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Finished CalculatePerCyclePerNucleotideErrorRate. It would be useful to extend this to looking for insertion/deletion errors by position as well, instead of simply providing counts for the number of reads with insertion/deletion events.

dnephi 2015-06-16

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changed /trunk/Documentation/USeqDocumentation/cmdLnMenus.html
changed /trunk/Source/edu/utah/seq/parsers/MergeBarcodedPairedAlignments.java
changed /trunk/build.properties
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