show warning when .somalier files have no sites with depth > 0 about somalier

[brentp]

can you show the stdout and stderr when you run:

somalier relate -o test -g group.txt cohort/*somalier
head test.samples.tsv

[taytayp]

Sure thing.

/somalier # somalier relate -o test -g group.txt cohort/*somalier
somalier version: 0.2.6
[somalier] time to read files and get per-sample stats for 2 samples: 0.00
[somalier] time to get expected relatedness from pedigree graph: 0.00
[somalier] time to calculate all vs all relatedness for all 1 combinations: 0.00
[somalier] wrote interactive HTML output for 1 pairs to: test.html
[somalier] wrote groups to: test.groups.tsv
[somalier] wrote samples to: test.samples.tsv
[somalier] wrote pair-wise relatedness metrics to: test.pairs.tsv
/somalier # head test.samples.tsv 
#sample	pedigree_sex	gt_depth_mean	gt_depth_sd	depth_mean	depth_sd	ab_mean	ab_std	n_hom_ref	n_het	n_hom_alt	n_unknown	p_middling_ab	X_depth_mean	X_n	X_hom_ref	X_het	X_hom_alt	Y_depth_mean	Y_n
TP19-09N_N		0.0	-nan	0.0	0.0	0.00	-nan	0	0	0	17384	0.000	0.00	0	0	0	0	0.00	0
TP19-09T_T		0.0	-nan	0.0	0.0	0.00	-nan	0	0	0	17384	0.000	0.00	0	0	0	0	0.00	0

[brentp]

Looks like you don't have any data in the .somalier files
can you re-extract the samples and show the output? perhaps you extracted with GRCh37 sites and your data is in 38? or vice-versa?

[taytayp]

Ah, looks like that did it! It's right that the graphs are relatively unimpressive right? There's just one comparison point between two samples, I assume.

#sample_a	sample_b	relatedness	hom_concordance	hets_a	hets_b	shared_hets	hom_alts_a	hom_alts_b	shared_hom_alts	ibs0	ibs2	n	x_ibs0	x_ibs2	expected_relatedness
TP19-09N_N	TP19-09T_T	0.999	1.000	5616	6333	5609	4791	5405	4789	0	14229	14235	0	282	-1.0

Thanks for the help, maybe a good error or warning would be to indicate the *somalier inputs are empty? Might save some users like me a headache.