Rename MANUAL.txt to MANUAL.md
Started fixing MD.
Rename INSTALL.txt to INSTALL.md
Update INSTALL.md
Fixed some MD, so that it renders well
Update errorhandle.py

added meaningful error code when a module was not found
Two hotfixes: runtime error when -m and -s specified for a PE lib (with no MP contamination obviously).
Empty repeat file in rare cases when --separate_repeats specified and no scaffolding is performed with an existing second library.
 Bumped up version number to 1.1.2.
Fixed runtime error bug for PE lib and empty repeat.fa file bug
Merge branch 'hotfix/1.1.1'
Fixed two bugs. Runtime error for PE lib without contiamination if -m ans -s specified and empty repeats.fa bug
Merge branch 'hotfix/1.1.1' into develop
The networkx package was updated to return a generator from connected_component_subgraphs. This caused len() to fail. Updated code to reflect this.
Merge pull request #7 from fadern/develop

Develop
Merge pull request #6 from rchikhi/patch-1

Update errorhandle.py
Merge pull request #5 from jvhaarst/master

Moved INSTALL.txt and MANUAL.txt to MarkDown versions
Changed dependency of pysam to require any version >=0.7
added less stringend dependency on pysam

Merge branch 'hotfix/pysam_dependency'
Added less stringent dependency on pysam. Previous dependency requeirment could cause error.

Merge branch 'hotfix/pysam_dependency' into develop
fixed pysam dependency bug.
Merge branch 'master' into develop
Added catch of exeption when no reads are mapped on contigs. More informative error message is given.
Added more informative error message when no reads are mapped to contigs.
Merge branch 'hotfix/no_mapped_reads_error'
Added more informative error message when no reads are mapped to contigs.
Merge branch 'hotfix/no_mapped_reads_error' into develop