0.5.3 fix

sigven · Nov 29, 2017 · 72f843a · 72f843a
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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
+* _November 29th 2017_: **0.5.3 release**
+   * Fixed bug with propagation of default options
 * _November 23rd 2017_: **0.5.2 release**
 * _November 15th 2017_: **0.5.1 pre-release**
   * Bug fixing (VCF validation)
@@ -21,8 +23,8 @@ 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.0.5.2.pcgr.html)
-* [Report for a colon adenocarcinoma sample (TCGA)](http://folk.uio.no/sigven/tumor_sample.COAD.0.5.2.pcgr.html)
+* [Report for a breast tumor sample (TCGA)](http://folk.uio.no/sigven/tumor_sample.BRCA.0.5.3.pcgr.html)
+* [Report for a colon adenocarcinoma sample (TCGA)](http://folk.uio.no/sigven/tumor_sample.COAD.0.5.3.pcgr.html)
 
 
 ### PCGR documentation
@@ -33,7 +35,7 @@ If you use PCGR, please cite our preprint paper:
 
 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). bioRxiv. doi:[10.1101/122366](https://doi.org/10.1101/122366)
 
-### Annotation resources included in PCGR (v0.5.2)
+### Annotation resources included in PCGR (v0.5.3)
 
 * [VEP v90](http://www.ensembl.org/info/docs/tools/vep/index.html) - Variant Effect Predictor release 90 (GENCODE v27 as the gene reference dataset)
 * [dBNSFP v3.4](https://sites.google.com/site/jpopgen/dbNSFP) - Database of non-synonymous functional predictions (March 2017)
@@ -71,18 +73,18 @@ A local installation of Python (it has been tested with [version 2.7.13](https:/
 3. Adjust the computing resources dedicated to the Docker, i.e.:
    - Memory: minimum 5GB
    - CPUs: minimum 4
-   - [How to - Mac OS X](https://docs.docker.com/docker-for-mac/#advanced)  
+   - [How to - Mac OS X](https://docs.docker.com/docker-for-mac/#advanced)
 
 #### STEP 2: Download PCGR
 
-1. Download and unpack the [latest software release (0.5.2)](https://github.com/sigven/pcgr/releases/tag/v0.5.2)
+1. Download and unpack the [latest software release (0.5.3)](https://github.com/sigven/pcgr/releases/tag/v0.5.3)
 2. Download and unpack the data bundle (approx. 16Gb) in the PCGR directory
-   * Download [the accompanying data bundle](https://drive.google.com/file/d/1NSeMWpLVMBcCEDYpOLsuWSnKfZEaamip/) from Google Drive to `~/pcgr-X.X` (replace _X.X_ with the version number, e.g `~/pcgr-0.5.2`)
+   * Download [the accompanying data bundle](https://drive.google.com/file/d/1NSeMWpLVMBcCEDYpOLsuWSnKfZEaamip/) from Google Drive to `~/pcgr-X.X` (replace _X.X_ with the version number, e.g `~/pcgr-0.5.3`)
    * Unpack the data bundle, e.g. through the following Unix command: `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 (0.5.2)](https://hub.docker.com/r/sigven/pcgr/) from DockerHub (approx 4.2Gb):
-   * `docker pull sigven/pcgr:0.5.2` (PCGR annotation engine)
+3. Pull the [PCGR Docker image (0.5.3)](https://hub.docker.com/r/sigven/pcgr/) from DockerHub (approx 4.2Gb):
+   * `docker pull sigven/pcgr:0.5.3` (PCGR annotation engine)
 
 #### STEP 3: Input preprocessing
 
@@ -128,7 +130,7 @@ 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-0.5.2
+					e.g. ~/pcgr-0.5.3
 	output_dir            Output directory
 	configuration_file    PCGR configuration file (TOML format)
 	sample_id             Tumor sample/cancer genome identifier - prefix for
@@ -162,9 +164,9 @@ The configuration file, formatted using [TOML](https://github.com/toml-lang/toml
 
