[FIX] Adapts to new seq_io and stream module.
Merge pull request #22 from weese/feature/stream/core-test-fixes

[FIX] fixed sequence_info confusion
[FIX] Adapts to new stream and seq_io module.
[NOP] Minor cosmetic change.
[NOP] Minor cosmetic change.
[FIX] Clears seq and meta before use in readRecord.
[FIX] Fixes read function for NewickTrees and some superfluous typedefs.
[INTERNAL] Some code cosmetics.
[INTERNAL] Some code cosmetics.
[FIX] Fixes limitation of number of fasta sequences accidentally introduced by previous commit.
Merge pull request #23 from rrahn/fix/stream/develop/pair_align

[FIX] Adapts to new stream and seq_io module.
Merge pull request #24 from rrahn/fix/stream/develop/seqan_tcoffee

Fix/stream/develop/seqan tcoffee
[FIX] Adapts to new I/O module.
[FIX] Removes unused typedefs.
Merge pull request #25 from weese/feature/stream/core-test-fixes

[FIX] implemented seek() for bgzf stream, fixed BAM index, fixed extra tests/demos
Merge pull request #27 from weese/feature/stream/core-test-fixes

[FIX] fixed bed test, added cartesian extension product to SmartFile, adapted sak
[INTERNAL] Uses tmp object to parse the file format extensions in OutputStreams constructor.
Merge pull request #26 from rrahn/fix/stream/develop/flexbar

Fix/stream/develop/flexbar
Merge pull request #28 from weese/feature/stream/core-test-fixes

[FIX] added support for file pipes and improved cartesian product of file extensions
Merge pull request #29 from weese/feature/stream/core-test-fixes

[FIX] added pipe support for razers