diff --git a/src/PyPop/xslt/__init__.py b/src/PyPop/xslt/__init__.py
index e69de29bb..1f33e8ba5 100644
--- a/src/PyPop/xslt/__init__.py
+++ b/src/PyPop/xslt/__init__.py
@@ -0,0 +1,101 @@
+#!/usr/bin/env python
+
+# This file is part of PyPop
+
+# Copyright (C) 2024
+# All Rights Reserved.
+
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2, or (at your option)
+# any later version.
+
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
+# 02111-1307, USA.
+
+# IN NO EVENT SHALL REGENTS BE LIABLE TO ANY PARTY FOR DIRECT,
+# INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING
+# LOST PROFITS, ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS
+# DOCUMENTATION, EVEN IF REGENTS HAS BEEN ADVISED OF THE POSSIBILITY
+# OF SUCH DAMAGE.
+
+# REGENTS SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT
+# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
+# FOR A PARTICULAR PURPOSE. THE SOFTWARE AND ACCOMPANYING
+# DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED "AS
+# IS". REGENTS HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT,
+# UPDATES, ENHANCEMENTS, OR MODIFICATIONS.
+
+"""
+Python XSLT extensions for handling things outside the scope of XSLT 1.0
+
+"""
+
+from lxml import etree
+from math import floor, log10, inf
+from numpy import format_float_scientific
+
+ns = etree.FunctionNamespace('http://pypop.org/lxml/functions')
+ns.prefix = 'es'
+
+def num_zeros(decimal):
+ return inf if decimal == 0 else -floor(log10(abs(decimal))) - 1
+
+def exponent_len(num):
+ # length of exponent, e.g.
+ # "e-3', would be two characters ('-3')
+ # "e-10" would be 3, ('-10')
+ return len(str(floor(log10(num))))
+
+@ns
+def format_number_fixed_width(context, *args):
+
+ num = float(args[0])
+ places = int(args[1])
+ zeros_before_sig_figs = num_zeros(num)
+
+ if zeros_before_sig_figs >= places and zeros_before_sig_figs != inf:
+ # get exponent size
+ exponent_size = exponent_len(num)
+ # need to reserve space for 'e', plus exponent characters
+ total_exponent_size = 1 + exponent_size
+ # use all remaining characters for precision
+ precision = places - total_exponent_size if places >= total_exponent_size else 0
+ # now format it
+ retval = format_float_scientific(num, exp_digits=1, precision=precision, trim='-')
+ else:
+ retval = "{0:.{1}f}".format(num, places)
+ return retval
+
+if __name__ == "__main__":
+
+ # some tests
+
+ ns['format_number_fixed_width'] = format_number_fixed_width
+
+ root = etree.XML('0.0000043')
+ doc = etree.ElementTree(root)
+
+ xslt = etree.XSLT(etree.XML('''
+
+
+
+ Yep [
+
+ ]
+
+
+ '''))
+
+ print(xslt(doc))
+
+
diff --git a/src/PyPop/xslt/emhaplofreq.xsl b/src/PyPop/xslt/emhaplofreq.xsl
index 81f65b56c..b0a29a976 100644
--- a/src/PyPop/xslt/emhaplofreq.xsl
+++ b/src/PyPop/xslt/emhaplofreq.xsl
@@ -476,7 +476,7 @@ MODIFICATIONS.
-
+
diff --git a/src/PyPop/xslt/hardyweinberg.xsl b/src/PyPop/xslt/hardyweinberg.xsl
index 21035a7ab..2475c40ae 100644
--- a/src/PyPop/xslt/hardyweinberg.xsl
+++ b/src/PyPop/xslt/hardyweinberg.xsl
@@ -482,9 +482,11 @@ MODIFICATIONS.
-
+
+
-
+
+
diff --git a/src/PyPop/xslt/lib.xsl b/src/PyPop/xslt/lib.xsl
index f69a555c9..61144316b 100644
--- a/src/PyPop/xslt/lib.xsl
+++ b/src/PyPop/xslt/lib.xsl
@@ -33,8 +33,11 @@ MODIFICATIONS.
-->
+ xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
+ xmlns:es="http://pypop.org/lxml/functions">
+
+
@@ -100,9 +103,18 @@ MODIFICATIONS.
-
+
+
+
+
+
+
+
+
+
+
+
diff --git a/tests/base.py b/tests/base.py
index b4727fd2e..05f0b44a3 100644
--- a/tests/base.py
+++ b/tests/base.py
@@ -62,6 +62,7 @@ def abspath_test_data(filename):
def filecmp_ignore_newlines(out_filename, gold_out_filename):
l1 = l2 = True
+ retval = True # default to match, unless there is a diff
# opening up files defaults to 'universal newlines' this ignores OS-specific newline differences
with open(out_filename, 'r') as f1, open(gold_out_filename, 'r') as f2:
while l1 and l2:
@@ -69,12 +70,14 @@ def filecmp_ignore_newlines(out_filename, gold_out_filename):
l2 = f2.readline()
if l1 != l2:
# generate the full-diff
- diff = unified_diff(open(out_filename, 'r').readlines(), open(gold_out_filename, 'r').readlines())
+ diff = unified_diff(open(gold_out_filename, 'r').readlines(), open(out_filename, 'r').readlines())
delta = ''.join(diff)
print (delta)
- return False
- return True
+ retval = False # mismatch
+ break
+
+ return retval
def filecmp_list_of_files(filename_list, gold_out_directory):
diff --git a/tests/data/gold-output/USAFEL-UchiTelle-small-Filters_CustomBinning-out.txt b/tests/data/gold-output/USAFEL-UchiTelle-small-Filters_CustomBinning-out.txt
index a7f7be2bd..2296e1a73 100644
--- a/tests/data/gold-output/USAFEL-UchiTelle-small-Filters_CustomBinning-out.txt
+++ b/tests/data/gold-output/USAFEL-UchiTelle-small-Filters_CustomBinning-out.txt
@@ -63,15 +63,15 @@ Total 1.00000 16 | Total 1.00000 16
----------------------
Table of genotypes, format of each cell is: observed/expected.
-01:01 0/0.0
-02:01 0/0.3 1/0.5
-02:10 0/0.1 0/0.5 0/0.1
-02:18 1/0.1 0/0.3 0/0.1 0/0.0
-03:01 0/0.1 0/0.5 1/0.3 0/0.1 0/0.1
-25:01 0/0.1 1/0.5 0/0.3 0/0.1 0/0.3 0/0.1
-32:04 0/0.2 0/0.8 1/0.4 0/0.2 1/0.4 1/0.4 0/0.3
-68:14 0/0.1 1/0.3 0/0.1 0/0.1 0/0.1 0/0.1 0/0.2 0/0.0
- 01:01 02:01 02:10 02:18 03:01 25:01 32:04 68:14
+01:01 0/3e-2
+02:01 0/0.2 1/0.5
+02:10 0/0.1 0/0.5 0/0.1
+02:18 1/6e-2 0/0.2 0/0.1 0/3e-2
+03:01 0/0.1 0/0.5 1/0.2 0/0.1 0/0.1
+25:01 0/0.1 1/0.5 0/0.2 0/0.1 0/0.2 0/0.1
+32:04 0/0.2 0/0.8 1/0.4 0/0.2 1/0.4 1/0.4 0/0.3
+68:14 0/6e-2 1/0.2 0/0.1 0/6e-2 0/0.1 0/0.1 0/0.2 0/3e-2
+ 01:01 02:01 02:10 02:18 03:01 25:01 32:04 68:14
[Cols: 1 to 8]
Observed Expected Chi-square DoF p-value
@@ -85,7 +85,7 @@ Table of genotypes, format of each cell is: observed/expected.
Common + lumped Value not calculated.
------------------------------------------------------------------------------------------
-All heterozygotes 7 6.75 0.01 1 0.9233
+All heterozygotes 7 6.75 9e-3 1 0.9233
------------------------------------------------------------------------------------------
Common heterozygotes by allele
@@ -124,16 +124,16 @@ Total 1.00000 20 | Total 1.00000 20
----------------------
Table of genotypes, format of each cell is: observed/expected.
- 01:02 0/0.4
-02:025 1/0.4 0/0.1
- 03:07 0/0.8 0/0.4 1/0.4
- 06:05 0/0.4 0/0.2 1/0.4 0/0.1
- 07:12 2/0.4 0/0.2 0/0.4 0/0.2 0/0.1
- 08:04 0/0.2 0/0.1 0/0.2 0/0.1 0/0.1 0/0.0
- 12:02 0/0.4 1/0.2 0/0.4 0/0.2 0/0.2 1/0.1 0/0.1
- 15:07 0/0.4 0/0.2 1/0.4 1/0.2 0/0.2 0/0.1 0/0.2 0/0.1
- 18:01 1/0.2 0/0.1 0/0.2 0/0.1 0/0.1 0/0.1 0/0.1 0/0.1 0/0.0
- 01:0202:025 03:07 06:05 07:12 08:04 12:02 15:07 18:01
+ 01:02 0/0.4
+02:025 1/0.4 0/0.1
+ 03:07 0/0.8 0/0.4 1/0.4
+ 06:05 0/0.4 0/0.2 1/0.4 0/0.1
+ 07:12 2/0.4 0/0.2 0/0.4 0/0.2 0/0.1
+ 08:04 0/0.2 0/0.1 0/0.2 0/0.1 0/0.1 0/3e-2
+ 12:02 0/0.4 1/0.2 0/0.4 0/0.2 0/0.2 1/0.1 0/0.1
+ 15:07 0/0.4 0/0.2 1/0.4 1/0.2 0/0.2 0/0.1 0/0.2 0/0.1
+ 18:01 1/0.2 0/0.1 0/0.2 0/0.1 0/0.1 0/5e-2 0/0.1 0/0.1 0/3e-2
+ 01:02 02:025 03:07 06:05 07:12 08:04 12:02 15:07 18:01
[Cols: 1 to 9]
Observed Expected Chi-square DoF p-value
diff --git a/tests/data/gold-output/USAFEL-UchiTelle-small-Filters_DigitBinning-out.txt b/tests/data/gold-output/USAFEL-UchiTelle-small-Filters_DigitBinning-out.txt
index 3f39c8c6e..b6d67ca20 100644
--- a/tests/data/gold-output/USAFEL-UchiTelle-small-Filters_DigitBinning-out.txt
+++ b/tests/data/gold-output/USAFEL-UchiTelle-small-Filters_DigitBinning-out.txt
@@ -61,13 +61,13 @@ Total1.00000 16 | Total1.00000 16
----------------------
Table of genotypes, format of each cell is: observed/expected.
-01 0/0.0
-02 1/0.4 1/1.5
-03 0/0.1 1/0.9 0/0.1
-25 0/0.1 1/0.9 0/0.3 0/0.1
-32 0/0.2 1/1.3 1/0.4 1/0.4 0/0.3
-68 0/0.1 1/0.4 0/0.1 0/0.1 0/0.2 0/0.0
- 01 02 03 25 32 68
+01 0/3e-2
+02 1/0.4 1/1.5
+03 0/0.1 1/0.9 0/0.1
+25 0/0.1 1/0.9 0/0.2 0/0.1
+32 0/0.2 1/1.3 1/0.4 1/0.4 0/0.3
+68 0/6e-2 1/0.4 0/0.1 0/0.1 0/0.2 0/3e-2
+ 01 02 03 25 32 68
[Cols: 1 to 6]
Observed Expected Chi-square DoF p-value
@@ -120,16 +120,16 @@ Total1.00000 20 | Total1.00000 20
----------------------
Table of genotypes, format of each cell is: observed/expected.
-01 0/0.4
-02 1/0.4 0/0.1
-03 0/0.8 0/0.4 1/0.4
-06 0/0.4 0/0.2 1/0.4 0/0.1
-07 2/0.4 0/0.2 0/0.4 0/0.2 0/0.1
-08 0/0.2 0/0.1 0/0.2 0/0.1 0/0.1 0/0.0
-12 0/0.4 1/0.2 0/0.4 0/0.2 0/0.2 1/0.1 0/0.1
-15 0/0.4 0/0.2 1/0.4 1/0.2 0/0.2 0/0.1 0/0.2 0/0.1
-18 1/0.2 0/0.1 0/0.2 0/0.1 0/0.1 0/0.1 0/0.1 0/0.1 0/0.0
- 01 02 03 06 07 08 12 15 18
+01 0/0.4
+02 1/0.4 0/0.1
+03 0/0.8 0/0.4 1/0.4
+06 0/0.4 0/0.2 1/0.4 0/0.1
+07 2/0.4 0/0.2 0/0.4 0/0.2 0/0.1
+08 0/0.2 0/0.1 0/0.2 0/0.1 0/0.1 0/3e-2
+12 0/0.4 1/0.2 0/0.4 0/0.2 0/0.2 1/0.1 0/0.1
+15 0/0.4 0/0.2 1/0.4 1/0.2 0/0.2 0/0.1 0/0.2 0/0.1
+18 1/0.2 0/0.1 0/0.2 0/0.1 0/0.1 0/5e-2 0/0.1 0/0.1 0/3e-2
+ 01 02 03 06 07 08 12 15 18
[Cols: 1 to 9]
Observed Expected Chi-square DoF p-value
diff --git a/tests/data/gold-output/USAFEL-UchiTelle-small-out-no-emhaplofreq-noguothompson-no-slatkin.txt b/tests/data/gold-output/USAFEL-UchiTelle-small-out-no-emhaplofreq-noguothompson-no-slatkin.txt
index 6e34bd7d2..6bcd58574 100644
--- a/tests/data/gold-output/USAFEL-UchiTelle-small-out-no-emhaplofreq-noguothompson-no-slatkin.txt
+++ b/tests/data/gold-output/USAFEL-UchiTelle-small-out-no-emhaplofreq-noguothompson-no-slatkin.txt
@@ -63,15 +63,15 @@ Total 1.00000 16 | Total 1.00000 16
----------------------
Table of genotypes, format of each cell is: observed/expected.
- 01:01 0/0.0
- 02:01 0/0.3 1/0.5
- 02:10 0/0.1 0/0.5 0/0.1
- 02:18 1/0.1 0/0.3 0/0.1 0/0.0
-03:012 0/0.1 0/0.5 1/0.3 0/0.1 0/0.1
- 25:01 0/0.1 1/0.5 0/0.3 0/0.1 0/0.3 0/0.1
- 32:04 0/0.2 0/0.8 1/0.4 0/0.2 1/0.4 1/0.4 0/0.3
- 68:14 0/0.1 1/0.3 0/0.1 0/0.1 0/0.1 0/0.1 0/0.2 0/0.0
- 01:01 02:01 02:10 02:1803:012 25:01 32:04 68:14
+ 01:01 0/3e-2
+ 02:01 0/0.2 1/0.5
+ 02:10 0/0.1 0/0.5 0/0.1
+ 02:18 1/6e-2 0/0.2 0/0.1 0/3e-2
+03:012 0/0.1 0/0.5 1/0.2 0/0.1 0/0.1
+ 25:01 0/0.1 1/0.5 0/0.2 0/0.1 0/0.2 0/0.1
+ 32:04 0/0.2 0/0.8 1/0.4 0/0.2 1/0.4 1/0.4 0/0.3
+ 68:14 0/6e-2 1/0.2 0/0.1 0/6e-2 0/0.1 0/0.1 0/0.2 0/3e-2
+ 01:01 02:01 02:10 02:18 03:012 25:01 32:04 68:14
[Cols: 1 to 8]
Observed Expected Chi-square DoF p-value
@@ -85,7 +85,7 @@ Table of genotypes, format of each cell is: observed/expected.
