move print_stats to base

code-deduplication: gsanders, mburnett
extract should_print_region_line method

code-deduplication: gsanders, mburnett
move print_region_list to base

code-deduplication: gsanders, mburnett
extract open_input_file method

code-deduplication: gsanders, mburnett
move parse_vcf_header to base

code-deduplication: gsanders, mburnett
move required_info_fields to base

code-deduplication: gsanders, mburnett
make filter_one_line more similar

code-deduplication: gsanders, mburnett
extract filter_sample_format_tag method

code-deduplication: gsanders, mburnett
extract get_readcounts_from_vcf_line method

code-deduplication: gsanders, mburnett
extract get_readcounts_from_vcf_line to base

code-deduplication: gsanders, mburnett
extract update_variant_for_sample

code-deduplication: gsanders, mburnett
move filter_one_sample to base

code-deduplication: gsanders, mburnett
replace magic "FT"/"DNFT" with method

code-deduplication: gsanders, mburnett
move pass_sample to base

code-deduplication: gsanders, mburnett
make fail_sample more similar

code-deduplication: gsanders, mburnett
add questions for gabe

code-deduplication: gsanders, mburnett
re-order methods to make diff more clear

code-deduplication: gsanders, mburnett
move get_all_sample_names_and_bam_paths and add_per_bam_params_to_input to base

code-deduplication: gsanders, mburnett
move generate_and_run_readcounts_in_parallel to base

code-deduplication: gsanders, mburnett
bugfix: don't use "FT" tag for Denovo Vcf Filter