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We'll see the following bases identified as ambiguous:
#chr position base
ambig 5 M
ambig 6 R
ambig 7 W
ambig 8 S
ambig 9 Y
ambig 10 K
It would be great if seqtk could support the following IUPAC ambiguities:
B C or G or T
D A or G or T
H A or C or T
V A or C or G
N any base
If I wrote any C at all, I'd make a PR, but as I don't I'll just leave an issue. It looks like the offending line is code like L812 and L438 which checks if the value obtained from bitcnt_table == 2, whereas there are ambiguities with values 3 and 4.
The text was updated successfully, but these errors were encountered:
Both cases are intentional. As its name implies, listhet gives the heterozygous positions. B/D/H/V/N are not hets. randbase is intended to work on hets only.
E.g. for a test sequence:
We'll see the following bases identified as ambiguous:
It would be great if seqtk could support the following IUPAC ambiguities:
If I wrote any C at all, I'd make a PR, but as I don't I'll just leave an issue. It looks like the offending line is code like L812 and L438 which checks if the value obtained from
bitcnt_table == 2
, whereas there are ambiguities with values 3 and 4.The text was updated successfully, but these errors were encountered: