estimate_purity is broken when only sample_id is provided

[rdmorin]

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"

[rdmorin]

@kristenadaley can you look into this?

[Kdreval]

This function also has other bugs that Jasper posted on Slack. I'll migrate this issue to the new repo for tracking