Lhc-python

Major changes:
* Added code for local, global and semi-global alignment.
* Added generalisation of loci tools.
* Added bitap for string matching.

Minor changes:
* Updated unit tests

Changes

* added bed filtering
* changed all genomic positions and intervals to use natural ordering
* added pysam as optional dependency. can now be used for all indexed sets

Fixed

* fixed relative position in nested intervals
* fixed nested interval relative position calculation

Fixes
- removed unused GffLine
- fixed genomic position **str**
- fixed nested genomic interval get_abs_pos bug
- fixed genomic interval creation bug
- fixed gbk sequence set access bugs

Changes
- added natural ordering
- added lru cache to inorder access interval set
- changed gff iterator to use intervals
- changed bed to use genomic interval
- changed gtf to use genomic interval
- made bed iterator more flexible
- converted to use updated vcf iterator
- added natural ordering option to vcf merger
- removed unused code

Fixes
- fixed vcf merge natural order argument
- fixed bed, gff and gtf iterators to use genomic intervals
- fixed info and qual in merge
- fixed sample fields in vcf merge
- fixed genomic position string representation
- fixed vcf merge natural ordering

Changes
- added total ordering to genomic position
- changed vcf iterator to use genomic position
- added hash to genomic position
- updated inorder access sets

Fixes
- fixed vcf iterator and set tests
- fixed vcf set

Fixes
- Fixed fasta fragment iterator. New chromosomes did not reset position to 0