Merge fastqs and bams

[anoronh4]

Addresses part 2 of #6

This PR adds the ability to handle multiple fastqs pairs per sample. The goals are:

1. Output one bam per sample
2. Add read group information in the primary bam based on the detected fastq header.
3. Produce merged reads for all applications other than default star alignment that take raw reads.

By itself, the code changes in this PR will assume that each fastq pair in the inputs has one read-group. Enabling splitting of fastqs can be added in a subsequent PR.