Mark DePristo 7b22467148 Bugfix: defaultBaseQualities actually works now ... -- It was being applied in the wrong order (after the first call to the underlying MalformedReadFilter) so if your first read was malformed you'd blow up there instead of being fixed properly. Added integration tests to ensure this continues to work. -- [delivers #49538319]		2013-06-17 14:37:27 -04:00
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sting	Bugfix: defaultBaseQualities actually works now	2013-06-17 14:37:27 -04:00