Comments (2)
Ah yes that makes a lot more sense than arrow.. not sure what I was thinking when I wrote that!
Thank you for your response. I will have to find a way to sanitise the BAMs beforehand I guess!
from oxbow.
Hi Jack,
Thanks for your interest in oxbow.
The InvalidReferenceSequenceName
error is coming from our upstream dependency noodles
which is reading/parsing the bam file. It looks like you're right that the brackets in the reference name are causing an issue. The name parsing happens in noodles
here. noodles
is aiming for compliance with file format specs (sam spec page 3 section 1.2.1) and errors out on this kind of thing.
Unfortunately, we don't have a way of handling nonconformant data with oxbow at the moment.
from oxbow.
Related Issues (16)
- Add support for reading extra tags from a BAM file. HOT 1
- pyoxbow: test suite HOT 1
- pyoxbow: sphinx API docs HOT 1
- oxbow: column selection HOT 1
- oxbow: nested field translation
- Reading VCF files? HOT 4
- Byte range mapping API
- Range query API
- Remote file access HOT 1
- Feature request: Return iterator of RecordBatches (in Python)
- read_bam shouldn't require BAM index
- Needs a logo HOT 1
- Status of CRAM support
- byte array offset overflow
- r-oxbow installation fails HOT 5
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 oxbow.