From 41a8f2381b0d2d2f7d6aa5d50dee93d96af3ff39 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Tue, 26 Jul 2016 10:49:46 +0600
Subject: Docs: genotype

---
 doc/Architecture.org                                  | 19 ++++++++++---------
 .../marker_regression/marker_regression_gn1.py        |  2 +-
 2 files changed, 11 insertions(+), 10 deletions(-)

diff --git a/doc/Architecture.org b/doc/Architecture.org
index e3bc8026..a1fcbef2 100644
--- a/doc/Architecture.org
+++ b/doc/Architecture.org
@@ -66,8 +66,9 @@ see the installation [[./README.org][instructions]].
 
 Genotypes are stored in genotype files. These are part of the GNU Guix
 distribution, see the installation [[./README.org][instructions]]. Genotype files are
-currently in GN1 format, and will be aligned with the [[http://kbroman.org/qtl2/pages/sampledata.html][R/qtl2
-formats]]. Currently it is for the stored file BXD.geno:
+currently in GN1 format, and will be aligned with the [[http://kbroman.org/qtl2/pages/sampledata.html][R/qtl2 formats]].
+
+GN1-style (still default GN2) for the stored file BXD.geno:
 
 #+begin_src js
 @name:BXD
@@ -130,21 +131,21 @@ genotype data is tagged as transposed:
 "founder_geno": "recla_foundergeno.csv",
 "founder_geno_transposed": true,
 "genotypes": {
-"1": "1",
-"2": "2",
-"3": "3"
+  "1": "1",
+  "2": "2",
+  "3": "3"
 },
 "pheno": "recla_pheno.csv",
 "pheno_transposed": false,
 "covar": "recla_covar.csv",
 "sex": {
-"covar": "Sex",
-"female": "female",
-"male": "male"
+  "covar": "Sex",
+  "female": "female",
+  "male": "male"
 },
 "x_chr": "X",
 "cross_info": {
-"covar": "ngen"
+  "covar": "ngen"
 },
 "gmap": "recla_gmap.csv",
 "pmap": "recla_pmap.csv",
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index 9573a9de..33ebc527 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -382,7 +382,7 @@ class MarkerRegression(object):
             self.GraphInterval = self.MbGraphInterval #Mb
         else:
             self.GraphInterval = self.cMGraphInterval #cM
-			
+
         ################################################################
         # Get Trait Values and Infomation
         ################################################################
-- 
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