New functionality for sect: ability to request median coverage for ea…

…ch sequence rather than the mean. This tends to give much better results as occasionally we have a few kmers with extremely high coverage in a sequence which skews the mean coverage.

Fixed a bug in the configuration.  Now correctly includes phthread library when linking the kat and test binaries.

Updated version to 1.0.7.

README.md

@@ -28,15 +28,13 @@ Generic installation description can be found in the INSTALL file. Short summary
       - gcc tool chain
       - make
       - jellyfish = V1.1.10 or V1.1.11 - http://www.cbcb.umd.edu/software/jellyfish/jellyfish-1.1.11.tar.gz **IMPORTANT NOTE**: Please use jellyfish V1.1, we currently do not support jellyfish 2.   We will update KAT to support newer versions of jellyfish in due course.
-      - seqan >= V1.4.1 - http://www.seqan.de
       - gnuplot (required for plotting at runtime, must be available on the path to use this functionality) - http://www.gnuplot.info
   - If you cloned the git repository you must first run "./autogen.sh" to create the configure and make files for your project.  Do not worry if this fails due to missing dependencies at this stage.  If you downloaded a source code distribution tarball then you can skip this step.
   - For a typical installation on a machine where you have root access type ```./configure; make; sudo make install;```
 
 The configure script can take several options as arguments.  One commonly modified option is ```--prefix```, which will install KAT to a custom directory.  By default this is "/usr/local", so the KAT executable would be found at "/usr/local/bin" by default.  In addition, some options specific to managing KAT dependencies located in non-standard locations are:
 
   - ```--with-jellyfish``` - for specifying a custom jellyfish directory
-  - ```--with-seqan``` - for specifying a custom seqan directory
   - ```--with-boost``` - for specifying a custom boost directory (boost is only required for unit testing)
   - ```--with-doxygen``` - for specifying a custom doxygen directory (doxygen is only required for generating code documention.
 
@@ -61,7 +59,7 @@ After KAT has been installed, the following tools should be available:
 
 Running ```kat --help``` will bring up a list of available tools within kat.  To get help on any of these subtools simple type: ```kat <tool> --help```.  For example: ```kat sect --help``` will show details on how to use the sequence coverage estimator tool.
 
-Some dependencies must be dynamically linked to "kat" at runtime.  Specifically, jellyfish and seqan must be available at runtime.  In addition, in order to use the plotting tools it is necessary for "gnuplot" to be available in the PATH.
+Specifically, jellyfish must be available for dynamic linking at runtime.  In addition, in order to use the plotting tools it is necessary for "gnuplot" to be available in the PATH.
 
 
 ##Extending KAT: