update docs

docs/_build/html/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: afd4f162f81866546b34bf43a60ac9dd
+config: 895eb4b97f76d81dda11c2de7331f3e9
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/_build/html/_sources/index.txt

@@ -10,7 +10,7 @@ corresponding `.vcf` file such as can occur from sample-swaps
 or pedigree misspecifications.
 
 The code to do this is quite simple. Below, we check for pedigree
-violations by looking at 5,000 sites (see docs for more details on selection)
+violations by looking at 5,000 sites (see :doc:`docs <relatedness>`  for more details on selection)
 and for sex discrepancies by looking at the non-PA regions of the X
 chromosome where males should have very few HET calls.
 
@@ -70,7 +70,7 @@ And we can see that there are no inferred errors along with other information us
 
 The `ped-check` file will contain `n_samples` \* `n_samples` number of rows like below::
 
-    ibs0	ibs2	ibs2*	n	rel	sample_a	sample_b	pedigree_distance	pedigree_parents	predicted_parents	parent_error
+    ibs0	ibs2	ibs2*	n	rel	sample_a	sample_b	pedigree_relatedness	pedigree_parents	predicted_parents	parent_error
     0.0801	0.0042	0.0165	4722	0.0245	NA12877	NA12878	0.0000	False	False	False
     0.0000	0.0125	0.0360	4723	0.5401	NA12877	NA12879	0.5000	True	True	False
     0.0000	0.0108	0.0390	4723	0.5482	NA12877	NA12880	0.5000	True	True	False
@@ -83,6 +83,9 @@ The `ped-check` file will contain `n_samples` \* `n_samples` number of rows like
 
 Using `IBS0`, we can infer the parent-child relationship of a pair of samples. If the inferred value
 doesn't match the relationship in the ped file, then the `parent_error` column will be `True`.
+We can see that the first line above has a high `ibs0` value (and low `rel` value) indicating it's
+not expected to be a parent-child relation while the rest have low `ibs0` (and high `rel` values).
+
 
 ..
     .. toctree::

docs/_build/html/_sources/relatedness.txt

@@ -0,0 +1,34 @@
+relatedness calculations
+========================
+
+Using cyvcf2, we can quickly calculate relatedness using the method
+described in http://www.nature.com/ng/journal/v42/n7/full/ng.608.html in
+equation 6.
+
+This is computationally intensive to calculate for the entire genome
+and other methods, such as KING (http://www.ncbi.nlm.nih.gov/pubmed/20926424)
+have fast methods to do this on the entire genome.
+
+The limitations of these methods is that they assume the average pair of samples
+is unrelated. 
+
+In `pedagree`, we use about 5,000 variants described in http://www.nature.com/nature/journal/v506/n7487/full/nature12975.html
+that are known to be targeted by most exome platforms, in hardy weinberg equilibrium in 1000 genomes,
+and mostly unlinked.
+
+When a user requests to calculate relatedness, we use those 5K sites and
+the genotypes from the 2504 1KG samples to provide a background of samples so
+that most samples are indeed unrelated. Since we are sampling on 5K sites,
+the calculations are quite fast (~5 minutes) and match very well what
+we get from a whole-genome scan because of the properties of those sites.
+Though we use the additional 2504 1KG samples internally, only the information
+from the ped/vcf file is returned.
+
+`pedagree` stores the relationships from the pedigree in a graph and can calculate
+the expected coefficient of relation from what is specified in the ped file.
+We can use this information to compare to what is calculated from the genotypes.
+
+sex QC
+------
+
+

docs/_build/html/_static/basic.css

@@ -4,7 +4,7 @@
  *
  * Sphinx stylesheet -- basic theme.
  *
- * :copyright: Copyright 2007-2014 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2015 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -197,7 +197,10 @@ h3:hover > a.headerlink,
 h4:hover > a.headerlink,
 h5:hover > a.headerlink,
 h6:hover > a.headerlink,
-dt:hover > a.headerlink {
+dt:hover > a.headerlink,
+caption:hover > a.headerlink,
+p.caption:hover > a.headerlink,
+div.code-block-caption:hover > a.headerlink {
     visibility: visible;
 }
 
