Aliases for the sam iterators for ease of use

The SamReader library is now fully contained of all the iterators and it
comes with readable aliases for SingleSamReader and PairSamReader.

This closes #17
Merge pull request #23 from MauricioCarneiro/mc_iterator_aliases

Aliases for the sam iterators for ease of use
escape the htslib directory in the Jamfile
add binary option to sam writer
Merge pull request #24 from MauricioCarneiro/develop

add binary option to sam writer
add missing accessors to the reverse flags to sam_body
Fix SamPairIterator

Problem
-------
paired iterator was not taking into account supplementary or secondary alignments.

Solution
--------
use a queue for all non-primary alignments and pass them through
individually after the properly paired reads.
Merge pull request #27 from MauricioCarneiro/mc_fix_paired_iterator

Fix SamPairIterator
rev up htslib
Refactor SamPairIterator

* refactor fetch_next_pair for clarity and reduce duplication
* switch to unique_ptr queue to avoid moving the header around
* make int conversions explicit between gamgee and htslib (to avoid warnings in the SamPairIterator)
Merge pull request #30 from MauricioCarneiro/mc_pair_iterator_refactor

Refactor SamPairIterator
Performance improvements on sam records

* strip away header from sam records
* make sam records hold pointers to the body unless copy constructor explicitly called
* modify iterators to own the memory allocation of the objects returned at each iteration
* explicitly tell users that the life of objects returned by reference is limited to the next iteration. Users can opt in on the copy constructor.
* add project website to the README
* small doxygen documentation fixes
Merge pull request #31 from MauricioCarneiro/develop

Performance improvements on sam records
Fix paired iterator and add tests

Add tests to single reader and paired reader over bans and sams
Travis-CI badge now points to the master branch only
Merge pull request #32 from MauricioCarneiro/mc_develop

Fix paired iterator and add tests
add make clean to htslib when rebuilding with -a
Move Fastq functionality into gamgee

* add exception safety and checked assignment to self to SamHeder's assignment operator
* make complement and reverse complement use std::transform instead of explicit loop
* add in place alternative for complement calculation
* add tests for complement
* rev up htslib
Merge pull request #33 from MauricioCarneiro/mc_develop

Add FASTQ functionality to Gamgee
add src dir to test Jamfile