0.6.2.1 release

sigven · May 14, 2018 · 306d6dd · 306d6dd
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diff --git a/README.md b/README.md
@@ -7,6 +7,8 @@ The Personal Cancer Genome Reporter (PCGR) is a stand-alone software package for
 ![PCGR overview](PCGR_workflow.png)
 
 ### News
+* _May 14th 2018_: **0.6.2.1 release**
+   * [CHANGELOG](http://pcgr.readthedocs.io/en/latest/CHANGELOG.html#may-14th-2018)
 * _May 9th 2018_: **0.6.2 release**
    * Fixed various bugs reported by users (see [CHANGELOG](http://pcgr.readthedocs.io/en/latest/CHANGELOG.html#may-9th-2018))
    * Data bundle update (ClinVar, KEGG, CIViC, UniProt, DiseaseOntology)
@@ -37,8 +39,8 @@ The Personal Cancer Genome Reporter (PCGR) is a stand-alone software package for
 
 
 ### Example reports
-* [Report for a breast tumor sample (TCGA)](http://folk.uio.no/sigven/tumor_sample.BRCA.pcgr_acmg.grch37.0.6.2.html)
-* [Report for a colon adenocarcinoma sample (TCGA)](http://folk.uio.no/sigven/tumor_sample.COAD.pcgr_acmg.grch37.0.6.2.html)
+* [Report for a breast tumor sample (TCGA)](http://folk.uio.no/sigven/tumor_sample.BRCA.pcgr_acmg.grch37.0.6.2.1.html)
+* [Report for a colon adenocarcinoma sample (TCGA)](http://folk.uio.no/sigven/tumor_sample.COAD.pcgr_acmg.grch37.0.6.2.1.html)
 
 
 ### PCGR documentation
@@ -49,7 +51,7 @@ If you use PCGR, please cite our recent publication:
 
 Sigve Nakken, Ghislain Fournous, Daniel Vodák, Lars Birger Aaasheim, Ola Myklebost, and Eivind Hovig. __Personal Cancer Genome Reporter: variant interpretation report for precision oncology__ (2017). _Bioinformatics_. 34(10):1778–1780. doi:[10.1093/bioinformatics/btx817](https://doi.org/10.1093/bioinformatics/btx817)
 
-### Annotation resources included in PCGR (0.6.2)
+### Annotation resources included in PCGR (0.6.2.1)
 
 * [VEP v92](http://www.ensembl.org/info/docs/tools/vep/index.html) - Variant Effect Predictor release 92 (GENCODE v28/v19 as the gene reference dataset)
 * [CIViC](http://civic.genome.wustl.edu) - Clinical interpretations of variants in cancer (May 8th 2018)
@@ -88,15 +90,15 @@ An installation of Python (version _3.6_) is required to run PCGR. Check that Py
 
 #### STEP 2: Download PCGR and data bundle
 
-1. Download and unpack the [latest software release (0.6.2)](https://github.com/sigven/pcgr/releases/tag/v0.6.2)
+1. Download and unpack the [latest software release (0.6.2.1)](https://github.com/sigven/pcgr/releases/tag/v0.6.2.1)
 2. Download and unpack the assembly-specific data bundle in the PCGR directory
    * [grch37 data bundle](https://drive.google.com/open?id=1cGBAmAh5t4miIeRrrd0zHsPCFToOr0Lf) (approx 9Gb)
    * [grch38 data bundle](https://drive.google.com/open?id=12q3rr7xpdBfaefRi0ysFHbH34kehNZOV) (approx 9Gb)
    * *Unpacking*: `gzip -dc pcgr.databundle.grch37.YYYYMMDD.tgz | tar xvf -`
 
     A _data/_ folder within the _pcgr-X.X_ software folder should now have been produced
-3. Pull the [PCGR Docker image (0.6.2)](https://hub.docker.com/r/sigven/pcgr/) from DockerHub (approx 5.1Gb):
-   * `docker pull sigven/pcgr:0.6.2` (PCGR annotation engine)
+3. Pull the [PCGR Docker image (0.6.2.1)](https://hub.docker.com/r/sigven/pcgr/) from DockerHub (approx 5.1Gb):
+   * `docker pull sigven/pcgr:0.6.2.1` (PCGR annotation engine)
 
