Documentation update

cobilab · Apr 12, 2019 · a49e26a · a49e26a
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diff --git a/manual/manual.pdf b/manual/manual.pdf
diff --git a/...sections/Amino_acid_sequence_tools/AC.tex → ...id_sequence_tools/AminoAcidCompressor.tex b/...sections/Amino_acid_sequence_tools/AC.tex → ...id_sequence_tools/AminoAcidCompressor.tex
@@ -1,5 +1,5 @@
-\section{Program gto\char`_ac}
-The \texttt{gto\char`_ac} is a new lossless compressor to compress efficiently amino acid sequences (proteins). It uses a cooperation between multiple context and substitutional tolerant context models. The cooperation between models is balanced with weights that benefit the models with better performance according to a forgetting function specific for each model.\\
+\section{Program gto\char`_amino\char`_acid\char`_compressor}
+The \texttt{gto\char`_amino\char`_acid\char`_compressor} is a new lossless compressor to compress efficiently amino acid sequences (proteins). It uses a cooperation between multiple context and substitutional tolerant context models. The cooperation between models is balanced with weights that benefit the models with better performance according to a forgetting function specific for each model.\\
 For help type:
 \begin{lstlisting}
 ./gto_amino_acid_compressor -h
@@ -8,7 +8,7 @@ \section{Program gto\char`_ac}
 
 \subsection*{Input parameters}
 
-The \texttt{gto\char`_ac} program needs a file with amino acid sequences to compress.\\
+The \texttt{gto\char`_amino\char`_acid\char`_compressor} program needs a file with amino acid sequences to compress.\\
 The attribution is given according to:
 \begin{lstlisting}
 Usage: ./gto_amino_acid_compressor [OPTION]... -r [FILE]  [FILE]:[...]                          

diff --git a/manual/sections/Amino_acid_sequence_tools/Amino_acid_sequence_tools.tex b/manual/sections/Amino_acid_sequence_tools/Amino_acid_sequence_tools.tex
@@ -15,4 +15,4 @@ \chapter{Amino acid sequence tools}
 
 \input{\AminoAcidSequenceToolsPath/AminoAcidToGroup.tex}
 \input{\AminoAcidSequenceToolsPath/AminoAcidToPseudoDNA.tex}
-\input{\AminoAcidSequenceToolsPath/AC.tex}
+\input{\AminoAcidSequenceToolsPath/AminoAcidCompressor.tex}
diff --git a/manual/sections/FASTQ_tools/FastqXS.tex b/manual/sections/FASTQ_tools/FastqXS.tex
@@ -1,5 +1,5 @@
-\section{Program gto\char`_xs}
-The \texttt{gto\char`_xs} is a skilled FASTQ read simulation tool, flexible, portable (does not need a reference sequence) and tunable in terms of sequence complexity. XS handles Ion Torrent, Roche-454, Illumina and ABI-SOLiD simulation sequencing types. It has several running modes, depending on the time and memory available, and is aimed at testing computing infrastructures, namely cloud computing of large-scale projects, and testing FASTQ compression algorithms. Moreover, XS offers the possibility of simulating the three main FASTQ components individually (headers, DNA sequences and quality-scores). Quality-scores can be simulated using uniform and Gaussian distributions.\\
+\section{Program gto\char`_fastq\char`_xs}
+The \texttt{gto\char`_fastq\char`_xs} is a skilled FASTQ read simulation tool, flexible, portable (does not need a reference sequence) and tunable in terms of sequence complexity. XS handles Ion Torrent, Roche-454, Illumina and ABI-SOLiD simulation sequencing types. It has several running modes, depending on the time and memory available, and is aimed at testing computing infrastructures, namely cloud computing of large-scale projects, and testing FASTQ compression algorithms. Moreover, XS offers the possibility of simulating the three main FASTQ components individually (headers, DNA sequences and quality-scores). Quality-scores can be simulated using uniform and Gaussian distributions.\\
 For help type:
 \begin{lstlisting}
 ./gto_xs -h
@@ -8,7 +8,7 @@ \section{Program gto\char`_xs}
 
 \subsection*{Input parameters}
 
-The \texttt{gto\char`_xs} program needs program needs a FASTQ file to compute.\\
+The \texttt{gto\char`_fastq\char`_xs} program needs program needs a FASTQ file to compute.\\
 The attribution is given according to:
 \begin{lstlisting}
 Usage: XS   [OPTION]... [FILE] 
@@ -68,7 +68,7 @@ \subsection*{Input parameters}
 \end{lstlisting}
 
 \subsection*{Output}
-The output of the \texttt{gto\char`_xs} program is a FASTQ file\\
+The output of the \texttt{gto\char`_fastq\char`_xs} program is a FASTQ file\\
 Using the input above using the common usage with 5 reads (-n 5), an output example for this is the following:
 \begin{lstlisting}
 @output.fastq.598 LQGQLWH01D5WVZ length=62