update for tidy

README.md

@@ -533,7 +533,7 @@ configuration file template can be found under ``R/sample_data``:
 
 ### Simplifying Combine Table
 
-As per release v1.3.0, VAST-TOOLS comes with a script to simplify and filter the table obtained in ``combine``, to make it more compatible with most R standard analyses. This module is called ``tidy``, and it parses INCLUSION tables (from ``combine``) event by event, printing out only the PSIs (i.e. no quality score) for those events that pass certain filters. Therefore, two main parameters need to be specified: (i) the minimum number of samples in which the event has sufficient read coverage (either as ``--min_N``, absolute number of samples, or as ``--min_Fr``, fraction of the total samples), and (ii) the minimum standard deviation of the PSIs of the events among the samples with good coverage (``--min_SD``). Several other parameters can be specified: ``--noVLOW``, excludes samples with VLOW coverage; ``--p_IR``, excludes samples that do not pass the binomial test for IR; ``--onlyEXSK``, only EX events are considered. For any given event, samples that do not meet the mininum coverage cut-off will be assigned a PSI = NA.
+As per release v1.3.0, VAST-TOOLS comes with a script to simplify and filter the table obtained in ``combine``, to make it more compatible with most R standard analyses. This module is called ``tidy``, and it parses INCLUSION tables (from ``combine``) event by event, printing out only the PSIs (i.e. no quality score) for those events that pass certain filters. Therefore, two main parameters need to be specified: (i) the minimum number of samples in which the event has sufficient read coverage (either as ``--min_N``, absolute number of samples, or as ``--min_Fr``, fraction of the total samples), and (ii) the minimum standard deviation of the PSIs of the events among the samples with good coverage (``--min_SD``). Several other parameters can be specified: ``--noVLOW``, excludes samples with VLOW coverage; ``--p_IR``, excludes samples that do not pass the binomial test for IR; ``--onlyEXSK``, only EX events are considered. For any given event, samples that do not meet the mininum coverage cut-off will be assigned a PSI = NA. From v2.2.2, ``tidy`` can also filter out events using ``--noB3`` and ``--min_ALT_use X``, as described for ``compare``.
 
 ``tidy`` can also be run using a config file (``--groups FILE``), in which TWO groups of samples are provided using the following format: