper old target
       if(OldTargetID >= 0) // -1 <-> "*"(unknown reference), -2 <-> uninitialized
       {
-  	// check previous occurence of that target
+  	// check previous occurrence of that target
   	if(seenRefSet.find(TargetName) != seenRefSet.end())
   	{
   	  if(IntOnly && Mult)
   	  {
   	    // require sorting and abort
-  	    cout << "\nBAM file MUST be sorted by target sequence names when 'intronsonly' and 'mult' options are active\n";
+  	    cout << "\nBAM file MUST be sorted by read names (samtools sort -n)  when 'intronsonly' and 'mult' options are active\n";
   	    return -1;
   	  }
   	}
@@ -1069,11 +1069,11 @@ int main(int argc, char* argv[])
     // TASK: else store alignment pointer into map
     // TASK: set new or reuse "pal"
 
-  } // end while (parsing through bam aligment lines)
+  } // end while (parsing through bam alignment lines)
 
 
-  // newline after display of the line count
-  cout << "\n";
+  // newline after display of the line count, has been commented out above
+  //cout << "\n";
 
   // print the last hints
   printHints(GFF, "");

auxprogs/bam2wig/Makefile

 # Makefile of bam2wig
 #
-# NOTE: Modify the variable TOOLDIR according to where your samtools/htslib/bcftools/tabix software has been installed
+# NOTE: Modify the variable TOOLDIR according to where your samtools/htslib/bcftools software has been installed
 # 
-# Created: 12-June-2012
-# Last modified: 10-NOV-2017
+# License: Artistic License, see file LICENSE.TXT or 
+#          https://opensource.org/licenses/artistic-license-1.0
 #
 
 ifndef TOOLDIR
 	TOOLDIR=$(HOME)/tools
-# replace with your own parent directory of samtools, htslib, bcftools, tabix
+# replace with your own parent directory of samtools, htslib, bcftools
 # if TOOLDIR is not specified as environment variable
 endif
 
 PROGRAM = bam2wig
 SOURCES = $(PROGRAM)
 OBJECTS = $(SOURCES:.c=.o)
-SAMTOOLS=$(TOOLDIR)/samtools/
-HTSLIB=$(TOOLDIR)/htslib/
-BCFTOOLS=$(TOOLDIR)/bcftools/
-TABIX=$(TOOLDIR)/tabix/
-INCLUDES=-I$(SAMTOOLS) -I. -I$(HTSLIB) -I$(BCFTOOLS) -I$(TABIX)
+SAMTOOLS=$(TOOLDIR)/samtools
+HTSLIB=$(TOOLDIR)/htslib
+BCFTOOLS=$(TOOLDIR)/bcftools
+INCLUDES=-I$(SAMTOOLS) -I. -I$(HTSLIB) -I$(BCFTOOLS)
 VPATH=$(SAMTOOLS)
 LIBS=$(SAMTOOLS)/libbam.a $(HTSLIB)/libhts.a -lcurses -lm -lz -lpthread -lcurl -lssl -lcrypto
 CFLAGS=-Wall -O2 $(INCLUDES)
@@ -27,6 +26,7 @@ CC=gcc
 
 $(PROGRAM) : bam2wig.o
 	$(CC) $(CFLAGS) $^ -o $@ $(LIBS) -lbz2 -llzma
+	mkdir -p ../../bin
 	cp bam2wig ../../bin/bam2wig
 
 bam2wig.o : bam2wig.c

auxprogs/bam2wig/README.txt

@@ -4,12 +4,11 @@ Installation instructions:
    * bcftools
    * htslib
    * samtools
-   * tabix
   You find those tools at https://github.com/samtools . bam2wig has been tested with samtools 0.2.0-rc7
 
-  We recommend that you install all four tools into one directory that we will further refer to as the
+  We recommend that you install all three tools into one directory that we will further refer to as the
   TOOLDIR. For example, you can install all tools into your home directory, which will result into
-  four folders in your home directory: bcftools, htslib, samtools and tabix.
+  three folders in your home directory: bcftools, htslib and samtools.
 
