original commit of all the code
Add a missing sript to the initial commit
Fix Some hard coded path to use the PATH instead
Propagate the force merge option
Add the names of the supported assembler
fix a bug in the force merged option
Resolve conflict
Merge branch 'master' of ssh://github.com/tcezard/RADmapper

Conflicts:
	bin/RAD_assemble_read2.py
	bin/RAD_assign_reads_to_consensus.py
	bin/RAD_bam_to_fastq.py
	bin/RAD_coverage_read1.py
	bin/RAD_genotype_to_pattern.py
	bin/RAD_merge_read1_and_read2.py
	bin/RAD_presence_absence_alleles.py
	bin/RAD_process_radtag.py
	bin/RAD_read_sifter_after_merge.py
	bin/RAD_set_read1_consensus_to_read2.py
	bin/RAD_smalt_align_reads_back_to_consensus.py
	lib/IO_interface/__init__.py
	lib/IO_interface/vcfIO.py
	lib/command_runner/__init__.py
	lib/utils/__init__.py
	lib/utils/parameters.py