[med-svn] [eigensoft] 09/12: Add at least one manpage where the executable does some sensible printout. Install examples

[Andreas Tille]

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commit 35dd40f6e2a0e2744105dbc03e29abe29f0c9f3c
Author: Andreas Tille <tille at debian.org>
Date:   Tue Jul 19 10:57:39 2016 +0200

    Add at least one manpage where the executable does some sensible printout.  Install examples
---
 debian/changelog              |  2 ++
 debian/copyright              |  1 +
 debian/examples               |  3 +++
 debian/manpages               |  1 +
 debian/mans/smarteigenstrat.1 | 34 ++++++++++++++++++++++++++++++++++
 5 files changed, 41 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index 4483761..bbbe8ee 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -7,6 +7,8 @@ eigensoft (6.1.2+dfsg-1) UNRELEASED; urgency=medium
   * cme fix dpkg-control
   * hardening=+bindnow
   * Leave only wrapper scripts in /usr/bin, executables go to /usr/lib/eigensoft
+  * add at least one manpage
+  * add examples
 
   [ Tatiana Malygina ]
   * Fix headers
diff --git a/debian/copyright b/debian/copyright
index dd58f4e..684d11d 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -16,6 +16,7 @@ Files-Excluded: bin/baseprog
                 */*.o
                 */*.a
                 */.*.swp
+                */lsqproject.pdf
 
 Files: *
 Copyright: 2010-2016 Alkes Price <aprice at hsph.harvard.edu>,
diff --git a/debian/examples b/debian/examples
new file mode 100644
index 0000000..4725453
--- /dev/null
+++ b/debian/examples
@@ -0,0 +1,3 @@
+CONVERTF
+EIGENSTRAT
+POPGEN
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..63ab24a
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/mans/*
diff --git a/debian/mans/smarteigenstrat.1 b/debian/mans/smarteigenstrat.1
new file mode 100644
index 0000000..f62372f
--- /dev/null
+++ b/debian/mans/smarteigenstrat.1
@@ -0,0 +1,34 @@
+.TH SMARTEIGENSTRAT "1" "July 2016" "smarteigenstrat 6.1.2" "User Commands"
+.SH NAME
+smarteigenstrat \- reduction of population bias for genetic analyses
+.SH SYNOPSIS
+.B smarteigenstrat
+\fB\-i\fR <genotypefile>  \fB\-a\fR <indivfile>  \fB\-b\fR <snpfile>  \fB\-p\fR <pcafile>   \fB\-o\fR <outputfile>      \fB\-l\fR <logfile>  \fB\-k\fR <numpca>  \fB\-q\fR <qtlmode>
+.SH DESCRIPTION
+The program \fBsmarteigenstrat\fR is part of EIGENSOFT.
+.P
+The EIGENSOFT package combines functionality from the group's population
+genetics methods (Patterson et al. 2006) and their EIGENSTRAT stratification
+method (Price et al. 2006). The EIGENSTRAT method uses principal components
+analysis to explicitly model ancestry differences between cases and
+controls along continuous axes of variation; the resulting correction is
+specific to a candidate marker's variation in frequency across ancestral
+populations, minimizing spurious associations while maximizing power to
+detect true associations. The EIGENSOFT package has a built-in plotting
+script and supports multiple file formats and quantitative phenotypes.
+.SH OPTIONS
+.TP
+\fB\-i\fR
+genotype file (PED, PACKEDPED, EIGENSTRAT, ANCESTRYMAP or PACKEDANCESTRYMAP format)\-o  output file (chisq)
+.TP
+\fB\-l\fR
+logfile (screen output,including error messages)
+.TP
+\fB\-q\fR
+YES for quantitative phenotype or NO otherwise
+.PP
+For quantitative phenotype, sixth column of .ped file or third column of EIGENSTRAT .ind file
+should be real numbers.  For non\-quantitative phenotype, sixth column of .ped or third column
+should be 'Case' or 'Control'
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

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