diff --git a/doc/conf.py b/doc/conf.py index f574141..eb5dfcb 100644 --- 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 index df4d96c..a217405 100644 --- a/doc/download.rst +++ b/doc/download.rst @@ -6,6 +6,7 @@ Download 20/20+ releases --------------- +* `2020plus v1.2.2 `_ - 9/10/2018 - Added option to handle mutational data sets where silent mutations are not reported * `2020plus v1.2.1 `_ - 8/2/2018 - Fixed bug where configuration file would not load * `2020plus v1.2.0 `_ - 3/21/2018 - Change to null distribution simulation * `2020plus v1.1.3 `_ - 8/17/2017 - Bug fixes for different versions of rpy2 diff --git a/doc/faq.rst b/doc/faq.rst index fb0e7ba..b7ac3ea 100644 --- 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 index 2e2defc..1bb7072 100644 --- a/doc/index.rst +++ b/doc/index.rst @@ -30,6 +30,7 @@ Contents: Releases -------- +* `2020plus v1.2.2 `_ - 9/10/2018 - Added option to handle mutational data sets where silent mutations are not reported * `2020plus v1.2.1 `_ - 8/2/2018 - Fixed bug where configuration file would not load * `2020plus v1.2.0 `_ - 3/21/2018 - Change to null distribution simulation * `2020plus v1.1.3 `_ - 8/17/2017 - Bug fixes for different versions of rpy2 diff --git a/src/__init__.py b/src/__init__.py index c68196d..bc86c94 100644 --- a/src/__init__.py +++ b/src/__init__.py @@ -1 +1 @@ -__version__ = "1.2.0" +__version__ = "1.2.2"