Common + lumped Value not calculated.
------------------------------------------------------------------------------------------
-All heterozygotes 7 6.75 0.01 1 0.9233
+All heterozygotes 7 6.75 9e-3 1 0.9233
------------------------------------------------------------------------------------------
Common heterozygotes by allele
@@ -124,16 +124,16 @@ Total 1.00000 20 | Total 1.00000 20
----------------------
Table of genotypes, format of each cell is: observed/expected.
- 01:02 0/0.4
-02:025 1/0.4 0/0.1
- 03:07 0/0.8 0/0.4 1/0.4
- 06:05 0/0.4 0/0.2 1/0.4 0/0.1
- 07:12 2/0.4 0/0.2 0/0.4 0/0.2 0/0.1
- 08:04 0/0.2 0/0.1 0/0.2 0/0.1 0/0.1 0/0.0
- 12:02 0/0.4 1/0.2 0/0.4 0/0.2 0/0.2 1/0.1 0/0.1
- 15:07 0/0.4 0/0.2 1/0.4 1/0.2 0/0.2 0/0.1 0/0.2 0/0.1
- 18:01 1/0.2 0/0.1 0/0.2 0/0.1 0/0.1 0/0.1 0/0.1 0/0.1 0/0.0
- 01:0202:025 03:07 06:05 07:12 08:04 12:02 15:07 18:01
+ 01:02 0/0.4
+02:025 1/0.4 0/0.1
+ 03:07 0/0.8 0/0.4 1/0.4
+ 06:05 0/0.4 0/0.2 1/0.4 0/0.1
+ 07:12 2/0.4 0/0.2 0/0.4 0/0.2 0/0.1
+ 08:04 0/0.2 0/0.1 0/0.2 0/0.1 0/0.1 0/3e-2
+ 12:02 0/0.4 1/0.2 0/0.4 0/0.2 0/0.2 1/0.1 0/0.1
+ 15:07 0/0.4 0/0.2 1/0.4 1/0.2 0/0.2 0/0.1 0/0.2 0/0.1
+ 18:01 1/0.2 0/0.1 0/0.2 0/0.1 0/0.1 0/5e-2 0/0.1 0/0.1 0/3e-2
+ 01:02 02:025 03:07 06:05 07:12 08:04 12:02 15:07 18:01
[Cols: 1 to 9]
Observed Expected Chi-square DoF p-value
diff --git a/tests/data/gold-output/USAFEL-UchiTelle-small-out-no-emhaplofreq-noguothompson.txt b/tests/data/gold-output/USAFEL-UchiTelle-small-out-no-emhaplofreq-noguothompson.txt
index 1eb670434..6fbcff606 100644
--- a/tests/data/gold-output/USAFEL-UchiTelle-small-out-no-emhaplofreq-noguothompson.txt
+++ b/tests/data/gold-output/USAFEL-UchiTelle-small-out-no-emhaplofreq-noguothompson.txt
@@ -63,15 +63,15 @@ Total 1.00000 16 | Total 1.00000 16
----------------------
Table of genotypes, format of each cell is: observed/expected.
- 01:01 0/0.0
- 02:01 0/0.3 1/0.5
- 02:10 0/0.1 0/0.5 0/0.1
- 02:18 1/0.1 0/0.3 0/0.1 0/0.0
-03:012 0/0.1 0/0.5 1/0.3 0/0.1 0/0.1
- 25:01 0/0.1 1/0.5 0/0.3 0/0.1 0/0.3 0/0.1
- 32:04 0/0.2 0/0.8 1/0.4 0/0.2 1/0.4 1/0.4 0/0.3
- 68:14 0/0.1 1/0.3 0/0.1 0/0.1 0/0.1 0/0.1 0/0.2 0/0.0
- 01:01 02:01 02:10 02:1803:012 25:01 32:04 68:14
+ 01:01 0/3e-2
+ 02:01 0/0.2 1/0.5
+ 02:10 0/0.1 0/0.5 0/0.1
+ 02:18 1/6e-2 0/0.2 0/0.1 0/3e-2
+03:012 0/0.1 0/0.5 1/0.2 0/0.1 0/0.1
+ 25:01 0/0.1 1/0.5 0/0.2 0/0.1 0/0.2 0/0.1
+ 32:04 0/0.2 0/0.8 1/0.4 0/0.2 1/0.4 1/0.4 0/0.3
+ 68:14 0/6e-2 1/0.2 0/0.1 0/6e-2 0/0.1 0/0.1 0/0.2 0/3e-2
+ 01:01 02:01 02:10 02:18 03:012 25:01 32:04 68:14
[Cols: 1 to 8]
Observed Expected Chi-square DoF p-value
@@ -85,7 +85,7 @@ Table of genotypes, format of each cell is: observed/expected.
Common + lumped Value not calculated.
------------------------------------------------------------------------------------------
-All heterozygotes 7 6.75 0.01 1 0.9233
+All heterozygotes 7 6.75 9e-3 1 0.9233
------------------------------------------------------------------------------------------
Common heterozygotes by allele
@@ -129,16 +129,16 @@ Total 1.00000 20 | Total 1.00000 20
----------------------
Table of genotypes, format of each cell is: observed/expected.
- 01:02 0/0.4
-02:025 1/0.4 0/0.1
- 03:07 0/0.8 0/0.4 1/0.4
- 06:05 0/0.4 0/0.2 1/0.4 0/0.1
- 07:12 2/0.4 0/0.2 0/0.4 0/0.2 0/0.1
- 08:04 0/0.2 0/0.1 0/0.2 0/0.1 0/0.1 0/0.0
- 12:02 0/0.4 1/0.2 0/0.4 0/0.2 0/0.2 1/0.1 0/0.1
- 15:07 0/0.4 0/0.2 1/0.4 1/0.2 0/0.2 0/0.1 0/0.2 0/0.1
- 18:01 1/0.2 0/0.1 0/0.2 0/0.1 0/0.1 0/0.1 0/0.1 0/0.1 0/0.0
- 01:0202:025 03:07 06:05 07:12 08:04 12:02 15:07 18:01
+ 01:02 0/0.4
+02:025 1/0.4 0/0.1
+ 03:07 0/0.8 0/0.4 1/0.4
+ 06:05 0/0.4 0/0.2 1/0.4 0/0.1
+ 07:12 2/0.4 0/0.2 0/0.4 0/0.2 0/0.1
+ 08:04 0/0.2 0/0.1 0/0.2 0/0.1 0/0.1 0/3e-2
+ 12:02 0/0.4 1/0.2 0/0.4 0/0.2 0/0.2 1/0.1 0/0.1
+ 15:07 0/0.4 0/0.2 1/0.4 1/0.2 0/0.2 0/0.1 0/0.2 0/0.1
+ 18:01 1/0.2 0/0.1 0/0.2 0/0.1 0/0.1 0/5e-2 0/0.1 0/0.1 0/3e-2
+ 01:02 02:025 03:07 06:05 07:12 08:04 12:02 15:07 18:01
[Cols: 1 to 9]
Observed Expected Chi-square DoF p-value
diff --git a/tests/data/gold-output/USAFEL-UchiTelle-small-out-no-emhaplofreq.txt b/tests/data/gold-output/USAFEL-UchiTelle-small-out-no-emhaplofreq.txt
index d87c54abb..5ff69ccf4 100644
--- a/tests/data/gold-output/USAFEL-UchiTelle-small-out-no-emhaplofreq.txt
+++ b/tests/data/gold-output/USAFEL-UchiTelle-small-out-no-emhaplofreq.txt
@@ -63,15 +63,15 @@ Total 1.00000 16 | Total 1.00000 16
----------------------
Table of genotypes, format of each cell is: observed/expected.
- 01:01 0/0.0
- 02:01 0/0.3 1/0.5
- 02:10 0/0.1 0/0.5 0/0.1
- 02:18 1/0.1 0/0.3 0/0.1 0/0.0
-03:012 0/0.1 0/0.5 1/0.3 0/0.1 0/0.1
- 25:01 0/0.1 1/0.5 0/0.3 0/0.1 0/0.3 0/0.1
- 32:04 0/0.2 0/0.8 1/0.4 0/0.2 1/0.4 1/0.4 0/0.3
- 68:14 0/0.1 1/0.3 0/0.1 0/0.1 0/0.1 0/0.1 0/0.2 0/0.0
- 01:01 02:01 02:10 02:1803:012 25:01 32:04 68:14
+ 01:01 0/3e-2
+ 02:01 0/0.2 1/0.5
+ 02:10 0/0.1 0/0.5 0/0.1
+ 02:18 1/6e-2 0/0.2 0/0.1 0/3e-2
+03:012 0/0.1 0/0.5 1/0.2 0/0.1 0/0.1
+ 25:01 0/0.1 1/0.5 0/0.2 0/0.1 0/0.2 0/0.1
+ 32:04 0/0.2 0/0.8 1/0.4 0/0.2 1/0.4 1/0.4 0/0.3
+ 68:14 0/6e-2 1/0.2 0/0.1 0/6e-2 0/0.1 0/0.1 0/0.2 0/3e-2
+ 01:01 02:01 02:10 02:18 03:012 25:01 32:04 68:14
[Cols: 1 to 8]
Observed Expected Chi-square DoF p-value
@@ -85,7 +85,7 @@ Table of genotypes, format of each cell is: observed/expected.
Common + lumped Value not calculated.
------------------------------------------------------------------------------------------
-All heterozygotes 7 6.75 0.01 1 0.9233
+All heterozygotes 7 6.75 9e-3 1 0.9233
------------------------------------------------------------------------------------------
Common heterozygotes by allele
@@ -138,16 +138,16 @@ Total 1.00000 20 | Total 1.00000 20
----------------------
Table of genotypes, format of each cell is: observed/expected.
- 01:02 0/0.4
-02:025 1/0.4 0/0.1
- 03:07 0/0.8 0/0.4 1/0.4
- 06:05 0/0.4 0/0.2 1/0.4 0/0.1
- 07:12 2/0.4 0/0.2 0/0.4 0/0.2 0/0.1
- 08:04 0/0.2 0/0.1 0/0.2 0/0.1 0/0.1 0/0.0
- 12:02 0/0.4 1/0.2 0/0.4 0/0.2 0/0.2 1/0.1 0/0.1
- 15:07 0/0.4 0/0.2 1/0.4 1/0.2 0/0.2 0/0.1 0/0.2 0/0.1
- 18:01 1/0.2 0/0.1 0/0.2 0/0.1 0/0.1 0/0.1 0/0.1 0/0.1 0/0.0
- 01:0202:025 03:07 06:05 07:12 08:04 12:02 15:07 18:01
+ 01:02 0/0.4
+02:025 1/0.4 0/0.1
+ 03:07 0/0.8 0/0.4 1/0.4
+ 06:05 0/0.4 0/0.2 1/0.4 0/0.1
+ 07:12 2/0.4 0/0.2 0/0.4 0/0.2 0/0.1
+ 08:04 0/0.2 0/0.1 0/0.2 0/0.1 0/0.1 0/3e-2
+ 12:02 0/0.4 1/0.2 0/0.4 0/0.2 0/0.2 1/0.1 0/0.1
+ 15:07 0/0.4 0/0.2 1/0.4 1/0.2 0/0.2 0/0.1 0/0.2 0/0.1
+ 18:01 1/0.2 0/0.1 0/0.2 0/0.1 0/0.1 0/5e-2 0/0.1 0/0.1 0/3e-2
+ 01:02 02:025 03:07 06:05 07:12 08:04 12:02 15:07 18:01
[Cols: 1 to 9]
Observed Expected Chi-square DoF p-value
diff --git a/tests/data/gold-output/USAFEL-UchiTelle-small-out.txt b/tests/data/gold-output/USAFEL-UchiTelle-small-out.txt
index 02d725d09..73e6c552b 100644
--- a/tests/data/gold-output/USAFEL-UchiTelle-small-out.txt
+++ b/tests/data/gold-output/USAFEL-UchiTelle-small-out.txt
@@ -63,15 +63,15 @@ Total 1.00000 16 | Total 1.00000 16
----------------------
Table of genotypes, format of each cell is: observed/expected.
- 01:01 0/0.0
- 02:01 0/0.3 1/0.5
- 02:10 0/0.1 0/0.5 0/0.1
- 02:18 1/0.1 0/0.3 0/0.1 0/0.0
-03:012 0/0.1 0/0.5 1/0.3 0/0.1 0/0.1
- 25:01 0/0.1 1/0.5 0/0.3 0/0.1 0/0.3 0/0.1
- 32:04 0/0.2 0/0.8 1/0.4 0/0.2 1/0.4 1/0.4 0/0.3
- 68:14 0/0.1 1/0.3 0/0.1 0/0.1 0/0.1 0/0.1 0/0.2 0/0.0
- 01:01 02:01 02:10 02:1803:012 25:01 32:04 68:14
+ 01:01 0/3e-2
+ 02:01 0/0.2 1/0.5
+ 02:10 0/0.1 0/0.5 0/0.1
+ 02:18 1/6e-2 0/0.2 0/0.1 0/3e-2
+03:012 0/0.1 0/0.5 1/0.2 0/0.1 0/0.1
+ 25:01 0/0.1 1/0.5 0/0.2 0/0.1 0/0.2 0/0.1
+ 32:04 0/0.2 0/0.8 1/0.4 0/0.2 1/0.4 1/0.4 0/0.3
+ 68:14 0/6e-2 1/0.2 0/0.1 0/6e-2 0/0.1 0/0.1 0/0.2 0/3e-2
+ 01:01 02:01 02:10 02:18 03:012 25:01 32:04 68:14
[Cols: 1 to 8]
Observed Expected Chi-square DoF p-value
@@ -85,7 +85,7 @@ Table of genotypes, format of each cell is: observed/expected.
Common + lumped Value not calculated.
------------------------------------------------------------------------------------------
-All heterozygotes 7 6.75 0.01 1 0.9233
+All heterozygotes 7 6.75 9e-3 1 0.9233
------------------------------------------------------------------------------------------
Common heterozygotes by allele
@@ -138,16 +138,16 @@ Total 1.00000 20 | Total 1.00000 20
----------------------
Table of genotypes, format of each cell is: observed/expected.
