renamed genomecoordinates to genomeregion
Added class to read indexed FASTA files
Added Pileup class to generate Pileup files. If the same flags and
settings are used, this will generate the same output as samtools
mpileup (but so far, for only one file).

Note: This class will not do base quality re-calculations.
Initial support for GTF files
Reworked FASTA to also have a NullFASTA implementation that will always
return 'N's
Pileup updates - bugfix with deletions. Made sure output was consistent
with samtools mpileup, wrt deletions.

Made more efficient to only load sequences as needed. Still need to test
with bam files with multiple references.
GTF CLI tool
Merge branch 'master' of git@github.com:ngsutils/ngsutilsj.git