Comments (4)
#1 hasn't been formalized. gfatools may support paths, but it won't happen soon.
It seems like one should be able to pick a vertex and do a BFS where only edges to ranks equal or lower than the starting segment (sample) are considered.
This works in simple cases, but generally not reliable. The better approach is to map sequences back to the graph and trace the alignment path.
from gfatools.
I see. But if the segment coordinates are stable relative to the linear reference (if my understanding is correct), then at least all the sample-specific segments, i.e., any new segments formed after the sample is added, can be "traced" along the reference, right? Why is it better to re-map and trace the alignment path?
from gfatools.
Here's where my confusion is coming from: the description in doc/rGRA.md and what I'm observing in my results tell me that the SO tag specifies the "offset on the stable sequence" which I presume to mean the input chromosome/scaffold/contig from the added sample. The illustration in that document suggests instead that the SO offset is relative to the reference sequence (only one segment shows the offest of 0 - the s1:chr1), which implies a single coordinate system for all sample segments. If it's the former, then my suggestion in the previous comment obviously won't work.
Or am I not interpreting the illustration correctly ?
Thank you
from gfatools.
Ok, I see it now. The illustration is for a case where all three samples have the first 5 bases in common, and so all have the same 0th coordinate, so to speak.
from gfatools.
Related Issues (20)
- Format clarification HOT 2
- Fields in bubble output HOT 1
- blacklisting region from a region file
- gfa view subgraph radius definition HOT 4
- Is there support for translation between stable coordinate and segment/local coordinate for GAF? HOT 1
- Add a License HOT 4
- can I convert single line path from complex structures into fasta files HOT 1
- GFA2 format from miniasm not properly converting to fasta HOT 1
- About "--bf" the bloom filter
- gfatools bubble doesn't work on GFA after bubble popping with gfatools asm
- conversion of GFA to rGFA HOT 2
- Invalid GAF is produced HOT 1
- "A" line produced by gfatools asm
- Can I extract path sequences from GFA or rGFA by pathname?
- meaning of NM:i:5 AS:f:56.3 dv:f:0.0694444 id:f:0.930556 cg:Z:4=1X2=1I38=1D5=1I5=1X13=? HOT 2
- How to convert fastG to GFA?
- Using `gfatools asm`
- The question about format of fasta using gfatoos gfa2fa
- Online GfaViewer on gfaServer HOT 2
- gfatools view to subset a gfa file HOT 2
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from gfatools.