- 01:02 0/0.4
-02:025 1/0.4 0/0.1
- 03:07 0/0.8 0/0.4 1/0.4
- 06:05 0/0.4 0/0.2 1/0.4 0/0.1
- 07:12 2/0.4 0/0.2 0/0.4 0/0.2 0/0.1
- 08:04 0/0.2 0/0.1 0/0.2 0/0.1 0/0.1 0/0.0
- 12:02 0/0.4 1/0.2 0/0.4 0/0.2 0/0.2 1/0.1 0/0.1
- 15:07 0/0.4 0/0.2 1/0.4 1/0.2 0/0.2 0/0.1 0/0.2 0/0.1
- 18:01 1/0.2 0/0.1 0/0.2 0/0.1 0/0.1 0/0.1 0/0.1 0/0.1 0/0.0
- 01:0202:025 03:07 06:05 07:12 08:04 12:02 15:07 18:01
+ 01:02 0/0.4
+02:025 1/0.4 0/0.1
+ 03:07 0/0.8 0/0.4 1/0.4
+ 06:05 0/0.4 0/0.2 1/0.4 0/0.1
+ 07:12 2/0.4 0/0.2 0/0.4 0/0.2 0/0.1
+ 08:04 0/0.2 0/0.1 0/0.2 0/0.1 0/0.1 0/3e-2
+ 12:02 0/0.4 1/0.2 0/0.4 0/0.2 0/0.2 1/0.1 0/0.1
+ 15:07 0/0.4 0/0.2 1/0.4 1/0.2 0/0.2 0/0.1 0/0.2 0/0.1
+ 18:01 1/0.2 0/0.1 0/0.2 0/0.1 0/0.1 0/5e-2 0/0.1 0/0.1 0/3e-2
+ 01:02 02:025 03:07 06:05 07:12 08:04 12:02 15:07 18:01
[Cols: 1 to 9]
Observed Expected Chi-square DoF p-value
diff --git a/tests/data/gold-output/USAFEL-UchiTelle_with_permu_tsv/USAFEL-UchiTelle-small-out.txt b/tests/data/gold-output/USAFEL-UchiTelle_with_permu_tsv/USAFEL-UchiTelle-small-out.txt
index 861b7f953..b4c750ba2 100644
--- a/tests/data/gold-output/USAFEL-UchiTelle_with_permu_tsv/USAFEL-UchiTelle-small-out.txt
+++ b/tests/data/gold-output/USAFEL-UchiTelle_with_permu_tsv/USAFEL-UchiTelle-small-out.txt
@@ -63,15 +63,15 @@ Total 1.00000 16 | Total 1.00000 16
----------------------
Table of genotypes, format of each cell is: observed/expected.
- 01:01 0/0.0
- 02:01 0/0.3 1/0.5
- 02:10 0/0.1 0/0.5 0/0.1
- 02:18 1/0.1 0/0.3 0/0.1 0/0.0
-03:012 0/0.1 0/0.5 1/0.3 0/0.1 0/0.1
- 25:01 0/0.1 1/0.5 0/0.3 0/0.1 0/0.3 0/0.1
- 32:04 0/0.2 0/0.8 1/0.4 0/0.2 1/0.4 1/0.4 0/0.3
- 68:14 0/0.1 1/0.3 0/0.1 0/0.1 0/0.1 0/0.1 0/0.2 0/0.0
- 01:01 02:01 02:10 02:1803:012 25:01 32:04 68:14
+ 01:01 0/3e-2
+ 02:01 0/0.2 1/0.5
+ 02:10 0/0.1 0/0.5 0/0.1
+ 02:18 1/6e-2 0/0.2 0/0.1 0/3e-2
+03:012 0/0.1 0/0.5 1/0.2 0/0.1 0/0.1
+ 25:01 0/0.1 1/0.5 0/0.2 0/0.1 0/0.2 0/0.1
+ 32:04 0/0.2 0/0.8 1/0.4 0/0.2 1/0.4 1/0.4 0/0.3
+ 68:14 0/6e-2 1/0.2 0/0.1 0/6e-2 0/0.1 0/0.1 0/0.2 0/3e-2
+ 01:01 02:01 02:10 02:18 03:012 25:01 32:04 68:14
[Cols: 1 to 8]
Observed Expected Chi-square DoF p-value
@@ -85,7 +85,7 @@ Table of genotypes, format of each cell is: observed/expected.
Common + lumped Value not calculated.
------------------------------------------------------------------------------------------
-All heterozygotes 7 6.75 0.01 1 0.9233
+All heterozygotes 7 6.75 9e-3 1 0.9233
------------------------------------------------------------------------------------------
Common heterozygotes by allele
@@ -138,16 +138,16 @@ Total 1.00000 20 | Total 1.00000 20
----------------------
Table of genotypes, format of each cell is: observed/expected.
- 01:02 0/0.4
-02:025 1/0.4 0/0.1
- 03:07 0/0.8 0/0.4 1/0.4
- 06:05 0/0.4 0/0.2 1/0.4 0/0.1
- 07:12 2/0.4 0/0.2 0/0.4 0/0.2 0/0.1
- 08:04 0/0.2 0/0.1 0/0.2 0/0.1 0/0.1 0/0.0
- 12:02 0/0.4 1/0.2 0/0.4 0/0.2 0/0.2 1/0.1 0/0.1
- 15:07 0/0.4 0/0.2 1/0.4 1/0.2 0/0.2 0/0.1 0/0.2 0/0.1
- 18:01 1/0.2 0/0.1 0/0.2 0/0.1 0/0.1 0/0.1 0/0.1 0/0.1 0/0.0
- 01:0202:025 03:07 06:05 07:12 08:04 12:02 15:07 18:01
+ 01:02 0/0.4
+02:025 1/0.4 0/0.1
+ 03:07 0/0.8 0/0.4 1/0.4
+ 06:05 0/0.4 0/0.2 1/0.4 0/0.1
+ 07:12 2/0.4 0/0.2 0/0.4 0/0.2 0/0.1
+ 08:04 0/0.2 0/0.1 0/0.2 0/0.1 0/0.1 0/3e-2
+ 12:02 0/0.4 1/0.2 0/0.4 0/0.2 0/0.2 1/0.1 0/0.1
+ 15:07 0/0.4 0/0.2 1/0.4 1/0.2 0/0.2 0/0.1 0/0.2 0/0.1
+ 18:01 1/0.2 0/0.1 0/0.2 0/0.1 0/0.1 0/5e-2 0/0.1 0/0.1 0/3e-2
+ 01:02 02:025 03:07 06:05 07:12 08:04 12:02 15:07 18:01
[Cols: 1 to 9]
Observed Expected Chi-square DoF p-value
diff --git a/tests/data/gold-output/custom-binning-G-Filter/BIGDAWG_SynthControl_Data-out.txt b/tests/data/gold-output/custom-binning-G-Filter/BIGDAWG_SynthControl_Data-out.txt
index 9ae221914..542e5e459 100644
--- a/tests/data/gold-output/custom-binning-G-Filter/BIGDAWG_SynthControl_Data-out.txt
+++ b/tests/data/gold-output/custom-binning-G-Filter/BIGDAWG_SynthControl_Data-out.txt
@@ -108,7 +108,7 @@ Table of genotypes, format of each cell is: observed/expected.
31:01:02G 3/3.0 6/5.7 2/2.8
32:01:01G 1/0.9 2/1.6 1/1.6 0/0.2
32:02 6/5.9 11/10.9 11/10.6 3/3.0 10/10.3
- 33:01:01 0/0.3 1/0.5 0/0.5 0/0.1 1/0.9 0/0.0
+ 33:01:01 0/0.3 1/0.5 0/0.5 0/0.1 1/0.9 0/2e-2
68:01:01G 2/2.3 4/4.3 4/4.2 1/1.2 8/8.1 0/0.4
68:06 5/4.9 9/9.1 9/8.9 3/2.5 17/17.1 1/0.8
29:01:01G29:02:01:02 31:01:02G 32:01:01G 32:02 33:01:01
@@ -122,119 +122,119 @@ Table of genotypes, format of each cell is: observed/expected.
------------------------------------------------------------------------------------------
Common N/A N/A 0.92 65 1.0000
------------------------------------------------------------------------------------------
- Lumped genotypes N/A N/A 0.01 1 0.9395
+ Lumped genotypes N/A N/A 6e-3 1 0.9395
------------------------------------------------------------------------------------------
Common + lumped N/A N/A 0.92 65 1.0000
------------------------------------------------------------------------------------------
- All homozygotes 63 63.35 0.00 1 0.9646
+ All homozygotes 63 63.35 2e-3 1 0.9646
------------------------------------------------------------------------------------------
- All heterozygotes 939 938.65 0.00 1 0.9908
+ All heterozygotes 939 938.65 1e-4 1 0.9908
------------------------------------------------------------------------------------------
Common heterozygotes by allele
-01:01:01G 152 152.25 0.00 0.9839
-02:01:01G 56 56.32 0.00 0.9658
-02:05:01G 132 131.94 0.00 0.9957
-03:01:01G 135 134.51 0.00 0.9662
-03:01:03 102 102.18 0.00 0.9858
-11:01:01G 110 111.05 0.01 0.9205
+01:01:01G 152 152.25 4e-4 0.9839
+02:01:01G 56 56.32 2e-3 0.9658
+02:05:01G 132 131.94 3e-5 0.9957
+03:01:01G 135 134.51 2e-3 0.9662
+03:01:03 102 102.18 3e-4 0.9858
+11:01:01G 110 111.05 1e-2 0.9205
23:01:01G 43 43.99 0.02 0.8814
-24:02:01G 145 144.70 0.00 0.9801
-24:02:04 56 56.32 0.00 0.9658
+24:02:01G 145 144.70 6e-4 0.9801
+24:02:04 56 56.32 2e-3 0.9658
25:01:01G 38 37.28 0.01 0.9061
-26:01:01G 92 91.40 0.00 0.9501
-26:08 105 104.85 0.00 0.9885
-29:01:01G 56 56.32 0.00 0.9658
-29:02:01:02 102 102.18 0.00 0.9858
+26:01:01G 92 91.40 4e-3 0.9501
+26:08 105 104.85 2e-4 0.9885
+29:01:01G 56 56.32 2e-3 0.9658
+29:02:01:02 102 102.18 3e-4 0.9858
31:01:02G 101 99.50 0.02 0.8803
-32:01:01G 30 29.55 0.01 0.9342
-32:02 183 182.44 0.00 0.9667
-33:01:01 9 8.96 0.00 0.9892
-68:01:01G 76 76.81 0.01 0.9267
-68:06 155 154.75 0.00 0.9838
+32:01:01G 30 29.55 7e-3 0.9342
+32:02 183 182.44 2e-3 0.9667
+33:01:01 9 8.96 2e-4 0.9892
+68:01:01G 76 76.81 8e-3 0.9267
+68:06 155 154.75 4e-4 0.9838
------------------------------------------------------------------------------------------
Common genotypes
-01:01:01G+01:01:01G 7 6.88 0.00 0.9621
+01:01:01G+01:01:01G 7 6.88 2e-3 0.9621
01:01:01G+02:05:01G 11 11.76 0.05 0.8241
-01:01:01G+03:01:01G 12 12.01 0.00 0.9975
-01:01:01G+03:01:03 9 8.95 0.00 0.9856
-01:01:01G+11:01:01G 10 9.77 0.01 0.9425
-01:01:01G+24:02:01G 13 13.00 0.00 0.9989
-01:01:01G+26:01:01G 8 7.95 0.00 0.9864
-01:01:01G+26:08 9 9.19 0.00 0.9488
-01:01:01G+29:02:01:02 9 8.95 0.00 0.9856
+01:01:01G+03:01:01G 12 12.01 1e-5 0.9975
+01:01:01G+03:01:03 9 8.95 3e-4 0.9856
+01:01:01G+11:01:01G 10 9.77 5e-3 0.9425
+01:01:01G+24:02:01G 13 13.00 2e-6 0.9989
+01:01:01G+26:01:01G 8 7.95 3e-4 0.9864
+01:01:01G+26:08 9 9.19 4e-3 0.9488
+01:01:01G+29:02:01:02 9 8.95 3e-4 0.9856
01:01:01G+31:01:02G 9 8.70 0.01 0.9183
01:01:01G+32:02 16 16.82 0.04 0.8424
01:01:01G+68:01:01G 7 6.63 0.02 0.8847
01:01:01G+68:06 14 14.00 0.00 0.9998
-02:01:01G+32:02 6 5.88 0.00 0.9590
-02:05:01G+02:05:01G 5 5.03 0.00 0.9890
-02:05:01G+03:01:01G 10 10.27 0.01 0.9318
+02:01:01G+32:02 6 5.88 3e-3 0.9590
+02:05:01G+02:05:01G 5 5.03 2e-4 0.9890
+02:05:01G+03:01:01G 10 10.27 7e-3 0.9318
02:05:01G+03:01:03 8 7.65 0.02 0.9001
02:05:01G+11:01:01G 8 8.36 0.02 0.9006
-02:05:01G+24:02:01G 11 11.12 0.00 0.9702
-02:05:01G+26:01:01G 7 6.80 0.01 0.9396
-02:05:01G+26:08 8 7.87 0.00 0.9617
+02:05:01G+24:02:01G 11 11.12 1e-3 0.9702
+02:05:01G+26:01:01G 7 6.80 6e-3 0.9396
+02:05:01G+26:08 8 7.87 2e-3 0.9617
02:05:01G+29:02:01:02 8 7.65 0.02 0.9001
02:05:01G+31:01:02G 8 7.44 0.04 0.8374
02:05:01G+32:02 14 14.38 0.01 0.9193
02:05:01G+68:01:01G 6 5.67 0.02 0.8893
-02:05:01G+68:06 12 11.98 0.00 0.9942
-03:01:01G+03:01:01G 5 5.25 0.01 0.9146
-03:01:01G+03:01:03 8 7.81 0.00 0.9471
+02:05:01G+68:06 12 11.98 5e-5 0.9942
+03:01:01G+03:01:01G 5 5.25 0.01 0.9145
+03:01:01G+03:01:03 8 7.81 4e-3 0.9471
03:01:01G+11:01:01G 8 8.54 0.03 0.8539
03:01:01G+24:02:01G 12 11.36 0.04 0.8493
-03:01:01G+26:01:01G 7 6.95 0.00 0.9837
-03:01:01G+26:08 8 8.03 0.00 0.9911
-03:01:01G+29:02:01:02 8 7.81 0.00 0.9471
+03:01:01G+26:01:01G 7 6.95 4e-4 0.9837
+03:01:01G+26:08 8 8.03 1e-4 0.9911
+03:01:01G+29:02:01:02 8 7.81 4e-3 0.9471
03:01:01G+31:01:02G 8 7.60 0.02 0.8838
-03:01:01G+32:02 15 14.69 0.01 0.9351
-03:01:01G+68:01:01G 6 5.79 0.01 0.9299
-03:01:01G+68:06 12 12.23 0.00 0.9480
+03:01:01G+32:02 15 14.69 7e-3 0.9351
+03:01:01G+68:01:01G 6 5.79 8e-3 0.9299
+03:01:01G+68:06 12 12.23 4e-3 0.9480
03:01:03+11:01:01G 6 6.36 0.02 0.8867
03:01:03+24:02:01G 8 8.46 0.03 0.8741
-03:01:03+26:01:01G 5 5.17 0.01 0.9391
-03:01:03+26:08 6 5.98 0.00 0.9941
-03:01:03+29:02:01:02 6 5.82 0.01 0.9406
+03:01:03+26:01:01G 5 5.17 6e-3 0.9391
+03:01:03+26:08 6 5.98 5e-5 0.9941
+03:01:03+29:02:01:02 6 5.82 6e-3 0.9406
03:01:03+31:01:02G 6 5.66 0.02 0.8859
-03:01:03+32:02 11 10.94 0.00 0.9856
-03:01:03+68:06 9 9.11 0.00 0.9715
+03:01:03+32:02 11 10.94 3e-4 0.9856
+03:01:03+68:06 9 9.11 1e-3 0.9715
11:01:01G+24:02:01G 10 9.24 0.06 0.8038
11:01:01G+26:01:01G 6 5.65 0.02 0.8839
11:01:01G+26:08 6 6.54 0.04 0.8340
11:01:01G+29:02:01:02 6 6.36 0.02 0.8867
-11:01:01G+31:01:02G 6 6.18 0.01 0.9414
-11:01:01G+32:02 12 11.95 0.00 0.9892
-11:01:01G+68:06 10 9.95 0.00 0.9876
-24:02:01G+24:02:01G 6 6.15 0.00 0.9518
+11:01:01G+31:01:02G 6 6.18 5e-3 0.9414
+11:01:01G+32:02 12 11.95 2e-4 0.9892
+11:01:01G+68:06 10 9.95 2e-4 0.9876
+24:02:01G+24:02:01G 6 6.15 4e-3 0.9518
24:02:01G+26:01:01G 8 7.52 0.03 0.8613
24:02:01G+26:08 9 8.70 0.01 0.9179
24:02:01G+29:02:01:02 8 8.46 0.03 0.8741
24:02:01G+31:01:02G 9 8.23 0.07 0.7873
-24:02:01G+32:02 16 15.90 0.00 0.9807
+24:02:01G+32:02 16 15.90 6e-4 0.9807
24:02:01G+68:01:01G 6 6.27 0.01 0.9149
-24:02:01G+68:06 13 13.24 0.00 0.9474
-24:02:04+32:02 6 5.88 0.00 0.9590
+24:02:01G+68:06 13 13.24 4e-3 0.9474
+24:02:04+32:02 6 5.88 3e-3 0.9590
26:01:01G+26:08 5 5.32 0.02 0.8905
-26:01:01G+29:02:01:02 5 5.17 0.01 0.9391
-26:01:01G+31:01:02G 5 5.03 0.00 0.9893
-26:01:01G+32:02 10 9.72 0.01 0.9296
-26:01:01G+68:06 8 8.10 0.00 0.9731
-26:08+29:02:01:02 6 5.98 0.00 0.9941
-26:08+31:01:02G 6 5.82 0.01 0.9391
-26:08+32:02 11 11.24 0.01 0.9420
+26:01:01G+29:02:01:02 5 5.17 6e-3 0.9391
+26:01:01G+31:01:02G 5 5.03 2e-4 0.9893
+26:01:01G+32:02 10 9.72 8e-3 0.9296
+26:01:01G+68:06 8 8.10 1e-3 0.9731
+26:08+29:02:01:02 6 5.98 5e-5 0.9941
+26:08+31:01:02G 6 5.82 6e-3 0.9391
+26:08+32:02 11 11.24 5e-3 0.9420
26:08+68:06 9 9.36 0.01 0.9061
-29:01:01G+32:02 6 5.88 0.00 0.9590
+29:01:01G+32:02 6 5.88 3e-3 0.9590
29:02:01:02+31:01:02G 6 5.66 0.02 0.8859
-29:02:01:02+32:02 11 10.94 0.00 0.9856
-29:02:01:02+68:06 9 9.11 0.00 0.9715
+29:02:01:02+32:02 11 10.94 3e-4 0.9856
+29:02:01:02+68:06 9 9.11 1e-3 0.9715
31:01:02G+32:02 11 10.64 0.01 0.9112
-31:01:02G+68:06 9 8.85 0.00 0.9611
-32:02+32:02 10 10.28 0.01 0.9300
-32:02+68:01:01G 8 8.10 0.00 0.9709
-32:02+68:06 17 17.12 0.00 0.9770
-68:01:01G+68:06 7 6.75 0.01 0.9223
-68:06+68:06 7 7.13 0.00 0.9624
+31:01:02G+68:06 9 8.85 2e-3 0.9611
+32:02+32:02 10 10.28 8e-3 0.9300
+32:02+68:01:01G 8 8.10 1e-3 0.9709
+32:02+68:06 17 17.12 8e-4 0.9770
+68:01:01G+68:06 7 6.75 1e-2 0.9223
+68:06+68:06 7 7.13 2e-3 0.9624
Total 702 700.68
------------------------------------------------------------------------------------------
@@ -279,16 +279,16 @@ Table of genotypes, format of each cell is: observed/expected.
