Comments (3)
Isn't there code in khmer that sniffs the file type? Much safer than relying on file extensions.
from kevlar.
Looks like #71 is relevant.
from kevlar.
Ideally, it would be great to have khmer detect the file type and handle accordingly. Unless I'm reading the code incorrectly, though, sketches stored on disk only indicate the storage type (bit, byte, or nibble), and do not store whether they are a *table or *graph data structure. So additional input is needed from the user anyway, and that might as well come in the form of a filename, with all the challenges that entails.
All of this is ripe for a fresh look once dib-lab/khmer#1595 is merged. @camillescott may well have already made some changes to the relevant code, but regardless we need to consider how we are going to support a growing list of hash functions (2bit, MurmurHash, rolling hash or hashes, more) and pre-processing options (consume with or without k-mer banding, consume with or without a mask, consume with or without [^ACGT]
preprocessing) in a maintainable way.
from kevlar.
Related Issues (20)
- Bug with log-space transformation
- Command or script for inspecting ambiguous calls
- MemoryError HOT 3
- Execution failed due to high FPR in case HOT 4
- Failed tests HOT 8
- Dead links to tutorial files HOT 3
- Empty files produced by kevlar split cause crash of kevlar assemble HOT 3
- python 3.6 install - pytest failures - 26 failed, 347 passed (pytest 5.3.5?) HOT 5
- Tutorial: Error on running kevlar filter HOT 9
- Clarification - how to avoid high FPR HOT 3
- kevlar memory error HOT 2
- partition, node error HOT 3
- Controls for simlike HOT 2
- VCF Parsing Issue HOT 1
- Where is kevlar? HOT 3
- How to just get the Kmer?
- Kevlar novel multithreading HOT 2
- count_control error: estimated false positive rate is 0.385 (FPR too high, bailing out!!! HOT 5
- > 30,000 variants reported from trio-analysis with FPR 0.001? HOT 6
- Is kevlar able to detect duplications/repeat expansions and in general CNV? HOT 1
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 kevlar.