Fix #174: bug in chromosome comparison
Fix #173: don't use SAM file from junctions script
Fix #171: Use 0 for mapq for unmapped read

There were some cases where one read of a pair is mapped and the
other isn't, and they both have mapq of 25. It should be 25 for
the mapped one and 0 for the other.
Change version to 2.0.5_04
Fix some tests
Merge branch 'release-2.0.5_04'