[BioC] makeGappedAlignmentPairs for broken pairs

Ido Tamir tamir at imp.ac.at
Thu Jan 16 11:57:25 CET 2014

is there a roadmap for allowing paired end reads where only one is mapped to be reported?
Basically I would like to have readGappedAlignmentPairs report them also.
One could reread the whole file and take only those reads where the  makeGappedAlignmentPairs test
was unsuccessfull.

thank you very much,

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