mod README

README.md

@@ -1,7 +1,7 @@
 # How to get cloneHD and filterHD?
 
 The current stable release, as well as pre-compiled executable binaries 
-for Mac OS X and GNU Linux (64bit), can be found [here](https://github.com/andrej-fischer/cloneHD/releases). 
+for Mac OS X and GNU Linux (64bit), can be found [here](https://github.com/andrej-fischer/cloneHD/releases). The cloneHD software is undergoing rapid development. Watch/Star this repo to receive updates.
 
 # Run a test with simulated data
 
@@ -20,6 +20,10 @@ For Mac OS X and GNU Linux (64bit), pre-compiled binaries are available [here](h
 
 in the `src` directory. The executables will be in `build`. For debugging with gdb, use `make -f Makefile.debug`.
 
+# Report bugs
+
+To report bugs, use the [issue](https://github.com/andrej-fischer/cloneHD/issues) interface of github.
+
 # What are cloneHD and filterHD for?
 
 cloneHD is a software for reconstructing the subclonal structure of a
@@ -76,20 +80,17 @@ The full documentation can be found in the `/docs/` subfolder. Click below.
    bias field for the tumor CNA data. Follow the logic of the example
    given here.
 
-*  If the matched-normal was sequenced at lower coverage than the tumor, it might be necessary 
-   to run filterHD with a higher-than-optimal diffusion constant (set with `--sigma [double]`)
-   to obtain a more faithful bias field. Otherwise, the filterHD solution is too stiff and 
-   you loose bias detail.
+*  If the matched-normal sample was sequenced at lower coverage than the tumor sample, it might be necessary to run filterHD with a higher-than-optimal diffusion constant (set with `--sigma [double]`) to obtain a more faithful bias field. Otherwise, the filterHD solution is too stiff and you loose bias detail.
 
-*  filterHD can sometimes run into local optima. It might be useful to
-   fix initial values for the parameters via `--jumpi [double]` etc.
+*  filterHD can sometimes run into local optima. In this case, it might be useful to
+   set initial values for the parameters via `--jumpi [double]` etc.
 
 *  By default, cloneHD runs with mass gauging enabled. This seems like
    an overkill, but is actually quite useful because you can see some
    alternative explanations during the course of the analysis.
 
 *  Don't put too much weight on the BIC criterion. It was calibrated
-   using simulated data. For real data, it should be supplied together with
+   using simulated data. For real data, it should be supplemented with
    common sense and biological knowledge. Use `--force [int]` to use a
    fixed number of subclones and `--max-tcn [int]` to set the maximum possible total
    copy number.