Manpages: fox a typo. Manual: bits of improvement.

doc/man/spell-marker.1.md

@@ -8,7 +8,7 @@ spell-marker – Compute the 1-point Parental Origin Probabilities in a pedigree
 
 # SYNOPSIS
 
-**spell-marker** [options...] [**--wd** *PATH*] **-n** *NAME* **-m** *GEN:FORMAT* *FILE* [**-m**...]
+**spell-marker** [options...] [**-wd** *PATH*] **-n** *NAME* **-m** *GEN:FORMAT* *FILE* [**-m**...]
 
 # DESCRIPTION
 

doc/man/spell-pedigree.1.md

@@ -8,7 +8,7 @@ spell-pedigree – Precompute the Markov Models for a pedigree
 
 # SYNOPSIS
 
-**spell-pedigree** [**-h**] [**--wd** *PATH*] **-n** *NAME* [**-s** *CHAR*] **-p** *FILE*
+**spell-pedigree** [**-h**] [**-wd** *PATH*] **-n** *NAME* [**-s** *CHAR*] **-p** *FILE*
 
 # DESCRIPTION
 

doc/man/spell-qtl.1.md

@@ -8,7 +8,7 @@ spell-qtl – Compute n-point Parental Origin Probabilities and perform QTL anal
 
 # SYNOPSIS
 
-**spell-qtl** [*options...*] [**--wd** *PATH*] **-n** *NAME* **-gm** *MAP* **-p** *GEN* *TRAITS* [**-p**...] [model and algorithms configuration...]
+**spell-qtl** [*options...*] [**-wd** *PATH*] **-n** *NAME* **-gm** *MAP* **-p** *GEN* *TRAITS* [**-p**...] [model and algorithms configuration...]
 
 # DESCRIPTION
 

doc/user_manual/makefile

@@ -4,8 +4,10 @@ SRCDIR = /home/sjasson/dev/spel
 
 EXAMPLE_DIR = $(SRCDIR)/examples/three_parents_F2
 
+all: user_manual.pdf
+
 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 outputs
-	pdflatex --shell-escape user_manual.tex && pdflatex --shell-escape user_manual.tex
+	pdflatex --shell-escape user_manual.tex && pdflatex --shell-escape user_manual.tex > /dev/null
 
 version.tex: 
 	git tag | tail -1 > version.tex
@@ -13,39 +15,40 @@ version.tex:
 spell-pedigree.tex: $(SRCDIR)/doc/man/spell-pedigree.1.md
 	/usr/bin/pandoc $(SRCDIR)/doc/man/spell-pedigree.1.md --listings -f markdown -t latex -o spell-pedigree.tex
 	sed -i s/\\label\{/\label\{spell-pedigree:/g spell-pedigree.tex
+	sed -i s/--/-\{\}-/g spell-pedigree.tex 
 
 spell-marker.tex: $(SRCDIR)/doc/man/spell-marker.1.md
 	/usr/bin/pandoc $(SRCDIR)/doc/man/spell-marker.1.md --listings -f markdown -t latex -o spell-marker.tex
 	sed -i s/\\label\{/\label\{spell-marker:/g spell-marker.tex
+	sed -i s/--/-\{\}-/g spell-marker.tex
 
 spell-qtl.tex: ../man/spell-qtl.1.md
 	/usr/bin/pandoc $(SRCDIR)/doc/man/spell-qtl.1.md --listings -f markdown -t latex -o spell-qtl.tex
 	sed -i s/\\label\{/\label\{spell-qtl:/g spell-qtl.tex
+	sed -i s/--/-\{\}-/g spell-qtl.tex
 
 spell-qtl-examples.tex: $(SRCDIR)/doc/man/spell-qtl-examples.1.md
 	/usr/bin/pandoc $(SRCDIR)/doc/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
+	sed -i s/--/-\{\}-/g spell-qtl-examples.tex
 
-
-input_files/example1.map input_files/example1_F2.phen input_files/example1_F2.gen input_files/example1.ped:input_files/%: $(EXAMPLE_DIR)/% input_dir
-	awk -v len=73 '{ if (length($$0) > len) print substr($$0, 1, len-3) "..."; else print; }' $< > $@
-
-input_dir:
+input_files/example1.map input_files/example1_F2.phen input_files/example1_F2.gen input_files/example1.ped:input_files/%: $(EXAMPLE_DIR)/%
 	mkdir -p input_files
+	awk -v len=69 '{ if (length($$0) > len) print substr($$0, 1, len-3) "..."; else print; }' $< > $@
 
-inputs: input_dir input_files/example1.map input_files/example1_F2.phen input_files/example1_F2.gen input_files/example1.ped
+inputs: input_files/example1.map input_files/example1_F2.phen input_files/example1_F2.gen input_files/example1.ped
 
 
-my_directory/my_name.spell-pedigree.data: $(EXAMPLE_DIR)/example1.ped
+my_directory/my_name.cache/my_name.spell-pedigree.data: $(EXAMPLE_DIR)/example1.ped
 	$(BINDIR)/spell-pedigree -wd my_directory -n my_name -p $<
 	
