samtools wrapper classes

[Peter]

samtools C api is very useful to handle bamfiles but the API requires a lot of manual allocation and deallocation of its structs, which is not very C++ friendly. In order to use this functionality in a C++ context e.g. in std::vector one need to have wrapper classes around these structs in same fashion as Matrix and Vector are wrappers around GSL structs.

[Peter]

(In [2864]) file structure and empty automake file for new bam namespace. refs #729

[Peter]

(In [2868]) refs #729. Add configure tests for samtools

[Peter]

(In [2869]) improve error messages. emove debug code. refs #729

[Peter]

(In [2874]) remove namespace bam. bam stuff will be put in omic namespace instead. refs #729

[Peter]

(In [2883]) New classes to wrap around functionality provided by samtools. refs #729

[Peter]

If configured --without-samtools Bam support is not compiled into libyat. For that reason, I chose to exclude Bam* header files from both installation and Doxygen input in that case. Is this desired behaviour? If not, it can easily be changed. (changing only one and not both a bit more tricky but doable.)

[Peter]

(In [2884]) add missing since tags. refs #729

[Peter]

(In [2888]) add example SAM file. refs #729

[Peter]

(In [2891]) check for samtools in configure; create bam file in 'make check' if we have samtools. refs #729

[Peter]

(In [2897]) prefer throwing yat::utility::runtime_error. refs #729

[Peter]

(In [2902]) test for bam_pair_analyse. refs #729

[Peter]

(In [2903]) refs #729. document bam_pair_analyse

[Peter]

(In [2904]) boost concept check. refs #729

[Peter]

(In [2910]) improve docs. closes #729