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Rm dupes #235

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Rm dupes #235

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averagehat
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Currently this includes #233 (which should be merged into dev). I did this to avoid manually merging later because they would otherwise have conflicts

This is for #217

Panciera and others added 30 commits March 23, 2016 13:47
Fixes issue where MiSeq reads were not being tagged correctly(#221)
…parse the rest of unparsed args if they exist and --qsub_ exist so error can be raised if wrong args exist
Parses all arguments(Closes #229)
@necrolyte2
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What is this PR for. It says RM dups but it seems like it is more about converting formats and such

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It's for #217 but it's not ready. Like it says it includes the bug fix to avoid merge conflicts later. Probably opened the PR prematurely

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