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Sequence Trimming - cleanup functions #352

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mothur-westcott opened this Issue Jul 7, 2017 · 0 comments

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mothur-westcott commented Jul 7, 2017

When I call…

                rSeq.printSequence(cout);

the output is the untrimmed sequence. but if I do rSeq.printUnAlignedSequence(cout); or cout << rSeq.getUnaligned().length() << endl;, I get the right output. Looking at the Sequence class, I’m not sure why the two print methods would give different results for unaligned sequences. Perhaps in Sequence::setUnaligned (called at L490 of qualityscores.cpp), we should set isaligned to FALSE. Alternatively we should use Sequence::trim at L490 of qualityscores.cpp, which does this naturally. I don’t think it impacts my application, but the print and trim calls seem like they need a tweak.

@mothur-westcott mothur-westcott added this to the Back Burner milestone Jul 7, 2017

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