estimate_purity is broken when only sample_id is provided

[Kdreval]

It looks like some updates have broken how estimate_purity would obtain the MAF data for a sample. This should be fixed so we can use the augment_ssm output with the auto-removal of variants with low read support.

pure=estimate_purity(sample_id="12-17272_tumorB")
fetching: slms-3
using flatfile: /projects/nhl_meta_analysis_scratch/gambl/results_local/gambl/battenberg_current/99-outputs/seg/genome--grch37/12-17272_tumorB--12-17272_normal_subclones.igv.seg
Rows: 45 Columns: 6
── Column specification ────────────────────────────────────────────────────────────────────────────────────────
Delimiter: "\t"
chr (2): ID, chrom
dbl (4): start, end, LOH_flag, log.ratio

ℹ Use spec() to retrieve the full column specification for this data.
ℹ Specify the column types or set show_col_types = FALSE to quiet this message.
Error in UseMethod("filter") :
no applicable method for 'filter' applied to an object of class "NULL"

[Kdreval]

Another issue with this function is:

• in some cases the calculated CCF is nonsensical
• it expects to read from file on disk instead of accepting input data frames
• it is hard-coded to only work with battenberg outputs
• it cannot accept level_3 inputs (more than 1 patient in the merged file)

More details and issues here

[Kdreval]

This is a migration of issue #100 from the parent repo

[rdmorin]

I believe these issues are all resolved in an overhaul I did today.