Open sjackman opened 9 years ago
From @jkbonfield on July 8, 2015 16:19
It took some head scratching to understand how j and is_flip work there. Confusing but probably less so that 1+(j!=is_flip)
:-)
From my reading of the code, is_flip represents the template orientation, correct? If so I agree that it would be useful to add it. I have no idea though what parses this name and how much we'd break by adding an additional field. Certainly wgsim_eval.pl would need changing, maybe more.
Note there is also a newer version in https://github.com/lh3/wgsim/, so it's forked out of samtools now it looks.
Which is the canonical version of wgsim, samtools/samtools
or lh3/wgsim
?
From @jkbonfield on July 9, 2015 8:25
I assume lh3/wgsim as it's newer and his README seems to imply this too. However I don't know for sure.
From @sjackman on February 26, 2015 17:51
The read ID output by wgsim does not include the orientation of the read,
is_flip
. It would be really useful to include the orientation.A read ID currently has six fields separated by underscores
@0_80_129_0:0:0_0:0:0_e/1
Can we add a seventh field that specifies
1
for reverse complement and0
otherwise? I'd be happy to submit a pull request if you agree.@0_80_129_0:0:0_0:0:0_e_0/1
or@0_80_129_0:0:0_0:0:0_e_1/1
https://github.com/samtools/samtools/blob/develop/misc/wgsim.c#L345-L347
Copied from original issue: samtools/samtools#355