ivar consensus: call reference at positions with low coverage

[alephreish]

I'm using ivar consensus to create updated reference sequences in simple cases (i.e. mapping of Sanger contigs to a reference assembly), similar to FastaAlternateReferenceMaker. For this to work, consensus should take reference residues at positions with low (zero) coverage, an option that AFAICT it does not have.

$ cat pile.txt
ref	1	A	0	*	*
ref	2	A	1	T	~
ref	3	T	0	*	*
ref	4	G	0	*	*
ref	5	G	0	*	*
$ ivar consensus -p cons -m 1 < pile.txt 
Minimum Quality: 20
Threshold: 0
Minimum depth: 1
Regions with depth less than minimum depth covered by: N
Reference length: 5
Positions with 0 depth: 4
Positions with depth below 1: 4
$ cat cons.fa 
>Consensus_cons_threshold_0_quality_20
NTNNN

A workaround is to mess with the pileup, forcing zero-depth positions to have the reference residue:

$ awk '!$4{$4=1;$5=".";$6="~"}1' OFS=\\t pile.txt | ivar consensus -p cons -m 1
Minimum Quality: 20
Threshold: 0
Minimum depth: 1
Regions with depth less than minimum depth covered by: N
Reference length: 5
Positions with 0 depth: 0
Positions with depth below 1: 0
$ cat cons.fa 
>Consensus_cons_threshold_0_quality_20
ATTGG

But I think it would be natural to add an argument (or to extend -n) that would indicate that the reference should be called for regions with zero coverage (perhaps in lower case).

[cmaceves]

got it, yeah that makes a lot of sense to me! could you please provide me some sample data?