Add tag DP_ACGT to GVCF

[martinghunt]

Adds new tag DP_ACGT to the GVCF file. It has read depths (from mpileup) for A-forward, A-reverse, C-forward, C-reverse, G-forward, G-reverse, T-forward, T-reverse. This is added to the GVCF when running clockwork variant_call_one_sample.

Add command line option --bam_file to clockwork gvcf_from_minos_and_samtools, which if used adds the new tag DP_ACGT to the output.