 The _examples_ folder contain input files from two tumor samples sequenced within TCGA. It also contains a PCGR configuration file. 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-0.5.2/examples/tumor_sample.COAD.vcf.gz`
-`--input_cna ~/pcgr-0.5.2/examples/tumor_sample.COAD.cna.tsv`
-` ~/pcgr-0.5.2 ~/pcgr-0.5.2/examples ~/pcgr-0.5.2/examples/pcgr_configuration.toml tumor_sample.COAD`
+`python pcgr.py --input_vcf ~/pcgr-0.5.3/examples/tumor_sample.COAD.vcf.gz`
+`--input_cna ~/pcgr-0.5.3/examples/tumor_sample.COAD.cna.tsv`
+` ~/pcgr-0.5.3 ~/pcgr-0.5.3/examples ~/pcgr-0.5.3/examples/pcgr_configuration_examples.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/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/doctrees/output.doctree b/docs/_build/doctrees/output.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: a37f4512adb7d594a1b2deb3b303056d
+config: 4a2fe4a2c5cd8e7cce3c94775d1a8b54
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/_build/html/_sources/about.rst.txt b/docs/_build/html/_sources/about.rst.txt
@@ -27,9 +27,9 @@ Example reports
 ~~~~~~~~~~~~~~~
 
 -  `Report for a breast tumor sample
-   (TCGA) <http://folk.uio.no/sigven/tumor_sample.BRCA.0.5.2.pcgr.html>`__
+   (TCGA) <http://folk.uio.no/sigven/tumor_sample.BRCA.0.5.3.pcgr.html>`__
 -  `Report for a colon adenocarcinoma sample
-   (TCGA) <http://folk.uio.no/sigven/tumor_sample.COAD.0.5.2.pcgr.html>`__
+   (TCGA) <http://folk.uio.no/sigven/tumor_sample.COAD.0.5.3.pcgr.html>`__
 
 Why use PCGR?
 ~~~~~~~~~~~~~

diff --git a/docs/_build/html/_sources/getting_started.rst.txt b/docs/_build/html/_sources/getting_started.rst.txt
@@ -55,15 +55,15 @@ Download PCGR
 ^^^^^^^^^^^^^
 
 -  Download and unpack the `latest software release
-   (0.5.2) <https://github.com/sigven/pcgr/releases/latest>`__
+   (0.5.3) <https://github.com/sigven/pcgr/releases/latest>`__
 
 -  Download and unpack the data bundle (approx. 16Gb) in the PCGR
    directory
 
    -  Download `the accompanying data
       bundle <https://drive.google.com/file/d/1NSeMWpLVMBcCEDYpOLsuWSnKfZEaamip/>`__
       from Google Drive to ``~/pcgr-X.X`` (replace *X.X* with the
-      version number, e.g. ``~/pcgr-0.5.2``)
+      version number, e.g. ``~/pcgr-0.5.3``)
    -  Decompress and untar the bundle, e.g. through the following Unix
       command:
       ``gzip -dc pcgr.databundle.GRCh37.YYYYMMDD.tgz | tar xvf -``
@@ -72,10 +72,10 @@ Download PCGR
    have been produced
 
 -  Pull the `PCGR Docker image -
-   0.5.2 <https://hub.docker.com/r/sigven/pcgr/>`__ from DockerHub
+   0.5.3 <https://hub.docker.com/r/sigven/pcgr/>`__ from DockerHub
    (approx 4.2Gb) :
 
-   -  ``docker pull sigven/pcgr:0.5.2`` (PCGR annotation engine)
+   -  ``docker pull sigven/pcgr:0.5.3`` (PCGR annotation engine)
 
 Run test - generation of clinical report for a cancer genome
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -94,7 +94,7 @@ 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-0.5.2
+                    e.g. ~/pcgr-0.5.3
     output_dir            Output directory
     configuration_file    PCGR configuration file (TOML format)
     sample_id             Tumor sample/cancer genome identifier - prefix for
@@ -135,10 +135,10 @@ sequenced within TCGA. It also contains a PCGR configuration file. 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-0.5.2/examples/tumor_sample.COAD.vcf.gz``
-``--input_cna ~/pcgr-0.5.2/examples/tumor_sample.COAD.cna.tsv``
-``~/pcgr-0.5.2 ~/pcgr-0.5.2/examples``
-\`\ ``~/pcgr-0.5.2/examples/pcgr_configuration.toml tumor_sample.COAD``
+``python pcgr.py --input_vcf ~/pcgr-0.5.3/examples/tumor_sample.COAD.vcf.gz``
+``--input_cna ~/pcgr-0.5.3/examples/tumor_sample.COAD.cna.tsv``
+``~/pcgr-0.5.3 ~/pcgr-0.5.3/examples``
+\`\ ``~/pcgr-0.5.3/examples/pcgr_configuration_examples.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/_sources/output.rst.txt b/docs/_build/html/_sources/output.rst.txt
@@ -212,9 +212,9 @@ below:
    -  Supporting scientific literature (key report elements)
 