@@ -314,6 +317,13 @@ table.docutils {
     border-collapse: collapse;
 }
 
+table caption span.caption-number {
+    font-style: italic;
+}
+
+table caption span.caption-text {
+}
+
 table.docutils td, table.docutils th {
     padding: 1px 8px 1px 5px;
     border-top: 0;
@@ -344,6 +354,25 @@ table.citation td {
     border-bottom: none;
 }
 
+/* -- figures --------------------------------------------------------------- */
+
+div.figure {
+    margin: 0.5em;
+    padding: 0.5em;
+}
+
+div.figure p.caption {
+    padding: 0.3em;
+}
+
+div.figure p.caption span.caption-number {
+    font-style: italic;
+}
+
+div.figure p.caption span.caption-text {
+}
+
+
 /* -- other body styles ----------------------------------------------------- */
 
 ol.arabic {
@@ -406,6 +435,10 @@ dl.glossary dt {
     font-size: 1.3em;
 }
 
+.sig-paren {
+    font-size: larger;
+}
+
 .versionmodified {
     font-style: italic;
 }
@@ -471,22 +504,51 @@ table.highlighttable td {
     padding: 0 0.5em 0 0.5em;
 }
 
-tt.descname {
+div.code-block-caption {
+    padding: 2px 5px;
+    font-size: small;
+}
+
+div.code-block-caption code {
+    background-color: transparent;
+}
+
+div.code-block-caption + div > div.highlight > pre {
+    margin-top: 0;
+}
+
+div.code-block-caption span.caption-number {
+    padding: 0.1em 0.3em;
+    font-style: italic;
+}
+
+div.code-block-caption span.caption-text {
+}
+
+div.literal-block-wrapper {
+    padding: 1em 1em 0;
+}
+
+div.literal-block-wrapper div.highlight {
+    margin: 0;
+}
+
+code.descname {
     background-color: transparent;
     font-weight: bold;
     font-size: 1.2em;
 }
 
-tt.descclassname {
+code.descclassname {
     background-color: transparent;
 }
 
-tt.xref, a tt {
+code.xref, a code {
     background-color: transparent;
     font-weight: bold;
 }
 
-h1 tt, h2 tt, h3 tt, h4 tt, h5 tt, h6 tt {
+h1 code, h2 code, h3 code, h4 code, h5 code, h6 code {
     background-color: transparent;
 }
 

docs/_build/html/_static/doctools.js

@@ -4,7 +4,7 @@
  *
  * Sphinx JavaScript utilities for all documentation.
  *
- * :copyright: Copyright 2007-2014 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2015 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -91,6 +91,30 @@ jQuery.fn.highlightText = function(text, className) {
   });
 };
 
+/*
+ * backward compatibility for jQuery.browser
+ * This will be supported until firefox bug is fixed.
+ */
+if (!jQuery.browser) {
+  jQuery.uaMatch = function(ua) {
+    ua = ua.toLowerCase();
+
+    var match = /(chrome)[ \/]([\w.]+)/.exec(ua) ||
+      /(webkit)[ \/]([\w.]+)/.exec(ua) ||
+      /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) ||
+      /(msie) ([\w.]+)/.exec(ua) ||
+      ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) ||
+      [];
+
+    return {
+      browser: match[ 1 ] || "",
+      version: match[ 2 ] || "0"
+    };
+  };
+  jQuery.browser = {};
+  jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true;
+}
+
 /**
  * Small JavaScript module for the documentation.
  */
@@ -152,9 +176,10 @@ var Documentation = {
 
   /**
    * workaround a firefox stupidity
+   * see: https://bugzilla.mozilla.org/show_bug.cgi?id=645075
    */
   fixFirefoxAnchorBug : function() {
-    if (document.location.hash && $.browser.mozilla)
+    if (document.location.hash)
       window.setTimeout(function() {
         document.location.href += '';
       }, 10);

docs/_build/html/_static/haiku.css

@@ -16,7 +16,7 @@
  *              Braden Ewing <brewin@gmail.com>
  *              Humdinger <humdingerb@gmail.com>
  *
- * :copyright: Copyright 2007-2014 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2015 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -307,7 +307,7 @@ td {
     vertical-align: top;
 }
 
-tt {
+code {
     background-color: #e2e2e2;
     font-size: 1.0em;
     font-family: monospace;