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Commit [r280]  Maximize  Restore  History

Added option to keep duplicate marked alignments. Now defaults to keeping them.

biotelerock 2015-01-01

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Parent: [r279]

Child: [r281]

changed /trunk/Source/edu/utah/seq/parsers/MergePairedAlignments.java
changed /trunk/Source/edu/utah/seq/parsers/PairedAlignmentChrParser.java
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