03:01:01G 16/15.9 4/3.8
03:01:02 15/14.8 7/7.0 3/3.3
04:01:01 20/20.4 10/9.7 9/9.0 6/6.2
-04:03:01G 1/0.7 0/0.3 0/0.3 1/0.4 0/0.0
- 04:04:01 1/0.7 0/0.3 0/0.3 1/0.4 0/0.0 0/0.0
+04:03:01G 1/0.7 0/0.3 0/0.3 1/0.4 0/6e-3
+ 04:04:01 1/0.7 0/0.3 0/0.3 1/0.4 0/1e-2 0/6e-3
07:01:01G 38/37.9 18/17.9 17/16.7 23/23.1 1/0.7 1/0.7 21/21.4
08:01:01G 38/38.5 18/18.2 17/17.0 23/23.4 1/0.7 1/0.7 43/43.5
11:01:01G 18/18.2 9/8.6 8/8.1 11/11.1 0/0.4 0/0.4 21/20.6
- 11:03 3/2.6 1/1.2 1/1.2 2/1.6 0/0.1 0/0.1 3/2.9
+ 11:03 3/2.6 1/1.2 1/1.2 2/1.6 0/5e-2 0/5e-2 3/2.9
11:04:01G 9/8.7 4/4.1 4/3.9 5/5.3 0/0.2 0/0.2 10/9.8
13:01:01 6/6.2 3/3.0 3/2.8 4/3.8 0/0.1 0/0.1 7/7.0
- 13:02:01 2/1.7 1/0.8 1/0.7 1/1.0 0/0.0 0/0.0 2/1.9
-13:03:01G 1/0.7 0/0.3 0/0.3 1/0.4 0/0.0 0/0.0 1/0.7
+ 13:02:01 2/1.7 1/0.8 1/0.7 1/1.0 0/3e-2 0/3e-2 2/1.9
+13:03:01G 1/0.7 0/0.3 0/0.3 1/0.4 0/1e-2 0/1e-2 1/0.7
14:01:01G 10/10.7 5/5.0 5/4.7 6/6.5 0/0.2 0/0.2 12/12.0
15:01:01G 46/46.7 22/22.1 21/20.6 28/28.4 1/0.9 1/0.9 52/52.7
01:01:01G03:01:01G 03:01:02 04:01:0104:03:01G 04:04:0107:01:01G
@@ -298,8 +298,8 @@ Table of genotypes, format of each cell is: observed/expected.
11:03 3/3.0 1/1.4 0/0.1
11:04:01G 10/10.0 5/4.7 1/0.7 1/1.1
13:01:01 7/7.2 3/3.4 0/0.5 2/1.6 1/0.6
- 13:02:01 2/1.9 1/0.9 0/0.1 0/0.4 0/0.3 0/0.0
-13:03:01G 1/0.7 0/0.4 0/0.1 0/0.2 0/0.1 0/0.0 0/0.0
+ 13:02:01 2/1.9 1/0.9 0/0.1 0/0.4 0/0.3 0/4e-2
+13:03:01G 1/0.7 0/0.4 0/5e-2 0/0.2 0/0.1 0/3e-2 0/6e-3
14:01:01G 12/12.2 6/5.8 1/0.8 3/2.8 2/2.0 1/0.5 0/0.2
15:01:01G 55/53.6 26/25.4 4/3.6 12/12.1 9/8.7 2/2.4 1/0.9
08:01:01G11:01:01G 11:0311:04:01G 13:01:01 13:02:0113:03:01G
@@ -317,76 +317,76 @@ Table of genotypes, format of each cell is: observed/expected.
------------------------------------------------------------------------------------------
Common + lumped N/A N/A 0.41 38 1.0000
------------------------------------------------------------------------------------------
- All homozygotes 114 114.54 0.00 1 0.9598
+ All homozygotes 114 114.54 3e-3 1 0.9598
------------------------------------------------------------------------------------------
- All heterozygotes 877 876.46 0.00 1 0.9855
+ All heterozygotes 877 876.46 3e-4 1 0.9855
------------------------------------------------------------------------------------------
Common heterozygotes by allele
-01:01:01G 224 224.42 0.00 0.9779
-03:01:01G 114 114.49 0.00 0.9634
-03:01:02 108 107.44 0.00 0.9571
-04:01:01 145 144.56 0.00 0.9710
-07:01:01G 249 248.27 0.00 0.9633
-08:01:01G 252 251.79 0.00 0.9896
-11:01:01G 130 130.11 0.00 0.9922
-11:03 20 19.80 0.00 0.9638
-11:04:01G 65 64.74 0.00 0.9737
+01:01:01G 224 224.42 8e-4 0.9779
+03:01:01G 114 114.49 2e-3 0.9634
+03:01:02 108 107.44 3e-3 0.9571
+04:01:01 145 144.56 1e-3 0.9710
+07:01:01G 249 248.27 2e-3 0.9633
+08:01:01G 252 251.79 2e-4 0.9896
+11:01:01G 130 130.11 1e-4 0.9922
+11:03 20 19.80 2e-3 0.9638
+11:04:01G 65 64.74 1e-3 0.9737
13:01:01 46 46.84 0.01 0.9026
-13:02:01 13 12.91 0.00 0.9811
-14:01:01G 78 78.61 0.00 0.9454
-15:01:01G 295 293.97 0.00 0.9523
+13:02:01 13 12.91 6e-4 0.9811
+14:01:01G 78 78.61 5e-3 0.9454
+15:01:01G 295 293.97 4e-3 0.9523
------------------------------------------------------------------------------------------
Common genotypes
-01:01:01G+01:01:01G 17 16.79 0.00 0.9595
-01:01:01G+03:01:01G 16 15.88 0.00 0.9762
-01:01:01G+03:01:02 15 14.84 0.00 0.9668
-01:01:01G+04:01:01 20 20.44 0.01 0.9230
-01:01:01G+07:01:01G 38 37.88 0.00 0.9844
-01:01:01G+08:01:01G 38 38.53 0.01 0.9319
-01:01:01G+11:01:01G 18 18.22 0.00 0.9582
-01:01:01G+11:04:01G 9 8.72 0.01 0.9249
-01:01:01G+13:01:01 6 6.25 0.01 0.9209
+01:01:01G+01:01:01G 17 16.79 3e-3 0.9595
+01:01:01G+03:01:01G 16 15.88 9e-4 0.9762
+01:01:01G+03:01:02 15 14.84 2e-3 0.9668
+01:01:01G+04:01:01 20 20.44 9e-3 0.9230
+01:01:01G+07:01:01G 38 37.88 4e-4 0.9844
+01:01:01G+08:01:01G 38 38.53 7e-3 0.9319
+01:01:01G+11:01:01G 18 18.22 3e-3 0.9581
+01:01:01G+11:04:01G 9 8.72 9e-3 0.9249
+01:01:01G+13:01:01 6 6.25 1e-2 0.9209
01:01:01G+14:01:01G 10 10.67 0.04 0.8365
01:01:01G+15:01:01G 46 46.73 0.01 0.9148
-03:01:01G+03:01:02 7 7.02 0.00 0.9948
+03:01:01G+03:01:02 7 7.02 4e-5 0.9948
03:01:01G+04:01:01 10 9.66 0.01 0.9139
-03:01:01G+07:01:01G 18 17.91 0.00 0.9835
-03:01:01G+08:01:01G 18 18.22 0.00 0.9589
+03:01:01G+07:01:01G 18 17.91 4e-4 0.9835
+03:01:01G+08:01:01G 18 18.22 3e-3 0.9589
03:01:01G+11:01:01G 9 8.62 0.02 0.8963
-03:01:01G+14:01:01G 5 5.05 0.00 0.9832
-03:01:01G+15:01:01G 22 22.10 0.00 0.9834
-03:01:02+04:01:01 9 9.03 0.00 0.9920
-03:01:02+07:01:01G 17 16.74 0.00 0.9489
-03:01:02+08:01:01G 17 17.03 0.00 0.9951
-03:01:02+11:01:01G 8 8.05 0.00 0.9852
-03:01:02+15:01:01G 21 20.65 0.01 0.9384
-04:01:01+04:01:01 6 6.22 0.01 0.9303
-04:01:01+07:01:01G 23 23.05 0.00 0.9915
-04:01:01+08:01:01G 23 23.45 0.01 0.9264
-04:01:01+11:01:01G 11 11.09 0.00 0.9785
+03:01:01G+14:01:01G 5 5.05 4e-4 0.9832
+03:01:01G+15:01:01G 22 22.10 4e-4 0.9834
+03:01:02+04:01:01 9 9.03 1e-4 0.9920
+03:01:02+07:01:01G 17 16.74 4e-3 0.9489
+03:01:02+08:01:01G 17 17.03 4e-5 0.9951
+03:01:02+11:01:01G 8 8.05 3e-4 0.9852
+03:01:02+15:01:01G 21 20.65 6e-3 0.9384
+04:01:01+04:01:01 6 6.22 8e-3 0.9303
+04:01:01+07:01:01G 23 23.05 1e-4 0.9915
+04:01:01+08:01:01G 23 23.45 9e-3 0.9264
+04:01:01+11:01:01G 11 11.09 7e-4 0.9785
04:01:01+11:04:01G 5 5.31 0.02 0.8939
04:01:01+14:01:01G 6 6.50 0.04 0.8459
-04:01:01+15:01:01G 28 28.44 0.01 0.9346
-07:01:01G+07:01:01G 21 21.36 0.01 0.9375
-07:01:01G+08:01:01G 43 43.46 0.00 0.9445
-07:01:01G+11:01:01G 21 20.55 0.01 0.9218
-07:01:01G+11:04:01G 10 9.84 0.00 0.9586
-07:01:01G+13:01:01 7 7.05 0.00 0.9857
-07:01:01G+14:01:01G 12 12.04 0.00 0.9910
-07:01:01G+15:01:01G 52 52.71 0.01 0.9222
-08:01:01G+08:01:01G 22 22.10 0.00 0.9825
-08:01:01G+11:01:01G 21 20.91 0.00 0.9840
-08:01:01G+11:04:01G 10 10.01 0.00 0.9985
-08:01:01G+13:01:01 7 7.17 0.00 0.9498
-08:01:01G+14:01:01G 12 12.25 0.00 0.9439
+04:01:01+15:01:01G 28 28.44 7e-3 0.9346
+07:01:01G+07:01:01G 21 21.36 6e-3 0.9375
+07:01:01G+08:01:01G 43 43.46 5e-3 0.9445
+07:01:01G+11:01:01G 21 20.55 1e-2 0.9218
+07:01:01G+11:04:01G 10 9.84 3e-3 0.9586
+07:01:01G+13:01:01 7 7.05 3e-4 0.9857
+07:01:01G+14:01:01G 12 12.04 1e-4 0.9910
+07:01:01G+15:01:01G 52 52.71 1e-2 0.9222
+08:01:01G+08:01:01G 22 22.10 5e-4 0.9825
+08:01:01G+11:01:01G 21 20.91 4e-4 0.9840
+08:01:01G+11:04:01G 10 10.01 4e-6 0.9985
+08:01:01G+13:01:01 7 7.17 4e-3 0.9498
+08:01:01G+14:01:01G 12 12.25 5e-3 0.9439
08:01:01G+15:01:01G 55 53.61 0.04 0.8499
-11:01:01G+14:01:01G 6 5.79 0.01 0.9312
+11:01:01G+14:01:01G 6 5.79 7e-3 0.9312
11:01:01G+15:01:01G 26 25.36 0.02 0.8986
-11:04:01G+15:01:01G 12 12.14 0.00 0.9689
+11:04:01G+15:01:01G 12 12.14 2e-3 0.9689
13:01:01+15:01:01G 9 8.69 0.01 0.9174
-14:01:01G+15:01:01G 15 14.85 0.00 0.9695
-15:01:01G+15:01:01G 32 32.51 0.01 0.9283
+14:01:01G+15:01:01G 15 14.85 1e-3 0.9695
+15:01:01G+15:01:01G 32 32.51 8e-3 0.9283
Total 889 891.48
------------------------------------------------------------------------------------------
@@ -443,12 +443,12 @@ Table of genotypes, format of each cell is: observed/expected.
