added reheader method
added gitignore for gem
Updated faidx method to run with no options
Added code for calmd
Added methods for targetcut and phase
added tests for index_stats, etch_with_function, fetch_reference, sort, mpileup, depth and index
Added test data and code for fixmate, flatstat and merge
added test for rmdup
wrote reheader and calmd methods plus tests
finished sam tests
Added pileup and vcf tests
Added pileup tests
Completed writing package methods. Wrote unit tests and created test data. Wrote rdoc for sam.rb
Included tutorial files
Added unit tests
Updated docs
Added visualisation of bam coverage
Merge pull request #30 from ethering/rewrite_no_wraps

Rewrite no wraps