Query sequence coverage for treesapp abundance

[cmorganl]

treesapp abundance calculates TPM or FPKM for entire query sequences. The depth of coverage, however, is unknown.

A new feature that reports the pile-up along each query sequence's length would be valuable in determining whether specific regions of query sequences (e.g. active sites) are actually covered or not.

A new field in the classifications.tsv file could report the percentage of a query sequence that was covered and a new BED table could report the depth across each character position.

[cmorganl]

In order for the alignments to work the full-length nucleotide ORFs should be written to the output directory as well. Sequences should be separated into FASTA files based on the reference packages they matched.