06:05:01 22/21.7 21/20.6 12/12.2 18/17.6 17/16.9 7/7.5
02:01:01G 03:01:01G 03:02:01 03:02:1203:03:02:03 04:01:01
[Cols: 1 to 6]
- 04:02:01 0/0.0
+ 04:02:01 0/2e-2
05:01:01:01 0/0.5 3/3.3
05:01:01:03 0/0.3 4/4.2 1/1.3
05:02:01 0/0.3 4/4.2 3/2.7 1/1.3
05:03:01:01 0/0.8 11/11.1 7/7.0 7/7.0 39/9.3
- 06:01:01G 0/0.0 1/0.5 0/0.3 0/0.3 1/0.9 0/0.0
+ 06:01:01G 0/4e-2 1/0.5 0/0.3 0/0.3 1/0.9 0/2e-2
06:02:01 0/1.0 14/14.0 9/8.9 9/8.9 0/23.5 1/1.1
06:03:01 8/0.3 4/4.1 2/2.6 2/2.6 6/6.9 0/0.3
06:05:01 0/0.8 11/10.8 7/6.8 7/6.8 0/18.1 1/0.8
@@ -473,94 +473,94 @@ Table of genotypes, format of each cell is: observed/expected.
All heterozygotes 855 913.64 3.76 1 0.0524
------------------------------------------------------------------------------------------
Common heterozygotes by allele
-02:01:01G 205 204.37 0.00 0.9650
-03:01:01G 196 195.85 0.00 0.9914
-03:02:01 122 121.57 0.00 0.9687
+02:01:01G 205 204.37 2e-3 0.9650
+03:01:01G 196 195.85 1e-4 0.9914
+03:02:01 122 121.57 2e-3 0.9687
03:02:12 152 170.36 1.98 0.1595
-03:03:02:03 164 163.83 0.00 0.9895
-04:01:01 76 76.81 0.01 0.9267
-04:02:01 8 7.97 0.00 0.9910
-05:01:01:01 109 108.40 0.00 0.9541
-05:01:01:03 71 70.34 0.01 0.9374
-05:02:01 71 70.34 0.01 0.9374
-05:03:01:01 115 174.41 20.24 0.0000*****
-06:01:01G 9 8.96 0.00 0.9892
+03:03:02:03 164 163.83 2e-4 0.9895
+04:01:01 76 76.81 8e-3 0.9267
+04:02:01 8 7.97 1e-4 0.9910
+05:01:01:01 109 108.40 3e-3 0.9541
+05:01:01:03 71 70.34 6e-3 0.9374
+05:02:01 71 70.34 6e-3 0.9374
+05:03:01:01 115 174.41 20.24 7e-6*****
+06:01:01G 9 8.96 2e-4 0.9892
06:02:01 190 214.29 2.75 0.0970
-06:03:01 70 69.41 0.00 0.9438
+06:03:01 70 69.41 5e-3 0.9438
06:05:01 152 170.36 1.98 0.1595
------------------------------------------------------------------------------------------
Common genotypes
-02:01:01G+02:01:01G 13 13.31 0.01 0.9315
+02:01:01G+02:01:01G 13 13.31 7e-3 0.9315
02:01:01G+03:01:01G 26 25.36 0.02 0.8988
-02:01:01G+03:02:01 15 14.99 0.00 0.9969
-02:01:01G+03:02:12 22 21.67 0.01 0.9436
+02:01:01G+03:02:01 15 14.99 2e-5 0.9969
+02:01:01G+03:02:12 22 21.67 5e-3 0.9436
02:01:01G+03:03:02:03 20 20.75 0.03 0.8695
-02:01:01G+04:01:01 9 9.22 0.01 0.9418
-02:01:01G+05:01:01:01 13 13.26 0.00 0.9439
+02:01:01G+04:01:01 9 9.22 5e-3 0.9418
+02:01:01G+05:01:01:01 13 13.26 5e-3 0.9439
02:01:01G+05:01:01:03 9 8.41 0.04 0.8401
02:01:01G+05:02:01 9 8.41 0.04 0.8401
02:01:01G+05:03:01:01 23 22.25 0.03 0.8732
-02:01:01G+06:02:01 28 28.13 0.00 0.9811
+02:01:01G+06:02:01 28 28.13 6e-4 0.9811
02:01:01G+06:03:01 8 8.30 0.01 0.9172
-02:01:01G+06:05:01 22 21.67 0.01 0.9436
-03:01:01G+03:01:01G 12 12.08 0.00 0.9826
-03:01:01G+03:02:01 14 14.27 0.01 0.9427
-03:01:01G+03:02:12 21 20.64 0.01 0.9366
-03:01:01G+03:03:02:03 20 19.76 0.00 0.9570
-03:01:01G+04:01:01 9 8.78 0.01 0.9415
+02:01:01G+06:05:01 22 21.67 5e-3 0.9436
+03:01:01G+03:01:01G 12 12.08 5e-4 0.9826
+03:01:01G+03:02:01 14 14.27 5e-3 0.9427
+03:01:01G+03:02:12 21 20.64 6e-3 0.9366
+03:01:01G+03:03:02:03 20 19.76 3e-3 0.9570
+03:01:01G+04:01:01 9 8.78 5e-3 0.9415
03:01:01G+05:01:01:01 13 12.62 0.01 0.9159
-03:01:01G+05:01:01:03 8 8.01 0.00 0.9961
-03:01:01G+05:02:01 8 8.01 0.00 0.9961
-03:01:01G+05:03:01:01 21 21.19 0.00 0.9675
-03:01:01G+06:02:01 27 26.79 0.00 0.9671
+03:01:01G+05:01:01:03 8 8.01 2e-5 0.9961
+03:01:01G+05:02:01 8 8.01 2e-5 0.9961
+03:01:01G+05:03:01:01 21 21.19 2e-3 0.9675
+03:01:01G+06:02:01 27 26.79 2e-3 0.9671
03:01:01G+06:03:01 7 7.90 0.10 0.7477
-03:01:01G+06:05:01 21 20.64 0.01 0.9366
-03:02:01+03:02:12 12 12.20 0.00 0.9553
-03:02:01+03:03:02:03 12 11.68 0.01 0.9246
-03:02:01+04:01:01 5 5.19 0.01 0.9337
+03:01:01G+06:05:01 21 20.64 6e-3 0.9366
+03:02:01+03:02:12 12 12.20 3e-3 0.9553
+03:02:01+03:03:02:03 12 11.68 9e-3 0.9246
+03:02:01+04:01:01 5 5.19 7e-3 0.9337
03:02:01+05:01:01:01 8 7.46 0.04 0.8433
03:02:01+05:03:01:01 13 12.52 0.02 0.8921
-03:02:01+06:02:01 16 15.83 0.00 0.9656
-03:02:01+06:05:01 12 12.20 0.00 0.9553
+03:02:01+06:02:01 16 15.83 2e-3 0.9656
+03:02:01+06:05:01 12 12.20 3e-3 0.9553
03:02:12+03:02:12 18 8.82 9.56 0.0020**
-03:02:12+03:03:02:03 17 16.89 0.00 0.9779
+03:02:12+03:03:02:03 17 16.89 8e-4 0.9779
03:02:12+04:01:01 7 7.50 0.03 0.8538
-03:02:12+05:01:01:01 11 10.79 0.00 0.9486
-03:02:12+05:01:01:03 7 6.85 0.00 0.9538
-03:02:12+05:02:01 7 6.85 0.00 0.9538
-03:02:12+05:03:01:01 0 18.11 18.11 0.0000****
-03:02:12+06:02:01 23 22.89 0.00 0.9817
+03:02:12+05:01:01:01 11 10.79 4e-3 0.9486
+03:02:12+05:01:01:03 7 6.85 3e-3 0.9538
+03:02:12+05:02:01 7 6.85 3e-3 0.9538
+03:02:12+05:03:01:01 0 18.11 18.11 2.1e-5****
+03:02:12+06:02:01 23 22.89 5e-4 0.9817
03:02:12+06:03:01 6 6.75 0.08 0.7716
-03:02:12+06:05:01 18 17.64 0.01 0.9311
-03:03:02:03+03:03:02:03 8 8.08 0.00 0.9765
-03:03:02:03+04:01:01 7 7.19 0.00 0.9448
+03:02:12+06:05:01 18 17.64 7e-3 0.9311
+03:03:02:03+03:03:02:03 8 8.08 9e-4 0.9765
+03:03:02:03+04:01:01 7 7.19 5e-3 0.9448
03:03:02:03+05:01:01:01 10 10.33 0.01 0.9184
03:03:02:03+05:01:01:03 7 6.56 0.03 0.8626
03:03:02:03+05:02:01 7 6.56 0.03 0.8626
03:03:02:03+05:03:01:01 18 17.34 0.03 0.8732
-03:03:02:03+06:02:01 22 21.92 0.00 0.9857
+03:03:02:03+06:02:01 22 21.92 3e-4 0.9857
03:03:02:03+06:03:01 6 6.47 0.03 0.8543
-03:03:02:03+06:05:01 17 16.89 0.00 0.9779
+03:03:02:03+06:05:01 17 16.89 8e-4 0.9779
04:01:01+05:03:01:01 8 7.70 0.01 0.9152
-04:01:01+06:02:01 10 9.74 0.01 0.9337
+04:01:01+06:02:01 10 9.74 7e-3 0.9337
04:01:01+06:05:01 7 7.50 0.03 0.8538
-05:01:01:01+05:03:01:01 11 11.08 0.00 0.9819
+05:01:01:01+05:03:01:01 11 11.08 5e-4 0.9819
05:01:01:01+06:02:01 14 14.00 0.00 0.9996
-05:01:01:01+06:05:01 11 10.79 0.00 0.9486
-05:01:01:03+05:03:01:01 7 7.03 0.00 0.9908
-05:01:01:03+06:02:01 9 8.89 0.00 0.9701
-05:01:01:03+06:05:01 7 6.85 0.00 0.9538
-05:02:01+05:03:01:01 7 7.03 0.00 0.9908
-05:02:01+06:02:01 9 8.89 0.00 0.9701
-05:02:01+06:05:01 7 6.85 0.00 0.9538
+05:01:01:01+06:05:01 11 10.79 4e-3 0.9486
+05:01:01:03+05:03:01:01 7 7.03 1e-4 0.9908
+05:01:01:03+06:02:01 9 8.89 1e-3 0.9701
+05:01:01:03+06:05:01 7 6.85 3e-3 0.9538
+05:02:01+05:03:01:01 7 7.03 1e-4 0.9908
+05:02:01+06:02:01 9 8.89 1e-3 0.9701
+05:02:01+06:05:01 7 6.85 3e-3 0.9538
05:03:01:01+05:03:01:01 39 9.29 94.95 0.0000*****
-05:03:01:01+06:02:01 0 23.50 23.50 0.0000*****
+05:03:01:01+06:02:01 0 23.50 23.50 1e-6*****
05:03:01:01+06:03:01 6 6.93 0.13 0.7228
-05:03:01:01+06:05:01 0 18.11 18.11 0.0000****
+05:03:01:01+06:05:01 0 18.11 18.11 2.1e-5****
06:02:01+06:02:01 27 14.85 9.93 0.0016**
06:02:01+06:03:01 8 8.77 0.07 0.7957
-06:02:01+06:05:01 23 22.89 0.00 0.9817
+06:02:01+06:05:01 23 22.89 5e-4 0.9817
06:03:01+06:05:01 6 6.75 0.08 0.7716
06:05:01+06:05:01 18 8.82 9.56 0.0020**
Total 926 924.16
diff --git a/tests/data/gold-output/custom-binning-P-Filter/BIGDAWG_SynthControl_Data-out.txt b/tests/data/gold-output/custom-binning-P-Filter/BIGDAWG_SynthControl_Data-out.txt
index e611ad447..0ef4a04b6 100644
--- a/tests/data/gold-output/custom-binning-P-Filter/BIGDAWG_SynthControl_Data-out.txt
+++ b/tests/data/gold-output/custom-binning-P-Filter/BIGDAWG_SynthControl_Data-out.txt
@@ -63,146 +63,154 @@ Total 1.00000 2004 | Total 1.00000 2004
----------------------
Table of genotypes, format of each cell is: observed/expected.