 #### STEP 3: Input preprocessing
 
@@ -157,7 +159,7 @@ A tumor sample report is generated by calling the Python script __pcgr.py__, whi
 
 	positional arguments:
 	pcgr_dir              PCGR base directory with accompanying data directory,
-				    e.g. ~/pcgr-0.6.2
+				    e.g. ~/pcgr-0.6.2.1
 	output_dir            Output directory
 	{grch37,grch38}       Genome assembly build: grch37 or grch38
 	configuration_file    PCGR configuration file (TOML format)
@@ -186,9 +188,9 @@ A tumor sample report is generated by calling the Python script __pcgr.py__, whi
 
 The _examples_ folder contain input files from two tumor samples sequenced within TCGA (**GRCh37** only). It also contains PCGR configuration files customized for these cases. A report for a colorectal tumor case can be generated by running the following command in your terminal window:
 
-`python pcgr.py --input_vcf ~/pcgr-0.6.2/examples/tumor_sample.COAD.vcf.gz`
-`--input_cna ~/pcgr-0.6.2/examples/tumor_sample.COAD.cna.tsv`
-` ~/pcgr-0.6.2 ~/pcgr-0.6.2/examples grch37 ~/pcgr-0.6.2/examples/pcgr_conf.COAD.toml tumor_sample.COAD`
+`python pcgr.py --input_vcf ~/pcgr-0.6.2.1/examples/tumor_sample.COAD.vcf.gz`
+`--input_cna ~/pcgr-0.6.2.1/examples/tumor_sample.COAD.cna.tsv`
+` ~/pcgr-0.6.2.1 ~/pcgr-0.6.2.1/examples grch37 ~/pcgr-0.6.2.1/examples/pcgr_conf.COAD.toml tumor_sample.COAD`
 
 
 This command will run the Docker-based PCGR workflow and produce the following output files in the _examples_ folder:

diff --git a/docs/CHANGELOG.md b/docs/CHANGELOG.md
@@ -1,6 +1,12 @@
 
 ## CHANGELOG
 
+#### 0.6.2.1 - May 14th 2018
+
+##### Fixed
+
+ * Bug in copy number annotation (broad/focal)
+
 #### 0.6.2 - May 9th 2018
 
 ##### Fixed

diff --git a/docs/CHANGELOG.rst b/docs/CHANGELOG.rst
@@ -1,6 +1,14 @@
 CHANGELOG
 ---------
 
+0.6.2.1 - May 14th 2018
+^^^^^^^^^^^^^^^^^^^^^^^
+
+Fixed
+'''''
+
+-  Bug in copy number annotation (broad/focal)
+
 0.6.2 - May 9th 2018
 ^^^^^^^^^^^^^^^^^^^^
 

diff --git a/docs/_build/doctrees/CHANGELOG.doctree b/docs/_build/doctrees/CHANGELOG.doctree
diff --git a/docs/_build/doctrees/about.doctree b/docs/_build/doctrees/about.doctree
diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle
diff --git a/docs/_build/doctrees/getting_started.doctree b/docs/_build/doctrees/getting_started.doctree
diff --git a/docs/_build/html/.buildinfo b/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: 04616fa05efaaa19416d1091e820f76a
+config: c0c8197050de327e0bb0458a914594e7
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/_build/html/CHANGELOG.html b/docs/_build/html/CHANGELOG.html
@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>CHANGELOG &mdash; Personal Cancer Genome Reporter 0.6.2 documentation</title>
+  <title>CHANGELOG &mdash; Personal Cancer Genome Reporter 0.6.2.1 documentation</title>
 
 
 
@@ -35,7 +35,7 @@
         <link rel="index" title="Index"
               href="genindex.html"/>
         <link rel="search" title="Search" href="search.html"/>
-    <link rel="top" title="Personal Cancer Genome Reporter 0.6.2 documentation" href="index.html"/>
+    <link rel="top" title="Personal Cancer Genome Reporter 0.6.2.1 documentation" href="index.html"/>
         <link rel="prev" title="Tier models" href="tier_systems.html"/> 
 
 
@@ -64,7 +64,7 @@
 
 
               <div class="version">
-                0.6.2
+                0.6.2.1
               </div>
 
