use examples from package

doc/user_manual/makefile

-user_manual.pdf : spell-pedigree.tex spell-marker.tex spell-qtl.tex spell-qtl-examples.tex version.tex user_manual.tex images/Spell-pipeline2.svg
+EXAMPLE_DIR = ~/INSTALL_DIR/SPELL_TEST/spell_qtl-0.1-alpha.1-Linux/share/spell-qtl/examples/three_parents_F2
+user_manual.pdf : spell-pedigree.tex spell-marker.tex spell-qtl.tex spell-qtl-examples.tex version.tex user_manual.tex images/Spell-pipeline2.svg inputs
 	pdflatex --shell-escape user_manual.tex && pdflatex --shell-escape user_manual.tex
 
 version.tex :
@@ -20,11 +21,21 @@ spell-qtl-examples.tex : ../man/spell-qtl-examples.1.md
 	/usr/bin/pandoc ../man/spell-qtl-examples.1.md --listings -f markdown -t latex -o spell-qtl-examples.tex
 	sed -i s/\\label\{/\label\{spell-qtl-examples:/g spell-qtl-examples.tex
 
+
+inputs : 
+	mkdir -p input_files
+	awk -v len=73 '{ if (length($$0) > len) print substr($$0, 1, len-3) "..."; else print; }' $(EXAMPLE_DIR)/example1.map > input_files/example1.map
+	awk -v len=73 '{ if (length($$0) > len) print substr($$0, 1, len-3) "..."; else print; }' $(EXAMPLE_DIR)/example1_F2.phen > input_files/example1_F2.phen
+	awk -v len=73 '{ if (length($$0) > len) print substr($$0, 1, len-3) "..."; else print; }' $(EXAMPLE_DIR)/example1_F2.gen > input_files/example1_F2.gen
+	awk -v len=73 '{ if (length($$0) > len) print substr($$0, 1, len-3) "..."; else print; }' $(EXAMPLE_DIR)/example1.ped > input_files/example1.ped
+
+
 clean:
 	rm -f *.aux *.log *.pdf *.toc *.out *.lol
 	rm -f version.tex
 	rm -f spell-pedigree.tex spell-marker.tex spell-qtl.tex spell-qtl-examples.tex
 	rm -f images/*.pdf images/*.pdf_tex
+	rm -rf input_files
 
 veryclean: clean
 	rm -f *~

doc/user_manual/user_manual.tex

@@ -336,19 +336,13 @@ Global software organization is displayed in figure \ref{fig:pipeline}. More det
 \subsubsection{File format}
 See \texttt{spell-pedigree} man page (at appendix \ref{ch:spell:predigree})
 \subsubsection{File sample}
-\begin{lstlisting}[frame=single,caption={[Pedigree (.ped input file)]Pedigree (.ped)}]
-Founders,1,0,0
-Founders,2,0,0
-Founders,3,0,0
-Founders,4,0,0
-F1,5,1,2
-F1,6,3,4
-CP,7,5,6
-F2,8,7,7
-F3,9,8,8
-F3,10,8,8
-F3,11,8,8
-\end{lstlisting}
+\lstinputlisting[numbers=left,
+		frame=single,
+		breaklines=false,
+		caption={[Pedigree (.ped input file)]Pedigree (selected lines from example1.ped from three\_parents\_F2 example)},
+		linerange={1-12,107-112}
+		]
+		{input_files/example1.ped}
 
 
 \subsection{Marker observations}
@@ -404,21 +398,15 @@ Note that \textbf{CP} and \textbf{ABHCD} formats imply user-made genotype infere
 Other allele code can be defined via a JSON file. (see in appendix \ref{spell-marker:marker-observation-format-specification} for format and \ref{spell-marker:example-the-02-abhcd-and-cp-formats} for sample files)
 
 \subsubsection{File sample}
-\begin{lstlisting}[frame=single,caption={[Marker alleles (.gen input file)]Marker alleles (.gen)}]
-data type random example
-42 42 0 0
-*M1 21221-0212-122-20000-101022220100202102200
-*M2 012120-0221010220101112222101211122120211-
-*M3 0221022000211200012112-020000-101221222202
-*M4 00112-021012200110101221221222112120100120
-*M5 2211-00211121002221--2-20002102-1011220211
-*M6 01211-201202221121002-12211200000001011001
-*M7 202212202-00--10-101221200-112001-110-220-
-*M8 222-22-02102002002220112-021-022--12012-11
-*M9 0210-10-1122212-21000-2200-121200200222211
-...
-\end{lstlisting}
-Note that \texttt{ data type} is irrelevant
+\lstinputlisting[numbers=left,
+		frame=single,
+		breaklines=false,
+		caption={[Marker alleles (.gen input file)]Marker alleles  (example1\_F2.gen from three\_parents\_F2 example)},
+		%linerange={1-8,35-39}
+		]
+		{input_files/example1_F2.gen}
+
+Note that line 1 \texttt{F2} after \texttt{ data type} is irrelevant
 
 \subsection{Genetic map}
 \subsubsection{File format}
@@ -431,24 +419,14 @@ One line per linkage group (space separated) :
 \end{itemize}
                
 \subsubsection{File sample}
-\begin{lstlisting}[frame=single,breaklines=false,caption={[Genetic Map (.map input file)] Genetic map (.map)}]
-*Chrom1 3 M11 10.5 M12 30.3 M13
-*Chrom2 17 M21 5.5 M22 0 M23 2 M24 5 M25 8 M26 11 M27 2.2 M28 2.5 M29 ...
-*Chrom3 8 M31 10 M32 10 M33 10 M34 10 M35 10 M36 10 M37 10 M38
-\end{lstlisting}
+\lstinputlisting[numbers=left,frame=single,breaklines=false,caption={[Genetic Map (.map input file)] Genetic map (example1.map from three\_parents\_F2 example)}]{input_files/example1.map}
 
 \subsection{Trait observations}
 \subsubsection{File format}
-As in MapMaker RAW format, without header : one line per trait beginning with starred (*) trait name followed by space separated observations (one numerical observation per individual, \texttt{ -} means unobserved).  
+As in MapMaker RAW format, without header : one line per trait beginning with starred (*) trait name followed by space separated observations (one numerical observation per individual, \texttt{ -} means unobserved). 
+ 
 \subsubsection{File sample}
-\begin{lstlisting}[frame=single,breaklines=false,caption={[Trait observations (.phen input file)]Trait observations (.phen)}]
-*trait_1 131.97 113.96 - 125.53 56.31 87.55 73.55 66.6 91.13 5.74 ... 
-*trait_2 149.12 -56.72 104.56 100.54 88.49 102.0 65.75 121.94 68.92 ...
-*trait_3 147.87 - - 38.53 103.83 95.51 20.05 72.69 66.74 136.95 78.57 ...
-*trait_4 57.52 143.51 128.02 41.53 122.34 100.11 123.41 74.11 119.22 ...
-*trait_5 125.69 197.13 - 152.77 74.41 188.16 64.8 108.04 89.6 154.62 ...
-...
-\end{lstlisting}
+\lstinputlisting[numbers=left,frame=single,breaklines=false,caption={[Trait observations (.phen input file)]Trait observations (example1\_F2.phen from three\_parents\_F2 example)}]{input_files/example1_F2.phen}
 
 \chapter{Generated outputs}
 \section{General organization}