updated version number

KarchinLab · Sep 11, 2018 · cc7d33e · cc7d33e
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diff --git a/doc/conf.py b/doc/conf.py
@@ -52,7 +52,7 @@
 # The short X.Y version.
 version = '1.2'
 # The full version, including alpha/beta/rc tags.
-release = '1.2.0'
+release = '1.2.2'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

diff --git a/doc/download.rst b/doc/download.rst
@@ -6,6 +6,7 @@ Download
 20/20+ releases
 ---------------
 
+* `2020plus v1.2.2 <https://github.com/KarchinLab/2020plus/archive/v1.2.2.tar.gz>`_ - 9/10/2018 - Added option to handle mutational data sets where silent mutations are not reported
 * `2020plus v1.2.1 <https://github.com/KarchinLab/2020plus/archive/v1.2.1.tar.gz>`_ - 8/2/2018 - Fixed bug where configuration file would not load
 * `2020plus v1.2.0 <https://github.com/KarchinLab/2020plus/archive/v1.2.0.tar.gz>`_ - 3/21/2018 - Change to null distribution simulation
 * `2020plus v1.1.3 <https://github.com/KarchinLab/2020plus/archive/v1.1.3.tar.gz>`_ - 8/17/2017 - Bug fixes for different versions of rpy2

diff --git a/doc/faq.rst b/doc/faq.rst
@@ -22,3 +22,10 @@ genes were established from cancer experts.
 
 You can substantially speed up run time by reducing the number of simulations.
 This can be done by reducing the NUMSIMULATIONS variable (e.g. from 100000 to 10000) in the `config.yaml` file or specification in the command line of snakemake via `--config NUMSIMULATIONS=10000`. This might result in a slight decrease in prediction performance but may be waranted for large data.
+
+**What happens if silent mutations were not recorded in my data set?** 
+
+Ocassionally, in the literature, studies may only report non-silent mutations
+from a sequencing study. If not accounted for, this may bias estimates of 
+statistical significance. To make an adjustment for this problem, provide the `drop_silent` option
+via the command line: `--config drop_silent="yes"`.
diff --git a/doc/index.rst b/doc/index.rst
@@ -30,6 +30,7 @@ Contents:
 Releases
 --------
 
+* `2020plus v1.2.2 <https://github.com/KarchinLab/2020plus/archive/v1.2.2.tar.gz>`_ - 9/10/2018 - Added option to handle mutational data sets where silent mutations are not reported
 * `2020plus v1.2.1 <https://github.com/KarchinLab/2020plus/archive/v1.2.1.tar.gz>`_ - 8/2/2018 - Fixed bug where configuration file would not load
 * `2020plus v1.2.0 <https://github.com/KarchinLab/2020plus/archive/v1.2.0.tar.gz>`_ - 3/21/2018 - Change to null distribution simulation
 * `2020plus v1.1.3 <https://github.com/KarchinLab/2020plus/archive/v1.1.3.tar.gz>`_ - 8/17/2017 - Bug fixes for different versions of rpy2

diff --git a/src/__init__.py b/src/__init__.py
@@ -1 +1 @@
-__version__ = "1.2.0"
+__version__ = "1.2.2"