 -  `View an example report for a breast tumor sample
-   (TCGA) <http://folk.uio.no/sigven/tumor_sample.BRCA.0.5.2.pcgr.html>`__
+   (TCGA) <http://folk.uio.no/sigven/tumor_sample.BRCA.0.5.3.pcgr.html>`__
 -  `View an example report for a colon adenocarcinoma sample
-   (TCGA) <http://folk.uio.no/sigven/tumor_sample.COAD.0.5.2.pcgr.html>`__
+   (TCGA) <http://folk.uio.no/sigven/tumor_sample.COAD.0.5.3.pcgr.html>`__
 
 The HTML reports have been tested using the following browsers:
 
@@ -694,7 +694,7 @@ The format of the compressed TSV file is the following:
 
 ::
 
-    1. chrom - chromosome  
+    1. chrom - chromosome
     2. segment_start - start of copy number segment
     3. segment_end - end of copy number segment
     4. segment_length_Mb - length of segment in Mb

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 0.5.2 documentation</title>
+  <title>About &mdash; Personal Cancer Genome Reporter 0.5.3 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 0.5.2 documentation" href="index.html"/>
+    <link rel="top" title="Personal Cancer Genome Reporter 0.5.3 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">
-                0.5.2
+                0.5.3
               </div>
 
 
@@ -169,9 +169,9 @@ <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.0.5.2.pcgr.html">Report for a breast tumor sample
+<li><a class="reference external" href="http://folk.uio.no/sigven/tumor_sample.BRCA.0.5.3.pcgr.html">Report for a breast tumor sample
 (TCGA)</a></li>
-<li><a class="reference external" href="http://folk.uio.no/sigven/tumor_sample.COAD.0.5.2.pcgr.html">Report for a colon adenocarcinoma sample
+<li><a class="reference external" href="http://folk.uio.no/sigven/tumor_sample.COAD.0.5.3.pcgr.html">Report for a colon adenocarcinoma sample
 (TCGA)</a></li>
 </ul>
 </div>
@@ -254,7 +254,7 @@ <h2>Contact<a class="headerlink" href="#contact" title="Permalink to this headli
     <script type="text/javascript">
         var DOCUMENTATION_OPTIONS = {
             URL_ROOT:'./',
-            VERSION:'0.5.2',
+            VERSION:'0.5.3',
             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 0.5.2 documentation</title>
+  <title>Annotation resources &mdash; Personal Cancer Genome Reporter 0.5.3 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 0.5.2 documentation" href="index.html"/>
+    <link rel="top" title="Personal Cancer Genome Reporter 0.5.3 documentation" href="index.html"/>
         <link rel="next" title="Input &amp; output" href="output.html"/>
         <link rel="prev" title="Getting started" href="getting_started.html"/> 
 
@@ -65,7 +65,7 @@
 
 
               <div class="version">
-                0.5.2
+                0.5.3
               </div>
 
 
@@ -334,7 +334,7 @@ <h2>Data quality<a class="headerlink" href="#data-quality" title="Permalink to t
     <script type="text/javascript">
         var DOCUMENTATION_OPTIONS = {
             URL_ROOT:'./',
-            VERSION:'0.5.2',
+            VERSION:'0.5.3',
             COLLAPSE_INDEX:false,
             FILE_SUFFIX:'.html',
             HAS_SOURCE:  true

diff --git a/docs/_build/html/genindex.html b/docs/_build/html/genindex.html
@@ -9,7 +9,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Index &mdash; Personal Cancer Genome Reporter 0.5.2 documentation</title>
+  <title>Index &mdash; Personal Cancer Genome Reporter 0.5.3 documentation</title>
 
 
 
@@ -36,7 +36,7 @@
         <link rel="index" title="Index"
               href="#"/>
         <link rel="search" title="Search" href="search.html"/>
-    <link rel="top" title="Personal Cancer Genome Reporter 0.5.2 documentation" href="index.html"/> 
+    <link rel="top" title="Personal Cancer Genome Reporter 0.5.3 documentation" href="index.html"/> 
 
 
   <script src="_static/js/modernizr.min.js"></script>
@@ -64,7 +64,7 @@
 
 
               <div class="version">
-                0.5.2
+                0.5.3
               </div>
 
 
@@ -173,7 +173,7 @@ <h1 id="index">Index</h1>
     <script type="text/javascript">
         var DOCUMENTATION_OPTIONS = {
             URL_ROOT:'./',
-            VERSION:'0.5.2',
+            VERSION:'0.5.3',
             COLLAPSE_INDEX:false,
             FILE_SUFFIX:'.html',
             HAS_SOURCE:  true