   Installation example:
 
@@ -29,10 +28,6 @@ Installation instructions:
   make
   sudo make install
   cd ..
-  git clone https://github.com/samtools/tabix.git
-  cd tabix
-  make
-  cd ..
   git clone https://github.com/samtools/samtools.git
   cd samtools
   autoheader
@@ -61,6 +56,3 @@ b) ./bam2wig -t "my_specified_track" -r chr3L test.s.bam
 
 Example (b) can only be done if an index file for test.s.bam exists. 
 Do "samtools index test.s.bam" and a file "test.s.bam.bai" will be generated.
-
-Tonatiuh Pena Centeno, Katharina Hoff
-29 November 2017

auxprogs/bam2wig/bam2wig.c

@@ -91,7 +91,7 @@ int main(int argc, char *argv[])
 	  }
 
 
-	// Initialising auxiliary data structures
+	// Initializing auxiliary data structures
 	data = calloc(1, sizeof(void*)); // data[0] is array for just one BAM file
 	// set the default region. left-shift "end" by appending 30 zeros (i.e. end=1073741824) 
 	beg = 0; end = 1<<30; tid = -1;  
@@ -116,6 +116,14 @@ int main(int argc, char *argv[])
 	if (tid >= 0) 
 	  { // if a region is specified and parsed successfully
 		bam_index_t *idx = bam_index_load(argv[optind]);  // load the index
+
+		if (idx == NULL)
+		  {
+		    fprintf(stderr, "Missing indexed BAM file!\n");
+		    fprintf(stderr, "See: samtools index\n");
+		    exit(1);
+		  }
+
 		data[0]->iter = bam_iter_query(idx, tid, beg, end); // set the iterator
 		bam_index_destroy(idx); // the index is not needed any more; phase out of the memory
 	  }

auxprogs/filterBam/src/filterBam.cc

@@ -149,7 +149,7 @@ int main(int argc, char *argv[])
   optionalCounters.outPaired = outPaired;
   optionalCounters.outUniq = outUniq;
   optionalCounters.outBest = outBest;
-  // Initialising options
+  // Initializing options
   struct globalOptions_t globalOptions;
   globalOptions = initOptions(argc, argv);
   bool best = globalOptions.best;

auxprogs/filterBam/src/functions/MatePairs.cc

@@ -55,7 +55,7 @@ MatePairs::MatePairs(const MatePairs &copyin)   // Copy constructor to handle pa
 	this->score = copyin.score; 	               
 }
 
-// Initialisation method
+// Initialization method
 MatePairs::MatePairs(int it, int jit, float score)
 {
 	this->alIt = it;
@@ -63,7 +63,7 @@ MatePairs::MatePairs(int it, int jit, float score)
 	this->score = score;
 }
 
-// Initialisation method
+// Initialization method
 void MatePairs::setValues(int it, int jit, float score)
 {
 	this->alIt = it;

auxprogs/filterBam/src/functions/PairednessCoverage.cc

@@ -51,7 +51,7 @@ PairednessCoverage::PairednessCoverage(const PairednessCoverage &copyin)   // Co
 	this->chr = copyin.chr; 	               
 }
 
-// Initialisation method
+// Initialization method
 PairednessCoverage::PairednessCoverage(int coord, int label, string chr)
 {
 	this->coord = coord; 	               
@@ -60,7 +60,7 @@ PairednessCoverage::PairednessCoverage(int coord, int label, string chr)
 }
 
 
-// Initialisation method
+// Initialization method
 void PairednessCoverage::setValues(int coord, int label, string chr)
 {
 	this->coord = coord;

auxprogs/filterBam/src/functions/SingleAlignment.cc

@@ -75,7 +75,7 @@ SingleAlignment::SingleAlignment(BamAlignment *al, float coverage, float percId,
 }
 
 
-// Initialisation method
+// Initialization method
 void SingleAlignment::setValues(BamAlignment *al, float coverage, float percId, const RefVector *refData)
 {
 	this->al = al;