-01:01P 7/6.9
-02:01P 5/4.8 1/0.8
-02:05P 11/11.8 4/4.1 5/5.0
-03:01P 21/21.0 7/7.3 18/17.9 16/16.0
-11:01P 10/9.8 4/3.4 8/8.4 14/14.9 4/3.5
-23:01P 4/3.7 1/1.3 3/3.2 5/5.7 2/2.6 1/0.5
-24:02P 18/17.8 6/6.2 15/15.2 27/27.1 14/12.7 5/4.8 11/11.5
-25:01P 3/3.1 1/1.1 3/2.7 5/4.8 2/2.2 1/0.9 4/4.1 0/0.4
-26:01P 8/8.0 3/2.8 7/6.8 12/12.1 6/5.7 2/2.2 11/10.3 2/1.8 2/2.3
- 26:08 9/9.2 3/3.2 8/7.9 14/14.0 6/6.5 3/2.5 12/11.9 2/2.1 5/5.3
-29:01P 5/4.8 2/1.7 4/4.1 7/7.3 4/3.4 1/1.3 6/6.2 1/1.1 3/2.8
-29:02P 9/8.9 3/3.1 8/7.7 14/13.6 6/6.4 2/2.4 11/11.6 2/2.0 5/5.2
-31:01P 9/8.7 3/3.0 8/7.4 14/13.3 6/6.2 2/2.4 12/11.3 2/2.0 5/5.0
-32:01P 2/2.5 1/0.9 2/2.1 4/3.8 2/1.8 1/0.7 3/3.2 1/0.6 1/1.4
- 32:02 16/16.8 6/5.9 14/14.4 26/25.6 12/12.0 5/4.6 22/21.8 4/3.8 10/9.7
-33:01P 1/0.7 0/0.3 1/0.6 2/1.1 0/0.5 0/0.2 1/1.0 0/0.2 0/0.4
-68:01P 7/6.6 2/2.3 6/5.7 10/10.1 4/4.7 2/1.8 8/8.6 2/1.5 4/3.8
- 68:06 14/14.0 5/4.9 12/12.0 21/21.3 10/10.0 4/3.8 18/18.1 3/3.2 8/8.1
- 01:01P 02:01P 02:05P 03:01P 11:01P 23:01P 24:02P 25:01P 26:01P
- [Cols: 1 to 9]
- 26:08 3/3.1
-29:01P 3/3.2 1/0.8
-29:02P 6/6.0 3/3.1 3/2.9
-31:01P 6/5.8 3/3.0 6/5.7 2/2.8
-32:01P 2/1.7 1/0.9 2/1.6 1/1.6 0/0.2
- 32:02 11/11.2 6/5.9 11/10.9 11/10.6 3/3.0 10/10.3
-33:01P 1/0.5 0/0.3 1/0.5 0/0.5 0/0.1 1/0.9 0/0.0
-68:01P 5/4.4 2/2.3 4/4.3 4/4.2 1/1.2 8/8.1 0/0.4 2/1.6
- 68:06 9/9.4 5/4.9 9/9.1 9/8.9 3/2.5 17/17.1 1/0.8 7/6.7 7/7.1
- 26:08 29:01P 29:02P 31:01P 32:01P 32:02 33:01P 68:01P 68:06
- [Cols: 10 to 18]
+01:01P 7/6.9
+02:01P 5/4.8 1/0.8
+02:05P 11/11.8 4/4.1 5/5.0
+03:01P 21/21.0 7/7.3 18/17.9 16/16.0
+11:01P 10/9.8 4/3.4 8/8.4 14/14.9 4/3.5
+23:01P 4/3.7 1/1.3 3/3.2 5/5.7 2/2.6 1/0.5
+24:02P 18/17.8 6/6.2 15/15.2 27/27.1 14/12.7 5/4.8 11/11.5
+25:01P 3/3.1 1/1.1 3/2.7 5/4.8 2/2.2 1/0.9 4/4.1
+26:01P 8/8.0 3/2.8 7/6.8 12/12.1 6/5.7 2/2.2 11/10.3
+ 26:08 9/9.2 3/3.2 8/7.9 14/14.0 6/6.5 3/2.5 12/11.9
+29:01P 5/4.8 2/1.7 4/4.1 7/7.3 4/3.4 1/1.3 6/6.2
+29:02P 9/8.9 3/3.1 8/7.7 14/13.6 6/6.4 2/2.4 11/11.6
+31:01P 9/8.7 3/3.0 8/7.4 14/13.3 6/6.2 2/2.4 12/11.3
+32:01P 2/2.5 1/0.9 2/2.1 4/3.8 2/1.8 1/0.7 3/3.2
+ 32:02 16/16.8 6/5.9 14/14.4 26/25.6 12/12.0 5/4.6 22/21.8
+33:01P 1/0.7 0/0.3 1/0.6 2/1.1 0/0.5 0/0.2 1/1.0
+68:01P 7/6.6 2/2.3 6/5.7 10/10.1 4/4.7 2/1.8 8/8.6
+ 68:06 14/14.0 5/4.9 12/12.0 21/21.3 10/10.0 4/3.8 18/18.1
+ 01:01P 02:01P 02:05P 03:01P 11:01P 23:01P 24:02P
+ [Cols: 1 to 7]
+25:01P 0/0.4
+26:01P 2/1.8 2/2.3
+ 26:08 2/2.1 5/5.3 3/3.1
+29:01P 1/1.1 3/2.8 3/3.2 1/0.8
+29:02P 2/2.0 5/5.2 6/6.0 3/3.1 3/2.9
+31:01P 2/2.0 5/5.0 6/5.8 3/3.0 6/5.7 2/2.8
+32:01P 1/0.6 1/1.4 2/1.7 1/0.9 2/1.6 1/1.6 0/0.2
+ 32:02 4/3.8 10/9.7 11/11.2 6/5.9 11/10.9 11/10.6 3/3.0
+33:01P 0/0.2 0/0.4 1/0.5 0/0.3 1/0.5 0/0.5 0/0.1
+68:01P 2/1.5 4/3.8 5/4.4 2/2.3 4/4.3 4/4.2 1/1.2
+ 68:06 3/3.2 8/8.1 9/9.4 5/4.9 9/9.1 9/8.9 3/2.5
+ 25:01P 26:01P 26:08 29:01P 29:02P 31:01P 32:01P
+ [Cols: 8 to 14]
+ 32:02 10/10.3
+33:01P 1/0.9 0/2e-2
+68:01P 8/8.1 0/0.4 2/1.6
+ 68:06 17/17.1 1/0.8 7/6.7 7/7.1
+ 32:02 33:01P 68:01P 68:06
+ [Cols: 15 to 18]
Observed Expected Chi-square DoF p-value
------------------------------------------------------------------------------------------
Common N/A N/A 1.05 59 1.0000
------------------------------------------------------------------------------------------
- Lumped genotypes N/A N/A 0.01 1 0.9420
+ Lumped genotypes N/A N/A 5e-3 1 0.9420
------------------------------------------------------------------------------------------
Common + lumped N/A N/A 1.05 59 1.0000
------------------------------------------------------------------------------------------
- All homozygotes 75 75.71 0.01 1 0.9348
+ All homozygotes 75 75.71 7e-3 1 0.9348
------------------------------------------------------------------------------------------
-All heterozygotes 927 926.29 0.00 1 0.9813
+All heterozygotes 927 926.29 5e-4 1 0.9813
------------------------------------------------------------------------------------------
Common heterozygotes by allele
-01:01P 152 152.25 0.00 0.9839
-02:01P 56 56.32 0.00 0.9658
-02:05P 132 131.94 0.00 0.9957
-03:01P 221 221.06 0.00 0.9968
-11:01P 110 111.05 0.01 0.9205
+01:01P 152 152.25 4e-4 0.9839
+02:01P 56 56.32 2e-3 0.9658
+02:05P 132 131.94 3e-5 0.9957
+03:01P 221 221.06 2e-5 0.9968
+11:01P 110 111.05 1e-2 0.9205
23:01P 43 43.99 0.02 0.8814
-24:02P 193 191.93 0.01 0.9386
+24:02P 193 191.93 6e-3 0.9386
25:01P 38 37.28 0.01 0.9061
-26:01P 92 91.40 0.00 0.9501
-26:08 105 104.85 0.00 0.9885
-29:01P 56 56.32 0.00 0.9658
-29:02P 102 102.18 0.00 0.9858
+26:01P 92 91.40 4e-3 0.9501
+26:08 105 104.85 2e-4 0.9885
+29:01P 56 56.32 2e-3 0.9658
+29:02P 102 102.18 3e-4 0.9858
31:01P 101 99.50 0.02 0.8803
-32:01P 30 29.55 0.01 0.9342
-32:02 183 182.44 0.00 0.9667
-33:01P 9 8.96 0.00 0.9892
-68:01P 76 76.81 0.01 0.9267
-68:06 155 154.75 0.00 0.9838
+32:01P 30 29.55 7e-3 0.9342
+32:02 183 182.44 2e-3 0.9667
+33:01P 9 8.96 2e-4 0.9892
+68:01P 76 76.81 8e-3 0.9267
+68:06 155 154.75 4e-4 0.9838
------------------------------------------------------------------------------------------
Common genotypes
-01:01P+01:01P 7 6.88 0.00 0.9621
+01:01P+01:01P 7 6.88 2e-3 0.9621
01:01P+02:05P 11 11.76 0.05 0.8241
-01:01P+03:01P 21 20.96 0.00 0.9925
-01:01P+11:01P 10 9.77 0.01 0.9425
-01:01P+24:02P 18 17.81 0.00 0.9640
-01:01P+26:01P 8 7.95 0.00 0.9864
-01:01P+26:08 9 9.19 0.00 0.9488
-01:01P+29:02P 9 8.95 0.00 0.9856
+01:01P+03:01P 21 20.96 9e-5 0.9925
+01:01P+11:01P 10 9.77 5e-3 0.9425
+01:01P+24:02P 18 17.81 2e-3 0.9640
+01:01P+26:01P 8 7.95 3e-4 0.9864
+01:01P+26:08 9 9.19 4e-3 0.9488
+01:01P+29:02P 9 8.95 3e-4 0.9856
01:01P+31:01P 9 8.70 0.01 0.9183
01:01P+32:02 16 16.82 0.04 0.8424
01:01P+68:01P 7 6.63 0.02 0.8847
01:01P+68:06 14 14.00 0.00 0.9998
02:01P+03:01P 7 7.32 0.01 0.9052
-02:01P+24:02P 6 6.22 0.01 0.9289
-02:01P+32:02 6 5.88 0.00 0.9590
-02:05P+02:05P 5 5.03 0.00 0.9890
-02:05P+03:01P 18 17.93 0.00 0.9863
+02:01P+24:02P 6 6.22 8e-3 0.9289
+02:01P+32:02 6 5.88 3e-3 0.9590
+02:05P+02:05P 5 5.03 2e-4 0.9890
+02:05P+03:01P 18 17.93 3e-4 0.9863
02:05P+11:01P 8 8.36 0.02 0.9006
-02:05P+24:02P 15 15.23 0.00 0.9521
-02:05P+26:01P 7 6.80 0.01 0.9396
-02:05P+26:08 8 7.87 0.00 0.9617
+02:05P+24:02P 15 15.23 4e-3 0.9521
+02:05P+26:01P 7 6.80 6e-3 0.9396
+02:05P+26:08 8 7.87 2e-3 0.9617
02:05P+29:02P 8 7.65 0.02 0.9001
02:05P+31:01P 8 7.44 0.04 0.8374
02:05P+32:02 14 14.38 0.01 0.9193
02:05P+68:01P 6 5.67 0.02 0.8893
-02:05P+68:06 12 11.98 0.00 0.9942
-03:01P+03:01P 16 15.97 0.00 0.9941
+02:05P+68:06 12 11.98 5e-5 0.9942
+03:01P+03:01P 16 15.97 6e-5 0.9941
03:01P+11:01P 14 14.90 0.05 0.8162
03:01P+23:01P 5 5.68 0.08 0.7751
-03:01P+24:02P 27 27.14 0.00 0.9781
-03:01P+26:01P 12 12.12 0.00 0.9726
-03:01P+26:08 14 14.01 0.00 0.9971
+03:01P+24:02P 27 27.14 8e-4 0.9781
+03:01P+26:01P 12 12.12 1e-3 0.9726
+03:01P+26:08 14 14.01 1e-5 0.9971
03:01P+29:01P 7 7.32 0.01 0.9052
-03:01P+29:02P 14 13.63 0.01 0.9212
+03:01P+29:02P 14 13.63 1e-2 0.9212
03:01P+31:01P 14 13.26 0.04 0.8381
-03:01P+32:02 26 25.63 0.01 0.9415
-03:01P+68:01P 10 10.10 0.00 0.9749
-03:01P+68:06 21 21.34 0.01 0.9420
+03:01P+32:02 26 25.63 5e-3 0.9415
+03:01P+68:01P 10 10.10 1e-3 0.9749
+03:01P+68:06 21 21.34 5e-3 0.9420
11:01P+24:02P 14 12.66 0.14 0.7064
11:01P+26:01P 6 5.65 0.02 0.8839
11:01P+26:08 6 6.54 0.04 0.8340
11:01P+29:02P 6 6.36 0.02 0.8867
-11:01P+31:01P 6 6.18 0.01 0.9414
-11:01P+32:02 12 11.95 0.00 0.9892
-11:01P+68:06 10 9.95 0.00 0.9876
+11:01P+31:01P 6 6.18 5e-3 0.9414
+11:01P+32:02 12 11.95 2e-4 0.9892
+11:01P+68:06 10 9.95 2e-4 0.9876
24:02P+24:02P 11 11.53 0.02 0.8752
24:02P+26:01P 11 10.30 0.05 0.8272
-24:02P+26:08 12 11.91 0.00 0.9789
-24:02P+29:01P 6 6.22 0.01 0.9289
+24:02P+26:08 12 11.91 7e-4 0.9789
+24:02P+29:01P 6 6.22 8e-3 0.9289
24:02P+29:02P 11 11.59 0.03 0.8631
24:02P+31:01P 12 11.26 0.05 0.8267
-24:02P+32:02 22 21.78 0.00 0.9622
+24:02P+32:02 22 21.78 2e-3 0.9622
24:02P+68:01P 8 8.58 0.04 0.8423
-24:02P+68:06 18 18.13 0.00 0.9754
+24:02P+68:06 18 18.13 9e-4 0.9754
26:01P+26:08 5 5.32 0.02 0.8905
-26:01P+29:02P 5 5.17 0.01 0.9391
-26:01P+31:01P 5 5.03 0.00 0.9893
-26:01P+32:02 10 9.72 0.01 0.9296
-26:01P+68:06 8 8.10 0.00 0.9731
-26:08+29:02P 6 5.98 0.00 0.9941
-26:08+31:01P 6 5.82 0.01 0.9391
-26:08+32:02 11 11.24 0.01 0.9420
+26:01P+29:02P 5 5.17 6e-3 0.9391
+26:01P+31:01P 5 5.03 2e-4 0.9893
+26:01P+32:02 10 9.72 8e-3 0.9296
+26:01P+68:06 8 8.10 1e-3 0.9731
+26:08+29:02P 6 5.98 5e-5 0.9941
+26:08+31:01P 6 5.82 6e-3 0.9391
+26:08+32:02 11 11.24 5e-3 0.9420
26:08+68:06 9 9.36 0.01 0.9061
-29:01P+32:02 6 5.88 0.00 0.9590
+29:01P+32:02 6 5.88 3e-3 0.9590
29:02P+31:01P 6 5.66 0.02 0.8859
-29:02P+32:02 11 10.94 0.00 0.9856
-29:02P+68:06 9 9.11 0.00 0.9715
+29:02P+32:02 11 10.94 3e-4 0.9856
+29:02P+68:06 9 9.11 1e-3 0.9715
31:01P+32:02 11 10.64 0.01 0.9112
-31:01P+68:06 9 8.85 0.00 0.9611
-32:02+32:02 10 10.28 0.01 0.9300
-32:02+68:01P 8 8.10 0.00 0.9709
-32:02+68:06 17 17.12 0.00 0.9770
-68:01P+68:06 7 6.75 0.01 0.9223
-68:06+68:06 7 7.13 0.00 0.9624
+31:01P+68:06 9 8.85 2e-3 0.9611
+32:02+32:02 10 10.28 8e-3 0.9300
+32:02+68:01P 8 8.10 1e-3 0.9709
+32:02+68:06 17 17.12 8e-4 0.9770
+68:01P+68:06 7 6.75 1e-2 0.9223
+68:06+68:06 7 7.13 2e-3 0.9624
Total 784 785.07
------------------------------------------------------------------------------------------
@@ -242,31 +250,36 @@ Total 1.00000 1982 | Total 1.00000 1982
-------------------------
Table of genotypes, format of each cell is: observed/expected.
