License fix merge

added new command line switches to README

adjusted merge_bed.py to new input format

added reads support filter example awk code

I fixed some stuff in the command line help and docs

added underscore to prefix description

* added lots of documentation to markdown

* find_circ.py:
	- no longer output dubious splices with NO_UNIQ_BRIDGES by default
	  switch --report_nobridges brings back old behaviour
* unmapped2anchors.py:
	- replaced with improved version from SVN that can split FASTA input
	  as well
* test_data/Makefile
	- supoprts three targets now: cdr1as_test, hek_test and hek_test2

* working on improved test cases that also showcase use of newer commandline switches/better output naming, etc.

  - now reports at which input line the exception was raised, helping to troubleshoot

* modified test_data to
  a) not redirect stderr anymore but explicitely store reads in a separate file
  b) contain deliberately broken input to test the reporting feature

  first commit, README converted to markdown and PDF generated with pandoc