Comments (3)
Hi Eric,
I don't really remember why that's there, but is it a problem to allow a user to set it?
I guess it could mess up other thresholds if other penalties/scores are not modified?
from bwa-meth.
I don't know enough about the flag to know for sure; just wanted to clarify the intended behavior. I think it's even possible to pass -B multiple times and override the user override.
It might be clearer to add -B to the argparse arguments with a default of 2 and a single int value as input?
from bwa-meth.
is there a "not" missing from your original issue? I don't see how it's possible to set -B:
https://github.com/brentp/bwa-meth/blob/master/bwameth.py#L358-L361
are you asking to make that available? I'd rather not unless you have compelling reason especially since bwa-meth has been unchanged for so long.
from bwa-meth.
Related Issues (20)
- Output of bwa-meth in BAM format HOT 1
- The link in `README.md` of the `compare/` folder is not working HOT 4
- [Release Request] make a release since bwa-mem2 index are not included in current version HOT 1
- bwa-meth index error HOT 12
- bwa-mem2 cannot recognize the input from the pipe HOT 5
- broken pipeline HOT 3
- `handle_header` mangles alt contigs HOT 2
- Unique mapped reads HOT 1
- Q: Issues with installation 0.2.5 HOT 1
- Timestamp checking of .fa files prevents me from running bwa-meth in the cloud HOT 2
- Meet Error When running bwa meth mem2
- Help command for aligner command does not work HOT 1
- unrecognized reference name during sam_parse HOT 9
- repeated alignment (bwa get stuck) HOT 2
- when running bwameth example, exception: AttributeError: module 'toolshed.files' has no attribute 'prefunc' HOT 2
- BWA-meth mapping issues
- Exception("bad or empty fastqs") HOT 2
- YC and MD tag issue HOT 3
- YC and YD tags 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 bwa-meth.