 
@@ -94,17 +94,21 @@
 <li class="toctree-l1"><a class="reference internal" href="output.html">Output</a></li>
 <li class="toctree-l1"><a class="reference internal" href="tier_systems.html">Tier models</a></li>
 <li class="toctree-l1 current"><a class="current reference internal" href="#">CHANGELOG</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="#may-9th-2018">0.6.2 - May 9th 2018</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="#may-14th-2018">0.6.2.1 - May 14th 2018</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="#fixed">Fixed</a></li>
+</ul>
+</li>
+<li class="toctree-l2"><a class="reference internal" href="#may-9th-2018">0.6.2 - May 9th 2018</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#id1">Fixed</a></li>
 <li class="toctree-l3"><a class="reference internal" href="#added">Added</a></li>
 </ul>
 </li>
 <li class="toctree-l2"><a class="reference internal" href="#may-2nd-2018">0.6.1 - May 2nd 2018</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="#id1">Fixed</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id2">Fixed</a></li>
 </ul>
 </li>
 <li class="toctree-l2"><a class="reference internal" href="#april-25th-2018">0.6.0 - April 25th 2018</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="#id2">Added</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id3">Added</a></li>
 <li class="toctree-l3"><a class="reference internal" href="#removed">Removed</a></li>
 <li class="toctree-l3"><a class="reference internal" href="#changed">Changed</a></li>
 </ul>
@@ -157,11 +161,20 @@
 
   <div class="section" id="changelog">
 <h1>CHANGELOG<a class="headerlink" href="#changelog" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="may-9th-2018">
-<h2>0.6.2 - May 9th 2018<a class="headerlink" href="#may-9th-2018" title="Permalink to this headline">¶</a></h2>
+<div class="section" id="may-14th-2018">
+<h2>0.6.2.1 - May 14th 2018<a class="headerlink" href="#may-14th-2018" title="Permalink to this headline">¶</a></h2>
 <div class="section" id="fixed">
 <h3>Fixed<a class="headerlink" href="#fixed" title="Permalink to this headline">¶</a></h3>
 <ul class="simple">
+<li>Bug in copy number annotation (broad/focal)</li>
+</ul>
+</div>
+</div>
+<div class="section" id="may-9th-2018">
+<h2>0.6.2 - May 9th 2018<a class="headerlink" href="#may-9th-2018" title="Permalink to this headline">¶</a></h2>
+<div class="section" id="id1">
+<h3>Fixed<a class="headerlink" href="#id1" title="Permalink to this headline">¶</a></h3>
+<ul class="simple">
 <li>Bug in copy number segment display (missing variable initalization)</li>
 <li>Typo in gnomAD filter statistic (fraction)</li>
 <li>Bug in mutational signature analysis for grch38 (forgot to pass
@@ -186,8 +199,8 @@ <h3>Added<a class="headerlink" href="#added" title="Permalink to this headline">
 </div>
 <div class="section" id="may-2nd-2018">
 <h2>0.6.1 - May 2nd 2018<a class="headerlink" href="#may-2nd-2018" title="Permalink to this headline">¶</a></h2>
-<div class="section" id="id1">
-<h3>Fixed<a class="headerlink" href="#id1" title="Permalink to this headline">¶</a></h3>
+<div class="section" id="id2">
+<h3>Fixed<a class="headerlink" href="#id2" title="Permalink to this headline">¶</a></h3>
 <ul class="simple">
 <li>Bug in tier assignment &#8216;pcgr_acmg&#8217; (case for no variants in
 tier1,2,3)</li>
@@ -203,8 +216,8 @@ <h3>Fixed<a class="headerlink" href="#id1" title="Permalink to this headline">¶
 </div>
 <div class="section" id="april-25th-2018">
 <h2>0.6.0 - April 25th 2018<a class="headerlink" href="#april-25th-2018" title="Permalink to this headline">¶</a></h2>
-<div class="section" id="id2">
-<h3>Added<a class="headerlink" href="#id2" title="Permalink to this headline">¶</a></h3>
+<div class="section" id="id3">
+<h3>Added<a class="headerlink" href="#id3" title="Permalink to this headline">¶</a></h3>
 <ul class="simple">
 <li>New argument in pcgr.py<ul>
 <li><em>assembly</em> (grch37/grch38)</li>
@@ -423,7 +436,7 @@ <h3>Changed<a class="headerlink" href="#changed" title="Permalink to this headli
     <script type="text/javascript">
         var DOCUMENTATION_OPTIONS = {
             URL_ROOT:'./',
-            VERSION:'0.6.2',
+            VERSION:'0.6.2.1',
             COLLAPSE_INDEX:false,
             FILE_SUFFIX:'.html',
             HAS_SOURCE:  true

diff --git a/docs/_build/html/_sources/CHANGELOG.rst.txt b/docs/_build/html/_sources/CHANGELOG.rst.txt
@@ -1,6 +1,14 @@
 CHANGELOG
 ---------
 