-01:01P 17/16.8
-03:01P 31/30.7 14/14.1
-04:01P 20/20.4 19/18.7 6/6.2
-04:03P 1/0.7 0/0.6 1/0.4 0/0.0
-04:04P 1/0.7 0/0.6 1/0.4 0/0.0 0/0.0
-07:01P 38/37.9 35/34.6 23/23.1 1/0.7 1/0.7 21/21.4
-08:01P 38/38.5 35/35.2 23/23.4 1/0.7 1/0.7 43/43.5 22/22.1
-11:01P 18/18.2 17/16.7 11/11.1 0/0.4 0/0.4 21/20.6 21/20.9 5/4.9
- 11:03 3/2.6 2/2.4 2/1.6 0/0.1 0/0.1 3/2.9 3/3.0 1/1.4 0/0.1
-11:04P 9/8.7 8/8.0 5/5.3 0/0.2 0/0.2 10/9.8 10/10.0 5/4.7 1/0.7
-13:01P 6/6.2 6/5.7 4/3.8 0/0.1 0/0.1 7/7.0 7/7.2 3/3.4 0/0.5
-13:02P 2/1.7 2/1.5 1/1.0 0/0.0 0/0.0 2/1.9 2/1.9 1/0.9 0/0.1
-13:03P 1/0.7 0/0.6 1/0.4 0/0.0 0/0.0 1/0.7 1/0.7 0/0.4 0/0.1
-14:01P 10/10.7 10/9.8 6/6.5 0/0.2 0/0.2 12/12.0 12/12.2 6/5.8 1/0.8
-15:01P 46/46.7 43/42.7 28/28.4 1/0.9 1/0.9 52/52.7 55/53.6 26/25.4 4/3.6
- 01:01P 03:01P 04:01P 04:03P 04:04P 07:01P 08:01P 11:01P 11:03
- [Cols: 1 to 9]
-11:04P 1/1.1
-13:01P 2/1.6 1/0.6
-13:02P 0/0.4 0/0.3 0/0.0
-13:03P 0/0.2 0/0.1 0/0.0 0/0.0
-14:01P 3/2.8 2/2.0 1/0.5 0/0.2 2/1.7
-15:01P 12/12.1 9/8.7 2/2.4 1/0.9 15/14.9 32/32.5
- 11:04P 13:01P 13:02P 13:03P 14:01P 15:01P
- [Cols: 10 to 15]
+01:01P 17/16.8
+03:01P 31/30.7 14/14.1
+04:01P 20/20.4 19/18.7 6/6.2
+04:03P 1/0.7 0/0.6 1/0.4 0/6e-3
+04:04P 1/0.7 0/0.6 1/0.4 0/1e-2 0/6e-3
+07:01P 38/37.9 35/34.6 23/23.1 1/0.7 1/0.7 21/21.4
+08:01P 38/38.5 35/35.2 23/23.4 1/0.7 1/0.7 43/43.5 22/22.1
+11:01P 18/18.2 17/16.7 11/11.1 0/0.4 0/0.4 21/20.6 21/20.9
+ 11:03 3/2.6 2/2.4 2/1.6 0/5e-2 0/5e-2 3/2.9 3/3.0
+11:04P 9/8.7 8/8.0 5/5.3 0/0.2 0/0.2 10/9.8 10/10.0
+13:01P 6/6.2 6/5.7 4/3.8 0/0.1 0/0.1 7/7.0 7/7.2
+13:02P 2/1.7 2/1.5 1/1.0 0/3e-2 0/3e-2 2/1.9 2/1.9
+13:03P 1/0.7 0/0.6 1/0.4 0/1e-2 0/1e-2 1/0.7 1/0.7
+14:01P 10/10.7 10/9.8 6/6.5 0/0.2 0/0.2 12/12.0 12/12.2
+15:01P 46/46.7 43/42.7 28/28.4 1/0.9 1/0.9 52/52.7 55/53.6
+ 01:01P 03:01P 04:01P 04:03P 04:04P 07:01P 08:01P
+ [Cols: 1 to 7]
+11:01P 5/4.9
+ 11:03 1/1.4 0/0.1
+11:04P 5/4.7 1/0.7 1/1.1
+13:01P 3/3.4 0/0.5 2/1.6 1/0.6
+13:02P 1/0.9 0/0.1 0/0.4 0/0.3 0/4e-2
+13:03P 0/0.4 0/5e-2 0/0.2 0/0.1 0/3e-2 0/6e-3
+14:01P 6/5.8 1/0.8 3/2.8 2/2.0 1/0.5 0/0.2 2/1.7
+15:01P 26/25.4 4/3.6 12/12.1 9/8.7 2/2.4 1/0.9 15/14.9
+ 11:01P 11:03 11:04P 13:01P 13:02P 13:03P 14:01P
+ [Cols: 8 to 14]
+15:01P 32/32.5
+ 15:01P
+ [Cols: 15 to 15]
Observed Expected Chi-square DoF p-value
------------------------------------------------------------------------------------------
@@ -276,71 +289,71 @@ Table of genotypes, format of each cell is: observed/expected.
------------------------------------------------------------------------------------------
Common + lumped N/A N/A 0.39 35 1.0000
------------------------------------------------------------------------------------------
- All homozygotes 121 121.56 0.00 1 0.9598
+ All homozygotes 121 121.56 3e-3 1 0.9598
------------------------------------------------------------------------------------------
-All heterozygotes 870 869.44 0.00 1 0.9850
+All heterozygotes 870 869.44 4e-4 1 0.9850
------------------------------------------------------------------------------------------
Common heterozygotes by allele
-01:01P 224 224.42 0.00 0.9779
-03:01P 208 207.90 0.00 0.9944
-04:01P 145 144.56 0.00 0.9710
-07:01P 249 248.27 0.00 0.9633
-08:01P 252 251.79 0.00 0.9896
-11:01P 130 130.11 0.00 0.9922
-11:03 20 19.80 0.00 0.9638
-11:04P 65 64.74 0.00 0.9737
+01:01P 224 224.42 8e-4 0.9779
+03:01P 208 207.90 5e-5 0.9944
+04:01P 145 144.56 1e-3 0.9710
+07:01P 249 248.27 2e-3 0.9633
+08:01P 252 251.79 2e-4 0.9896
+11:01P 130 130.11 1e-4 0.9922
+11:03 20 19.80 2e-3 0.9638
+11:04P 65 64.74 1e-3 0.9737
13:01P 46 46.84 0.01 0.9026
-13:02P 13 12.91 0.00 0.9811
-14:01P 78 78.61 0.00 0.9454
-15:01P 295 293.97 0.00 0.9523
+13:02P 13 12.91 6e-4 0.9811
+14:01P 78 78.61 5e-3 0.9454
+15:01P 295 293.97 4e-3 0.9523
------------------------------------------------------------------------------------------
Common genotypes
-01:01P+01:01P 17 16.79 0.00 0.9595
-01:01P+03:01P 31 30.72 0.00 0.9598
-01:01P+04:01P 20 20.44 0.01 0.9230
-01:01P+07:01P 38 37.88 0.00 0.9844
-01:01P+08:01P 38 38.53 0.01 0.9319
-01:01P+11:01P 18 18.22 0.00 0.9582
-01:01P+11:04P 9 8.72 0.01 0.9249
-01:01P+13:01P 6 6.25 0.01 0.9209
+01:01P+01:01P 17 16.79 3e-3 0.9595
+01:01P+03:01P 31 30.72 3e-3 0.9598
+01:01P+04:01P 20 20.44 9e-3 0.9230
+01:01P+07:01P 38 37.88 4e-4 0.9844
+01:01P+08:01P 38 38.53 7e-3 0.9319
+01:01P+11:01P 18 18.22 3e-3 0.9581
+01:01P+11:04P 9 8.72 9e-3 0.9249
+01:01P+13:01P 6 6.25 1e-2 0.9209
01:01P+14:01P 10 10.67 0.04 0.8365
01:01P+15:01P 46 46.73 0.01 0.9148
-03:01P+03:01P 14 14.05 0.00 0.9893
-03:01P+04:01P 19 18.69 0.01 0.9436
-03:01P+07:01P 35 34.65 0.00 0.9526
-03:01P+08:01P 35 35.25 0.00 0.9671
-03:01P+11:01P 17 16.67 0.01 0.9356
-03:01P+11:04P 8 7.98 0.00 0.9937
+03:01P+03:01P 14 14.05 2e-4 0.9893
+03:01P+04:01P 19 18.69 5e-3 0.9436
+03:01P+07:01P 35 34.65 4e-3 0.9526
+03:01P+08:01P 35 35.25 2e-3 0.9671
+03:01P+11:01P 17 16.67 7e-3 0.9356
+03:01P+11:04P 8 7.98 6e-5 0.9937
03:01P+13:01P 6 5.72 0.01 0.9053
-03:01P+14:01P 10 9.76 0.01 0.9398
-03:01P+15:01P 43 42.75 0.00 0.9691
-04:01P+04:01P 6 6.22 0.01 0.9303
-04:01P+07:01P 23 23.05 0.00 0.9915
-04:01P+08:01P 23 23.45 0.01 0.9264
-04:01P+11:01P 11 11.09 0.00 0.9785
+03:01P+14:01P 10 9.76 6e-3 0.9398
+03:01P+15:01P 43 42.75 2e-3 0.9691
+04:01P+04:01P 6 6.22 8e-3 0.9303
+04:01P+07:01P 23 23.05 1e-4 0.9915
+04:01P+08:01P 23 23.45 9e-3 0.9264
+04:01P+11:01P 11 11.09 7e-4 0.9785
04:01P+11:04P 5 5.31 0.02 0.8939
04:01P+14:01P 6 6.50 0.04 0.8459
-04:01P+15:01P 28 28.44 0.01 0.9346
-07:01P+07:01P 21 21.36 0.01 0.9375
-07:01P+08:01P 43 43.46 0.00 0.9445
-07:01P+11:01P 21 20.55 0.01 0.9218
-07:01P+11:04P 10 9.84 0.00 0.9586
-07:01P+13:01P 7 7.05 0.00 0.9857
-07:01P+14:01P 12 12.04 0.00 0.9910
-07:01P+15:01P 52 52.71 0.01 0.9222
-08:01P+08:01P 22 22.10 0.00 0.9825
-08:01P+11:01P 21 20.91 0.00 0.9840
-08:01P+11:04P 10 10.01 0.00 0.9985
-08:01P+13:01P 7 7.17 0.00 0.9498
-08:01P+14:01P 12 12.25 0.00 0.9439
+04:01P+15:01P 28 28.44 7e-3 0.9346
+07:01P+07:01P 21 21.36 6e-3 0.9375
+07:01P+08:01P 43 43.46 5e-3 0.9445
+07:01P+11:01P 21 20.55 1e-2 0.9218
+07:01P+11:04P 10 9.84 3e-3 0.9586
+07:01P+13:01P 7 7.05 3e-4 0.9857
+07:01P+14:01P 12 12.04 1e-4 0.9910
+07:01P+15:01P 52 52.71 1e-2 0.9222
+08:01P+08:01P 22 22.10 5e-4 0.9825
+08:01P+11:01P 21 20.91 4e-4 0.9840
+08:01P+11:04P 10 10.01 4e-6 0.9985
+08:01P+13:01P 7 7.17 4e-3 0.9498
+08:01P+14:01P 12 12.25 5e-3 0.9439
08:01P+15:01P 55 53.61 0.04 0.8499
-11:01P+14:01P 6 5.79 0.01 0.9312
+11:01P+14:01P 6 5.79 7e-3 0.9312
11:01P+15:01P 26 25.36 0.02 0.8986
-11:04P+15:01P 12 12.14 0.00 0.9689
+11:04P+15:01P 12 12.14 2e-3 0.9689
13:01P+15:01P 9 8.69 0.01 0.9174
-14:01P+15:01P 15 14.85 0.00 0.9695
-15:01P+15:01P 32 32.51 0.01 0.9283
+14:01P+15:01P 15 14.85 1e-3 0.9695
+15:01P+15:01P 32 32.51 8e-3 0.9283
Total 915 916.92
------------------------------------------------------------------------------------------
@@ -379,29 +392,31 @@ Total 1.00000 2004 | Total 1.00000 2004
-------------------------
Table of genotypes, format of each cell is: observed/expected.
- 02:01P 13/13.3
- 03:01P 26/25.4 12/12.1
-03:02:12 22/21.7 21/20.6 18/8.8
- 03:02P 15/15.0 14/14.3 12/12.2 4/4.2
- 03:03P 20/20.7 20/19.8 17/16.9 12/11.7 8/8.1
- 04:01P 9/9.2 9/8.8 7/7.5 5/5.2 7/7.2 2/1.6
-04:02:01 0/0.9 0/0.9 0/0.8 0/0.5 0/0.7 0/0.3 0/0.0
- 05:01P 22/21.7 21/20.6 18/17.6 13/12.2 17/16.9 8/7.5 0/0.8 8/8.8
- 05:02P 9/8.4 8/8.0 7/6.8 5/4.7 7/6.6 3/2.9 0/0.3 7/6.8 1/1.3
- 05:03P 23/22.2 21/21.2 0/18.1 13/12.5 18/17.3 8/7.7 0/0.8 18/18.1 7/7.0
- 06:01P 1/1.0 1/1.0 1/0.8 1/0.6 1/0.8 0/0.4 0/0.0 1/0.8 0/0.3
- 06:02P 28/28.1 27/26.8 23/22.9 16/15.8 22/21.9 10/9.7 0/1.0 23/22.9 9/8.9
- 06:03P 8/8.3 7/7.9 6/6.8 4/4.7 6/6.5 3/2.9 8/0.3 6/6.8 2/2.6
- 06:05P 22/21.7 21/20.6 18/17.6 12/12.2 17/16.9 7/7.5 0/0.8 18/17.6 7/6.8
- 02:01P 03:01P03:02:12 03:02P 03:03P 04:01P04:02:01 05:01P 05:02P
- [Cols: 1 to 9]
- 05:03P 39/9.3
- 06:01P 1/0.9 0/0.0
- 06:02P 0/23.5 1/1.1 27/14.9
- 06:03P 6/6.9 0/0.3 8/8.8 1/1.3
- 06:05P 0/18.1 1/0.8 23/22.9 6/6.8 18/8.8
- 05:03P 06:01P 06:02P 06:03P 06:05P
- [Cols: 10 to 14]
+ 02:01P 13/13.3
+ 03:01P 26/25.4 12/12.1
+03:02:12 22/21.7 21/20.6 18/8.8
+ 03:02P 15/15.0 14/14.3 12/12.2 4/4.2
+ 03:03P 20/20.7 20/19.8 17/16.9 12/11.7 8/8.1
+ 04:01P 9/9.2 9/8.8 7/7.5 5/5.2 7/7.2 2/1.6
+04:02:01 0/0.9 0/0.9 0/0.8 0/0.5 0/0.7 0/0.3 0/2e-2
+ 05:01P 22/21.7 21/20.6 18/17.6 13/12.2 17/16.9 8/7.5 0/0.8
+ 05:02P 9/8.4 8/8.0 7/6.8 5/4.7 7/6.6 3/2.9 0/0.3
+ 05:03P 23/22.2 21/21.2 0/18.1 13/12.5 18/17.3 8/7.7 0/0.8
+ 06:01P 1/1.0 1/1.0 1/0.8 1/0.6 1/0.8 0/0.4 0/4e-2
+ 06:02P 28/28.1 27/26.8 23/22.9 16/15.8 22/21.9 10/9.7 0/1.0
+ 06:03P 8/8.3 7/7.9 6/6.8 4/4.7 6/6.5 3/2.9 8/0.3
+ 06:05P 22/21.7 21/20.6 18/17.6 12/12.2 17/16.9 7/7.5 0/0.8
+ 02:01P 03:01P 03:02:12 03:02P 03:03P 04:01P 04:02:01
+ [Cols: 1 to 7]
+ 05:01P 8/8.8
+ 05:02P 7/6.8 1/1.3
+ 05:03P 18/18.1 7/7.0 39/9.3
+ 06:01P 1/0.8 0/0.3 1/0.9 0/2e-2
+ 06:02P 23/22.9 9/8.9 0/23.5 1/1.1 27/14.9
+ 06:03P 6/6.8 2/2.6 6/6.9 0/0.3 8/8.8 1/1.3
+ 06:05P 18/17.6 7/6.8 0/18.1 1/0.8 23/22.9 6/6.8 18/8.8
+ 05:01P 05:02P 05:03P 06:01P 06:02P 06:03P 06:05P
+ [Cols: 8 to 14]
Observed Expected Chi-square DoF p-value
------------------------------------------------------------------------------------------
@@ -416,90 +431,90 @@ Table of genotypes, format of each cell is: observed/expected.