-my_directory/my_name.spell-marker.data: my_directory/my_name.spell-pedigree.data $(EXAMPLE_DIR)/example1_F2.gen $(EXAMPLE_DIR)/example1_F2C.gen
+my_directory/my_name.cache/my_name.spell-marker.data: my_directory/my_name.cache/my_name.spell-pedigree.data $(EXAMPLE_DIR)/example1_F2.gen $(EXAMPLE_DIR)/example1_F2C.gen
 	$(BINDIR)/spell-marker -wd my_directory -n my_name -m F2:A/B $(EXAMPLE_DIR)/example1_F2.gen -m F2C:A/C $(EXAMPLE_DIR)/example1_F2C.gen -o F2,F2C -O1 -Op
 
-my_directory/my_name.n-point/ch1/F2/my_name.ch1.F2.0.csv:  my_directory/my_name.spell-marker.data $(EXAMPLE_DIR)/example1_F2.phen $(EXAMPLE_DIR)/example1_F2C.phen $(EXAMPLE_DIR)/example1.map
+my_directory/my_name.n-point/ch1/F2/my_name.ch1.F2.0.csv:  my_directory/my_name.cache/my_name.spell-marker.data $(EXAMPLE_DIR)/example1_F2.phen $(EXAMPLE_DIR)/example1_F2C.phen $(EXAMPLE_DIR)/example1.map
 	$(BINDIR)/spell-qtl -wd my_directory -n my_name -P auto -p F2 $(EXAMPLE_DIR)/example1_F2.phen -p F2C $(EXAMPLE_DIR)/example1_F2C.phen -gm $(EXAMPLE_DIR)/example1.map output-nppop
 
-my_directory/my_name.report/t1/t1_report.txt: my_directory/my_name.spell-marker.data $(EXAMPLE_DIR)/example1_F2.phen $(EXAMPLE_DIR)/example1_F2C.phen $(EXAMPLE_DIR)/example1.map
+my_directory/my_name.report/t1/t1_report.txt: my_directory/my_name.cache/my_name.spell-marker.data $(EXAMPLE_DIR)/example1_F2.phen $(EXAMPLE_DIR)/example1_F2C.phen $(EXAMPLE_DIR)/example1.map
 	$(BINDIR)/spell-qtl -wd my_directory -n my_name -P auto -p F2 $(EXAMPLE_DIR)/example1_F2.phen -p F2C $(EXAMPLE_DIR)/example1_F2C.phen -gm $(EXAMPLE_DIR)/example1.map
 	
 outputs: my_directory/my_name.report/t1/t1_report.txt my_directory/my_name.n-point/ch1/F2/my_name.ch1.F2.0.csv

doc/user_manual/user_manual.tex

@@ -19,7 +19,8 @@
 
 \lstset{
 breakatwhitespace=false,
-breaklines=true
+breaklines=true,
+basicstyle=\ttfamily
 }
 
 
@@ -28,20 +29,20 @@ breaklines=true
   \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
 
 
-
-\newcommand\myfolder[2][white]{%
-\begin{tikzpicture}[overlay]
-\begin{scope}[xshift=20pt]
-\filldraw[rounded corners=1pt,fill=#1,draw=white,double=black]
-  (-23pt,10pt) -- ++(3pt,5pt) -- ++(18pt,0pt) -- ++(40:3pt) -- ++(9pt,0pt) -- ++(-40:3pt)
-  -- (20pt,15pt) -- (23pt,10pt) -- cycle;
-\filldraw[rounded corners,draw=white,double=black,top color=#1,bottom color=#1!30]
-  (-22pt,-12pt) -- ++(44pt,0pt) -- (25pt,12pt) coordinate (topr) -- ++(-50pt,0pt) coordinate (topl) -- cycle;
-\end{scope}  
-\end{tikzpicture}%
-\makebox[35pt]{\raisebox{-3pt}{{\ttfamily/#2}}}%
-}
-
+% 
+% \newcommand\myfolder[2][white]{%
+% \begin{tikzpicture}[overlay]
+% \begin{scope}[xshift=20pt]
+% \filldraw[rounded corners=1pt,fill=#1,draw=white,double=black]
+%   (-23pt,10pt) -- ++(3pt,5pt) -- ++(18pt,0pt) -- ++(40:3pt) -- ++(9pt,0pt) -- ++(-40:3pt)
+%   -- (20pt,15pt) -- (23pt,10pt) -- cycle;
+% \filldraw[rounded corners,draw=white,double=black,top color=#1,bottom color=#1!30]
+%   (-22pt,-12pt) -- ++(44pt,0pt) -- (25pt,12pt) coordinate (topr) -- ++(-50pt,0pt) coordinate (topl) -- cycle;
+% \end{scope}  
+% \end{tikzpicture}%
+% \makebox[35pt]{\raisebox{-3pt}{{\ttfamily/#2}}}%
+% }
+%