+0.6.2.1 - May 14th 2018
+^^^^^^^^^^^^^^^^^^^^^^^
+
+Fixed
+'''''
+
+-  Bug in copy number annotation (broad/focal)
+
 0.6.2 - May 9th 2018
 ^^^^^^^^^^^^^^^^^^^^
 

diff --git a/docs/_build/html/_sources/about.rst.txt b/docs/_build/html/_sources/about.rst.txt
@@ -26,9 +26,9 @@ Example reports
 ~~~~~~~~~~~~~~~
 
 -  `Report for a breast tumor sample
-   (TCGA) <http://folk.uio.no/sigven/tumor_sample.BRCA.pcgr_acmg.grch37.0.6.2.html>`__
+   (TCGA) <http://folk.uio.no/sigven/tumor_sample.BRCA.pcgr_acmg.grch37.0.6.2.1.html>`__
 -  `Report for a colon adenocarcinoma sample
-   (TCGA) <http://folk.uio.no/sigven/tumor_sample.COAD.pcgr_acmg.grch37.0.6.2.html>`__
+   (TCGA) <http://folk.uio.no/sigven/tumor_sample.COAD.pcgr_acmg.grch37.0.6.2.1.html>`__
 
 Why use PCGR?
 ~~~~~~~~~~~~~

diff --git a/docs/_build/html/_sources/getting_started.rst.txt b/docs/_build/html/_sources/getting_started.rst.txt
@@ -45,7 +45,7 @@ STEP 2: Download PCGR and data bundle
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 1. Download and unpack the `latest software release
-   (0.6.2) <https://github.com/sigven/pcgr/releases/tag/v0.6.2>`__
+   (0.6.2.1) <https://github.com/sigven/pcgr/releases/tag/v0.6.2.1>`__
 2. Download and unpack the assembly-specific data bundle in the PCGR
    directory
 
@@ -61,10 +61,10 @@ STEP 2: Download PCGR and data bundle
    A *data/* folder within the *pcgr-X.X* software folder should now
    have been produced
 3. Pull the `PCGR Docker image
-   (0.6.2) <https://hub.docker.com/r/sigven/pcgr/>`__ from DockerHub
+   (0.6.2.1) <https://hub.docker.com/r/sigven/pcgr/>`__ from DockerHub
    (approx 5.1Gb):
 
-   -  ``docker pull sigven/pcgr:0.6.2`` (PCGR annotation engine)
+   -  ``docker pull sigven/pcgr:0.6.2.1`` (PCGR annotation engine)
 
 STEP 3: Input preprocessing
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -151,7 +151,7 @@ A tumor sample report is generated by calling the Python script
 
     positional arguments:
     pcgr_dir              PCGR base directory with accompanying data directory,
-                    e.g. ~/pcgr-0.6.2
+                    e.g. ~/pcgr-0.6.2.1
     output_dir            Output directory
     {grch37,grch38}       Genome assembly build: grch37 or grch38
     configuration_file    PCGR configuration file (TOML format)
@@ -181,9 +181,9 @@ configuration files customized for these samples. A report for a
 colorectal tumor case can be generated by running the following command
 in your terminal window:
 
-``python pcgr.py --input_vcf ~/pcgr-0.6.2/examples/tumor_sample.COAD.vcf.gz``
-``--input_cna ~/pcgr-0.6.2/examples/tumor_sample.COAD.cna.tsv``
-``~/pcgr-0.6.2 ~/pcgr-0.6.2/examples grch37 ~/pcgr-0.6.2/examples/pcgr_conf.COAD.toml tumor_sample.COAD``
+``python pcgr.py --input_vcf ~/pcgr-0.6.2.1/examples/tumor_sample.COAD.vcf.gz``
+``--input_cna ~/pcgr-0.6.2.1/examples/tumor_sample.COAD.cna.tsv``
+``~/pcgr-0.6.2.1 ~/pcgr-0.6.2.1/examples grch37 ~/pcgr-0.6.2.1/examples/pcgr_conf.COAD.toml tumor_sample.COAD``
 