All heterozygotes 851 909.45 3.76 1 0.0526
------------------------------------------------------------------------------------------
Common heterozygotes by allele
-02:01P 205 204.37 0.00 0.9650
-03:01P 196 195.85 0.00 0.9914
+02:01P 205 204.37 2e-3 0.9650
+03:01P 196 195.85 1e-4 0.9914
03:02:12 152 170.36 1.98 0.1595
-03:02P 122 121.57 0.00 0.9687
-03:03P 164 163.83 0.00 0.9895
-04:01P 76 76.81 0.01 0.9267
-04:02:01 8 7.97 0.00 0.9910
+03:02P 122 121.57 2e-3 0.9687
+03:03P 164 163.83 2e-4 0.9895
+04:01P 76 76.81 8e-3 0.9267
+04:02:01 8 7.97 1e-4 0.9910
05:01P 172 170.36 0.02 0.9002
-05:02P 71 70.34 0.01 0.9374
-05:03P 115 174.41 20.24 0.0000*****
-06:01P 9 8.96 0.00 0.9892
+05:02P 71 70.34 6e-3 0.9374
+05:03P 115 174.41 20.24 7e-6*****
+06:01P 9 8.96 2e-4 0.9892
06:02P 190 214.29 2.75 0.0970
-06:03P 70 69.41 0.00 0.9438
+06:03P 70 69.41 5e-3 0.9438
06:05P 152 170.36 1.98 0.1595
------------------------------------------------------------------------------------------
Common genotypes
-02:01P+02:01P 13 13.31 0.01 0.9315
+02:01P+02:01P 13 13.31 7e-3 0.9315
02:01P+03:01P 26 25.36 0.02 0.8988
-02:01P+03:02:12 22 21.67 0.01 0.9436
-02:01P+03:02P 15 14.99 0.00 0.9969
+02:01P+03:02:12 22 21.67 5e-3 0.9436
+02:01P+03:02P 15 14.99 2e-5 0.9969
02:01P+03:03P 20 20.75 0.03 0.8695
-02:01P+04:01P 9 9.22 0.01 0.9418
-02:01P+05:01P 22 21.67 0.01 0.9436
+02:01P+04:01P 9 9.22 5e-3 0.9418
+02:01P+05:01P 22 21.67 5e-3 0.9436
02:01P+05:02P 9 8.41 0.04 0.8401
02:01P+05:03P 23 22.25 0.03 0.8732
-02:01P+06:02P 28 28.13 0.00 0.9811
+02:01P+06:02P 28 28.13 6e-4 0.9811
02:01P+06:03P 8 8.30 0.01 0.9172
-02:01P+06:05P 22 21.67 0.01 0.9436
-03:01P+03:01P 12 12.08 0.00 0.9826
-03:01P+03:02:12 21 20.64 0.01 0.9366
-03:01P+03:02P 14 14.27 0.01 0.9427
-03:01P+03:03P 20 19.76 0.00 0.9570
-03:01P+04:01P 9 8.78 0.01 0.9415
-03:01P+05:01P 21 20.64 0.01 0.9366
-03:01P+05:02P 8 8.01 0.00 0.9961
-03:01P+05:03P 21 21.19 0.00 0.9675
-03:01P+06:02P 27 26.79 0.00 0.9671
+02:01P+06:05P 22 21.67 5e-3 0.9436
+03:01P+03:01P 12 12.08 5e-4 0.9826
+03:01P+03:02:12 21 20.64 6e-3 0.9366
+03:01P+03:02P 14 14.27 5e-3 0.9427
+03:01P+03:03P 20 19.76 3e-3 0.9570
+03:01P+04:01P 9 8.78 5e-3 0.9415
+03:01P+05:01P 21 20.64 6e-3 0.9366
+03:01P+05:02P 8 8.01 2e-5 0.9961
+03:01P+05:03P 21 21.19 2e-3 0.9675
+03:01P+06:02P 27 26.79 2e-3 0.9671
03:01P+06:03P 7 7.90 0.10 0.7477
-03:01P+06:05P 21 20.64 0.01 0.9366
+03:01P+06:05P 21 20.64 6e-3 0.9366
03:02:12+03:02:12 18 8.82 9.56 0.0020**
-03:02:12+03:02P 12 12.20 0.00 0.9553
-03:02:12+03:03P 17 16.89 0.00 0.9779
+03:02:12+03:02P 12 12.20 3e-3 0.9553
+03:02:12+03:03P 17 16.89 8e-4 0.9779
03:02:12+04:01P 7 7.50 0.03 0.8538
-03:02:12+05:01P 18 17.64 0.01 0.9311
-03:02:12+05:02P 7 6.85 0.00 0.9538
-03:02:12+05:03P 0 18.11 18.11 0.0000****
-03:02:12+06:02P 23 22.89 0.00 0.9817
+03:02:12+05:01P 18 17.64 7e-3 0.9311
+03:02:12+05:02P 7 6.85 3e-3 0.9538
+03:02:12+05:03P 0 18.11 18.11 2.1e-5****
+03:02:12+06:02P 23 22.89 5e-4 0.9817
03:02:12+06:03P 6 6.75 0.08 0.7716
-03:02:12+06:05P 18 17.64 0.01 0.9311
-03:02P+03:03P 12 11.68 0.01 0.9246
-03:02P+04:01P 5 5.19 0.01 0.9337
+03:02:12+06:05P 18 17.64 7e-3 0.9311
+03:02P+03:03P 12 11.68 9e-3 0.9246
+03:02P+04:01P 5 5.19 7e-3 0.9337
03:02P+05:01P 13 12.20 0.05 0.8178
03:02P+05:03P 13 12.52 0.02 0.8921
-03:02P+06:02P 16 15.83 0.00 0.9656
-03:02P+06:05P 12 12.20 0.00 0.9553
-03:03P+03:03P 8 8.08 0.00 0.9765
-03:03P+04:01P 7 7.19 0.00 0.9448
-03:03P+05:01P 17 16.89 0.00 0.9779
+03:02P+06:02P 16 15.83 2e-3 0.9656
+03:02P+06:05P 12 12.20 3e-3 0.9553
+03:03P+03:03P 8 8.08 9e-4 0.9765
+03:03P+04:01P 7 7.19 5e-3 0.9448
+03:03P+05:01P 17 16.89 8e-4 0.9779
03:03P+05:02P 7 6.56 0.03 0.8626
03:03P+05:03P 18 17.34 0.03 0.8732
-03:03P+06:02P 22 21.92 0.00 0.9857
+03:03P+06:02P 22 21.92 3e-4 0.9857
03:03P+06:03P 6 6.47 0.03 0.8543
-03:03P+06:05P 17 16.89 0.00 0.9779
+03:03P+06:05P 17 16.89 8e-4 0.9779
04:01P+05:01P 8 7.50 0.03 0.8566
04:01P+05:03P 8 7.70 0.01 0.9152
-04:01P+06:02P 10 9.74 0.01 0.9337
+04:01P+06:02P 10 9.74 7e-3 0.9337
04:01P+06:05P 7 7.50 0.03 0.8538
05:01P+05:01P 8 8.82 0.08 0.7829
-05:01P+05:02P 7 6.85 0.00 0.9538
-05:01P+05:03P 18 18.11 0.00 0.9802
-05:01P+06:02P 23 22.89 0.00 0.9817
+05:01P+05:02P 7 6.85 3e-3 0.9538
+05:01P+05:03P 18 18.11 6e-4 0.9802
+05:01P+06:02P 23 22.89 5e-4 0.9817
05:01P+06:03P 6 6.75 0.08 0.7716
-05:01P+06:05P 18 17.64 0.01 0.9311
-05:02P+05:03P 7 7.03 0.00 0.9908
-05:02P+06:02P 9 8.89 0.00 0.9701
-05:02P+06:05P 7 6.85 0.00 0.9538
+05:01P+06:05P 18 17.64 7e-3 0.9311
+05:02P+05:03P 7 7.03 1e-4 0.9908
+05:02P+06:02P 9 8.89 1e-3 0.9701
+05:02P+06:05P 7 6.85 3e-3 0.9538
05:03P+05:03P 39 9.29 94.95 0.0000*****
-05:03P+06:02P 0 23.50 23.50 0.0000*****
+05:03P+06:02P 0 23.50 23.50 1e-6*****
05:03P+06:03P 6 6.93 0.13 0.7228
-05:03P+06:05P 0 18.11 18.11 0.0000****
+05:03P+06:05P 0 18.11 18.11 2.1e-5****
06:02P+06:02P 27 14.85 9.93 0.0016**
06:02P+06:03P 8 8.77 0.07 0.7957
-06:02P+06:05P 23 22.89 0.00 0.9817
+06:02P+06:05P 23 22.89 5e-4 0.9817
06:03P+06:05P 6 6.75 0.08 0.7716
06:05P+06:05P 18 8.82 9.56 0.0020**
Total 960 958.82
diff --git a/tests/test_AlleleColon.py b/tests/test_AlleleColon.py
index f332026fc..056e93fbd 100644
--- a/tests/test_AlleleColon.py
+++ b/tests/test_AlleleColon.py
@@ -9,7 +9,7 @@ def test_AlleleColon_HardyWeinberg():
assert exit_code == 0
# compare with md5sum of output file
with open("Test_Allele_Colon_HardyWeinberg-out.txt", 'rb') as out_handle:
- assert hashlib.md5(out_handle.read()).hexdigest() == '245a8a8493506c0b65ba9a3469173b13'
+ assert hashlib.md5(out_handle.read()).hexdigest() == 'aa0ad448139a3ea9c65ffa913ef97930'
def test_AlleleColon_Emhaplofreq():
exit_code = run_pypop_process('./tests/data/Test_Allele_Colon_Emhaplofreq.ini', './tests/data/Test_Allele_Colon_Emhaplofreq.pop')
diff --git a/tests/test_GenotypeCommon.py b/tests/test_GenotypeCommon.py
index de4222e77..903ab61bf 100644
--- a/tests/test_GenotypeCommon.py
+++ b/tests/test_GenotypeCommon.py
@@ -9,7 +9,7 @@ def test_GenotypeCommon_HardyWeinberg():
assert exit_code == 0
# compare with md5sum of output file
with open("BIGDAWG_SynthControl_Data-out.txt", 'rb') as out_handle:
- assert hashlib.md5(out_handle.read()).hexdigest() == 'db4bc1113e9eab337561f7510e73381f'
+ assert hashlib.md5(out_handle.read()).hexdigest() == '7162aa0715ccfd1cb7b666409d839129'
def test_GenotypeCommonDash_HardyWeinberg():
exit_code = run_pypop_process('./tests/data/WS_BDCtrl_Test_HW.ini', './tests/data/BIGDAWG_SynthControl_Data_dash.pop')
@@ -17,4 +17,4 @@ def test_GenotypeCommonDash_HardyWeinberg():
assert exit_code == 0
# compare with md5sum of output file
with open("BIGDAWG_SynthControl_Data_dash-out.txt", 'rb') as out_handle:
- assert hashlib.md5(out_handle.read()).hexdigest() == '36053392f9dd25c9a2a6bb1fc6db242a'
+ assert hashlib.md5(out_handle.read()).hexdigest() == 'ee7d37fb5a21419d917bf343f2315083'
diff --git a/tests/test_XSLT.py b/tests/test_XSLT.py
new file mode 100644
index 000000000..d8582b415
--- /dev/null
+++ b/tests/test_XSLT.py
@@ -0,0 +1,58 @@
+import subprocess
+import hashlib
+import pytest
+import os.path
+import tempfile
+from lxml import etree
+from base import abspath_test_data, in_temp_dir
+from PyPop.xslt import format_number_fixed_width
+
+def _run_format_function(root, num, places):
+ xpath_str = "es:format_number_fixed_width('%s', %d)" % (num, places)
+ output = str(root.xpath(xpath_str))
+ # print(num, output)
+ return output
+
+def test_format_number_fixed_width():
+
+ test_cases = [
+ # in_str # out_str #places
+ ('0.032', '0.03200', 5), # pad out with leading zeros
+ ('0.0433', '0.04330', 5),
+ ('0.04333', '0.04333', 5),
+ ('0.000004333', '4.33e-6', 5), # converts to scientific notation to fit in the 5 character ('places') limit
+ ('0.0000000004333', '4.3e-10', 5),
+ ('0.00000433', '0.000004', 6), # does not convert to scientific notation, because we have 6 characters
+ ('0.00000491', '0.000005', 6), # check rounding!
+ ('0.000000433', '4.33e-7', 6), # again need scientific notation to fit
+ ('0.000000', '0.0000', 4), # handle zero as float, not sci notation
+ ('0.02726', '0.0273', 4), # rounding test
+ ('0.02725', '0.0272', 4), # note that is somewhat unexpected: Python rounding for '5' can be weird, see: https://docs.python.org/3/library/functions.html#round
+ ]
+
+ # empty XML to test against
+ root = etree.XML('')
+
+ for test_case in test_cases:
+ in_str, out_str, places = test_case
+ assert out_str == _run_format_function(root, in_str, places)
+
+def test_formatting_with_XML_doc():
+
+ # read and parse stylesheet
+ styledoc = etree.parse(abspath_test_data('src/PyPop/xslt/text.xsl'))
+ style = etree.XSLT(styledoc)
+
+ # parse output XML file
+ doc = etree.parse(abspath_test_data('./tests/data/BIGDAWG_SynthControl_Data-out.xml'))
+
+ # process via stylesheet
+ result = style(doc, **{"new-hardyweinberg-format": "1",
+ "use-python-extensions": "1"})
+
+ # save result to file
+ result.write_output('BIGDAWG_SynthControl_Data-out.txt')
+
+ # check exit code
+ assert True == True
+
diff --git a/website/docs/guide-chapter-instructions.rst b/website/docs/guide-chapter-instructions.rst
index 26b3ffe8d..60c51ea68 100644
--- a/website/docs/guide-chapter-instructions.rst
+++ b/website/docs/guide-chapter-instructions.rst
@@ -8,6 +8,21 @@ results. The text output, generated from the XML file via XSLT, contains
a human-readable summary of the XML results. Below we discuss the output
contained in this text file.
+.. warning::
+
+ The text output we discuss below is strictly intended for
+ consumption by an end-user, or incorporation into a paper. You
+ should never extract information from this text file output to
+ perform any downstream analyses (e.g. don't take the values in the
+ output and paste them into another program). This is because the
+ results are rounded for space, and you may lose a lot of precision
+ if you use any floating-point output in further analyses.
+
+ You should use the :ref:`TSV outputs ` for
+ maximum precision (which, in turn, are derived from the raw XML
+ output) for such analyses.
+
+
.. _instructions-pop-summary:
Population summary