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\chapter{Generated outputs}
\section{General organization}

General output directory organization is  : 

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    parent anchor=south,
    anchor=west,
    calign=first,
    %edge={rounded corners},
    edge path={
      \noexpand\path [draw, \forestoption{edge}]
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      (!u.south west) +(15pt,0) |- (.child anchor)\forestoption{edge label};
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    },
    before typesetting nodes={
      if n=1
        {insert before={[,phantom,minimum height=10pt]}}
        {}
    },
    fit=band,
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    s sep=0pt, %vertical base separator... see also l
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    before computing xy={l=20pt},
  }
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[my\_directory \textsf{\textsl{(directory)}}
	[my\_name.1-point \textsf{\textsl{(directory)}}
		[my\_name.pedigree-and-probabilities.M\_1\_10.csv \textsf{\textsl{(text file)}} ]
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		[...]
	]
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	[my\_name.cache \textsf{\textsl{(directory)}}
		[my\_name.spell-marker.data \textsf{\textsl{(binary file)}}]
		[my\_name.spell-pedigree.data \textsf{\textsl{(binary file)}}]
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	]
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	[my\_name.n-point \textsf{\textsl{(directory)}}
		[ch1 \textsf{\textsl{(directory)}}
			[F2 \textsf{\textsl{(directory)}}
				[my\_name.ch1.F2.0.csv \textsf{\textsl{(text file)}}]
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				[...]
			]
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			[F2C \textsf{\textsl{(directory)}}
				[my\_name.ch1.F2.0.csv \textsf{\textsl{(text file)}}]
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				[...]
			]
		]
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		[ch2 \textsf{\textsl{(directory)}}
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			[...]
		]
	]
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	[my\_name.report \textsf{\textsl{(directory)}}
		[full\_map.txt \textsf{\textsl{(text file)}}]
		[t1 \textsf{\textsl{(directory)}}
			[ch1:124.34\_LOD.txt \textsf{\textsl{(text file)}}]
			[Model\_Cross\_ch1:114.96\_ch1:124.34\_ch1:150\_XtX\_inv.txt \textsf{\textsl{(text file)}}]
			[Model\_Cross\_ch1:114.96\_ch1:124.34\_ch1:150\_X.txt \textsf{\textsl{(text file)}}]
			[t1\_report.txt \textsf{\textsl{(text file)}}]
			[trait\_values.txt \textsf{\textsl{(text file)}}]
		]
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	]
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	[my\_name.spell-qtl.log \textsf{\textsl{(text file)}}
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	]
]
\end{forest}


\begin{itemize}
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\item A common working directory must be set for all 3 executables using the commandline option \texttt{-wd my\_directory} or \texttt{-{}-work-directory my\_directory}. Every result produced during analysis will be output into this directory.
\item A configuration name using commandline option \texttt{-n my\_name} or \texttt{-{}-name my\_name} is used to prefix the subdirectories and output files.
\item Parental Origin Probabilities are output as CSV files:
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\begin{description}
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\item [1-point] one file per marker (with pedigree-like structure). Use option \texttt{-O1} in command \texttt{spell-marker} to output these files.
\item [n-point] one file per linkage group per generation per individual. Use option \texttt{output-nppop} in command \texttt{spell-qtl} to output these files.
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\end{description}
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\item A report containing:
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\begin{itemize}
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\item A text-mode rendering of the genetic map with the detected QTLs and their respective confidence intervals,
\item The model matrix and the variance-covariance matrix for each selected set of loci used by the detection algorithm,
\item The detailed final model including variance-covariance matrix, coefficients, contrasts, and contrasts significance.
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\end{itemize}
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\item A cache of intermediate computation results.
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\end{itemize}

\section{Output files samples}
\subsection{1-point POP}
\lstinputlisting[numbers=left,
		frame=single,
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		caption={[1-point output file] 1-point output file (selected lines from file \texttt{my\_name.pedigree-and-probabilities.M\_1\_1.csv}  in directory \texttt{my\_directory/my\_name.1-point/} )  },
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		linerange={1-12,107-112}
]{my_directory/my_name.1-point/my_name.pedigree-and-probabilities.M_1_1.csv}

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Note that you must use the \texttt{-O1} commandline option in \texttt{spell-marker} in order to generate these files (see \vref{spell-marker:output-modes}.) 
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\subsection{n-point POP}
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\lstinputlisting[numbers=left,
		frame=single,
		caption={[n-point output file] n-point output file (\texttt{my\_name.ch1.F2.0.csv}  in directory \texttt{my\_directory/my\_name.n-point/ch1/F2/} )  },
]
{output_files/my_name.ch1.F2.0.csv}

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Note that you must use the \texttt{output-nppop} processing option in \texttt{spell-qtl} in order to generate these files (see \vref{spell-qtl:processing-options}.)
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\subsection{full map}

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The special text file named \texttt{full\_map.txt} is produced at the root of the \texttt{my name.report} directory. The full genetic map is drawn using text characters. Any detected QTL (for any trait under study) is inserted in this map with its confidence interval (figure \vref{fig:full-map}). 
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\begin{figure}[h]
\includegraphics[width=1.0\textwidth]{full_map.png}
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\caption{screen capture of \texttt{less -RS full\_map.txt} in an \textit{ad hoc} resized terminal. Chromosome names are printed in light blue. The chromosome and the marker names are in white. The detected QTL and its confidence interval are added in green, labeled with trait name (\texttt{t1}), \texttt{@},  QTL position (\texttt{135.34}) and confidence interval (\texttt{[129.246:140.84]})}
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\label{fig:full-map}
\end{figure}

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Note that you must use the \texttt{cat} or \texttt{less -RS} command in order to see it properly. \texttt{more} command, \texttt{less} command or your favorite text editor may fail to read special characters. 
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\subsection{Trait by trait reports}
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For every trait under analysis, a report directory is generated (this directory name is the trait name). Within this directory the report file itself is named after the trait name followed by \texttt{\_report.txt}
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This file is divided in several parts. For the sample file \vref{sample:report} they are :
\begin{description}
\item[General information (lines 1-7)] Trait name and what was detected (QTLs positions and confidence intervals)
\item[R2 (lines 12-20)] Part of the variance explained by each QTL
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\item[Coefficients (lines 22-54)] Cross effects and QTLs allele effects are displayed with their estimated vairiance-covariance matrix
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\item[Contrasts (lines 57-79 and 81-103)] Spell-QTL computes all tractable contrasts and tests their significances. Spell-QTL displays a contrasts section for each comparable effect group. 
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\item[Final Model (lines 105-325)] The final linear model for this detection is then displayed in human readable form. (It is available in computer readable form in files \texttt{trait\_values.txt} and  \texttt{Model\_*X.txt})
\item[Final Model inversion (lines 328-351)] $(X^tX)^{-1}$ matrix from linear model solving in human readable form. (It is available in computer readable form in file \texttt{Model\_*\_XtX\_inv.txt}).
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\end{description}

\lstinputlisting[numbers=left,
		frame=single,
		caption={[report file] sample report file (\texttt{t1\_report.txt}  in directory \texttt{my\_directory/my\_name.report/t1} )  },
		label={sample:report}
]
{output_files/t1_report.txt}