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Added option to NBP to parse bam files, updated the bisulfite tutorial/ user guide to recommend dropping dups with MarkDuplicates.jar

biotelerock 2013-05-30

changed /trunk/Documentation/USeqDocumentation/releaseNotes.txt
changed /trunk/Documentation/USeqDocumentation/usageBisSeq.html
changed /trunk/Source/edu/utah/seq/parsers/NovoalignBisulfiteParser.java
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