esiragusa/seqan — pull request #16 by weese (2014-09-02 19:58:58+00:00)
Title: [FEATURE] added SmartFile class to replace former BamStream/GffStream/SequenceStream

* The new generic base class `SmartFile` can be specialized with one representative Format Tag (`Fastq`, `Bam`, `Gff`) and a direction (`Input`, `Output`)
* I provided shortcuts e.g. `BamFileIn`, `GffFileOut`, `SeqFileIn`

Additionally, I ported sam2matrix, samcat and all Bam/Gff tests to the new interface.