Comments (9)
Here's how you output dot format:
vg view -d x.vg >x.dot
Every tool in vg
is self-documenting. Just add -h
or --help
to the command line.
Also, any graph output can be piped into any other program. So you can pick up a tiny bit of one graph and then pipe it into vg view
or vg align
. For example, here we can index a graph we've made, then pick up the node with id 50 and its neighbors (defined by a BFS search with up to 5 steps):
vg index -s x.vg
vg find -n 50 -c 5 x.vg | vg view -d - | dot -Tpng -o barrio50.png
These should be added to the documentation. My preference is to start documenting things on the wiki.
from vg.
cool, thanks @ekg. I'm happy to add some documentation things as I play around with vg
a bit; are you suggesting creating this repo's GitHub wiki? Do you envision the README remaining a/the main source of documentation?
Also, while we're here, any interest in making some of the unchecked boxes from the README into issues?
from vg.
I think we should start the wiki. The readme should be shorter and more
clear so people don't get confused.
And the unchecked boxes should absolutely be issues. It hasn't been an..
Issue because its been just me for the past four months. Pick your favorite
and let's jam.
On Mar 13, 2015 8:46 PM, "Ryan Williams" [email protected] wrote:
cool, thanks @ekg https://github.com/ekg. I'm happy to add some
documentation things as I play around with vg a bit; are you suggesting
creating this repo's GitHub wiki? Do you envision the README remaining
a/the main source of documentation?Also, while we're here, any interest in making some of the unchecked boxes
from the README into issues?—
Reply to this email directly or view it on GitHub
#7 (comment).
from vg.
Have you had a chance to experiment further?
from vg.
Sorry for the radio silence, was traveling and otherwise preoccupied but have time to work on variant-graph-related things now. Beginning the "empty checkbox" -> issue migration now, wave me off if that's not a good idea!
from vg.
No, it's great! Go for it. Will you be interested in working on development?
On Apr 14, 2015 8:06 PM, "Ryan Williams" [email protected] wrote:
Sorry for the radio silence, was traveling and otherwise preoccupied but
have time to work on variant-graph-related things now. Beginning the "empty
checkbox" -> issue migration now, wave me off if that's not a good idea!—
Reply to this email directly or view it on GitHub
#7 (comment).
from vg.
Interested for sure; not sure I should commit to anything yet but if you have suggestions for pieces I could bite off easily I am all ears. I have yet to use vg
beyond running it on its own test cases and trying to follow the GA4GH discussion around sub-graphs vs. side-graphs.
I've been thinking a lot (and coding a little) about what a good, interactive, web-based graph-viz story would look like. Can take that discussion over to #8 though.
from vg.
from vg.
That sounds good @ekg; I don't see your email here but mine is [email protected] if you want to shoot me a note; setting up a call or something sounds great.
from vg.
Related Issues (20)
- GAF file empty with vg giraffe HOT 3
- Low-complexity pruning is slow in surjection
- Turn off surjection anchor limit by default
- Bump necessary magic numbers for long-read index types HOT 1
- vg autoindex --workflow mpmap HOT 1
- GAF nodes do not correspond to VCF nodes HOT 3
- Fastq analysis in euka HOT 2
- Protobuf errors mapping HOT 4
- vg augment crashes in combination with giraffe .gam outputs HOT 5
- when i do the code :vg stats -a var1.gam > var1.stats ,show me a bug HOT 2
- vg surject and pack fail on GraphAligner produced .gam HOT 4
- About the usage of vg deconstruct HOT 5
- Right method to annotate genes on pangenome graph HOT 1
- vg call report missing allele HOT 2
- vg call error HOT 2
- How do different methods affect precision? HOT 4
- Giraffe alignment is very slow and produces warning[vg::Watchdog] messages unless rescue is disabled HOT 12
- Giraffe needs to better deal with systems where multiple processes opening the distance index causes slowdowns
- Any option like BWA MEM '-C'?
- vg convert failes while converting gbz to xg with signal 6 error HOT 6
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from vg.