readAlignmentatCpGIsland: Reads a sequence alignment from a BAM file at the given...
In ndbrown6/EMseq: Enzymatic Methylation sequencing

Reads paired-end sequences from a BAM file given the coordinates of a CpG Isalnd and returns the corresponding sequence alignment and base qualities

1	readAlignmentatCpGIsland(bam, bai, chromosome, start, end, strand)

`bam`	character string specifying path to BAM file
`bai`	character string specifying path to index file. Should not contain extension
`chromosome`	character [X, Y, MT] or numeric [1-22] string of query chomosome
`start`	numeric string defining start of genomic coordinate to query
`end`	numeric string defining end of genomic coordinate to query
`strand`	character string specifying which reads to return. Forward (+) or reverse (-)