US: Common difference identification about sequencetubemap

[glennhickey]

Yeah, it would be handy to see differences in the reads that are not in the graph. This is a hard problem in general, but for SNPs it shouldn't be too bad. A SNP Edit in the GAM would look like

 {"to_length": 1, "from_length": 1, "sequence": "T"}

and in this case, the display should print a T at the appropriate position on the read. Presumably small inserts could be done in a similar manner by printing the sequence (or maybe insertion length). They look like (no from_length or from_length 0):

 {"to_length": 2, "sequence": "T"}

Deletes seem much harder as you would have to display a new edge to the graph. Deletion edits have the to_length field set to 0

 {"from_length": 2}

[wolfib]

How about displaying deletions by changing the read color from red to reddish transparent in the relevant region and not adding any extra edges?

[adamnovak]

That might work.

…

On Fri, Jul 28, 2017 at 8:13 AM, Wolfgang Beyer ***@***.***> wrote: How about displaying deletions by changing the read color from red to reddish transparent in the relevant region and not adding any extra edges? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#8 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AE0_X46GTzXMAQ3NJUTYpgPT2aM5eVOGks5sSfqrgaJpZM4OedxN> .

[adamnovak]

We don't do anything special for this, but I don't think we really need to. Seeing several mismatches/indels at the same position is enough.