 This command will run the Docker-based PCGR workflow and produce the
 following output files in the *examples* folder:

diff --git a/docs/_build/html/about.html b/docs/_build/html/about.html
@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>About &mdash; Personal Cancer Genome Reporter 0.6.2 documentation</title>
+  <title>About &mdash; Personal Cancer Genome Reporter 0.6.2.1 documentation</title>
 
 
 
@@ -35,7 +35,7 @@
         <link rel="index" title="Index"
               href="genindex.html"/>
         <link rel="search" title="Search" href="search.html"/>
-    <link rel="top" title="Personal Cancer Genome Reporter 0.6.2 documentation" href="index.html"/>
+    <link rel="top" title="Personal Cancer Genome Reporter 0.6.2.1 documentation" href="index.html"/>
         <link rel="next" title="Getting started" href="getting_started.html"/>
         <link rel="prev" title="Welcome to Personal Cancer Genome Reporter’s documentation!" href="index.html"/> 
 
@@ -65,7 +65,7 @@
 
 
               <div class="version">
-                0.6.2
+                0.6.2.1
               </div>
 
 
@@ -170,9 +170,9 @@ <h2>What is the Personal Cancer Genome Reporter (PCGR)?<a class="headerlink" hre
 <div class="section" id="example-reports">
 <h2>Example reports<a class="headerlink" href="#example-reports" title="Permalink to this headline">¶</a></h2>
 <ul class="simple">
-<li><a class="reference external" href="http://folk.uio.no/sigven/tumor_sample.BRCA.pcgr_acmg.grch37.0.6.2.html">Report for a breast tumor sample
+<li><a class="reference external" href="http://folk.uio.no/sigven/tumor_sample.BRCA.pcgr_acmg.grch37.0.6.2.1.html">Report for a breast tumor sample
 (TCGA)</a></li>
-<li><a class="reference external" href="http://folk.uio.no/sigven/tumor_sample.COAD.pcgr_acmg.grch37.0.6.2.html">Report for a colon adenocarcinoma sample
+<li><a class="reference external" href="http://folk.uio.no/sigven/tumor_sample.COAD.pcgr_acmg.grch37.0.6.2.1.html">Report for a colon adenocarcinoma sample
 (TCGA)</a></li>
 </ul>
 </div>
@@ -256,7 +256,7 @@ <h2>Contact<a class="headerlink" href="#contact" title="Permalink to this headli
     <script type="text/javascript">
         var DOCUMENTATION_OPTIONS = {
             URL_ROOT:'./',
-            VERSION:'0.6.2',
+            VERSION:'0.6.2.1',
             COLLAPSE_INDEX:false,
             FILE_SUFFIX:'.html',
             HAS_SOURCE:  true

diff --git a/docs/_build/html/annotation_resources.html b/docs/_build/html/annotation_resources.html
@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Annotation resources &mdash; Personal Cancer Genome Reporter 0.6.2 documentation</title>
+  <title>Annotation resources &mdash; Personal Cancer Genome Reporter 0.6.2.1 documentation</title>
 
 
 
@@ -35,7 +35,7 @@
         <link rel="index" title="Index"
               href="genindex.html"/>
         <link rel="search" title="Search" href="search.html"/>
-    <link rel="top" title="Personal Cancer Genome Reporter 0.6.2 documentation" href="index.html"/>
+    <link rel="top" title="Personal Cancer Genome Reporter 0.6.2.1 documentation" href="index.html"/>
         <link rel="next" title="Input" href="input.html"/>
         <link rel="prev" title="Getting started" href="getting_started.html"/> 
 
@@ -65,7 +65,7 @@
 
 
               <div class="version">
-                0.6.2
+                0.6.2.1
               </div>
 
 
@@ -334,7 +334,7 @@ <h3>Data quality<a class="headerlink" href="#data-quality" title="Permalink to t
     <script type="text/javascript">
         var DOCUMENTATION_OPTIONS = {
             URL_ROOT:'./',
-            VERSION:'0.6.2',
+            VERSION:'0.6.2.1',
             COLLAPSE_INDEX:false,
             FILE_SUFFIX:'.html',
             HAS_SOURCE:  true