Update README.md (#170)

updated README before the release.

README.md

@@ -1,29 +1,12 @@
 # Smudgeplot 
 
-<font size ="4">**_Version: 0.3.0 Oriel_**</font>
+<font size ="4">**_Version: 0.4.0 Arched_**</font>
 
-<font size ="4">**_Authors: [Gene W Myers](https://github.com/thegenemyers) and [Kamil S. Jaron](https://github.com/KamilSJaron)._**</font>
-
-This is a merger of PloidyPlot from https://github.com/KamilSJaron/MERQURY.FK & Smudgeplot. 
-
-The big changes are
- + the search for the kmer pair will be within both canonical and non-canonical k-mer sets (Gene demonstrated it makes a difference)
- + the tool will be supporting FastK kmer counter only
- + the backend by Gene is paralelized and massively faster
- + the intermediate file will be a flat file with the 2d histogram with cov1, cov2, freq columns (as opposed to list of coverages of pairs cov1 cov2);
- + at least for now WE LOSE the ability to extract sequences of the kmers in the pair; this functionality will hopefully restore at some point together with functionality to assess the quality of assembly.
- + we added "run all" functionality for people that want "FastK database -> plot" type of solution.
- + completelly revamped plot showing how all individual kmer pairs insead of agregating them into squares
- + new smudge detection algorithm based on grid projection on the smudge plane (working, but under revisions at the moment)
- + R package smudgeplot was retired and is no longer used
-
-We keep the same pythonic interface, the interface of older smudgeplot and this version are very similar and largely compatible.
-
-Current state: RUNNING; beta-testing;
+<font size ="4">**_Authors: [Gene W Myers](https://github.com/thegenemyers) and [Kamil S. Jaron](https://github.com/KamilSJaron), Tianyi Ma._**</font>
 
 ### Install the whole thing
 
-This version of smudgeplot operates on FastK k-mer databases. So, before installing smudgeplot, please install [FastK](https://github.com/thegenemyers/FASTK). The smudgeplot installation consist of one R package, and three executables. One of the three needs to be compiled - that is the C-backend to search for all the k-mer pairs.
+This version of smudgeplot operates on FastK k-mer databases. So, before installing smudgeplot, please install [FastK](https://github.com/thegenemyers/FASTK). The smudgeplot installation consist of one python, two R scripts and the C-backend to search for all the k-mer pairs (hetmers) that needs to be compilet.
 
 #### Quick
 
@@ -94,7 +77,7 @@ The y-axis scaling is by default 100, one can spcify argument `ylim` to scale it
 smudgeplot.py all -o data/Scer/trial_run_ylim70 data/Scer/kmerpairs_text.smu -ylim 70
 ```
 
-And that's it for now! I will be streamlining this over the next few days so hopefully it will all work with a single command;
+There is also a plotting module that requires the coverage and a list of smudges and their respective sizes listed in a tabular file. This plotting module does not inference and should be used only if you know the right answers already. 
 
 ### How smudgeplot works