Snippy_Variants: Calculate % reads aligned

[emmadoughty]

🆒

📌 Explain the Request

Please add output for % reads aligned for Anippy_Variants

📚 Context

Currently, Snipy_Variants provides an output column of # reads aligned, but this isn't put in context of the total number of reads in the sample. It would be very helpful to have a % calculated to be able to see if there are any major differences in the samples vs the ref, or any contamination indicated by low % reads aligned.

📈 Desired Behavior

Add extra output column with %reads aligned

ℹ️ Additional Information

[jrotieno]

Looking at #592, I think we may have the numbers already available and only need to be calculated. For example, If I look at this new combined QC output:

samplename	reads_aligned_to_reference	variants_total	percent_ref_coverage	#rname	startpos	endpos	numreads	covbases	coverage	meandepth	meanbaseq	meanmapq	#rname	startpos	endpos	numreads	covbases	coverage	meandepth	meanbaseq	meanmapq
ERR10913488	3504551	84125	84.5073	AE003852	1	2961182	2376498	2615376	88.322	114.7	34.2	58.6	AE003853	1	1072319	654185	830592	77.4575	87.0957	34.2	59

we can see that 3504551 were aligned to reference, whereas 2376498 and 654185 (total: 3030683) were mapped to chromosomes 1 and 2, and 86.5% of the reads.