Comments (6)
I don't have any specific merge functions in libBigWig, you would iterate over the intervals in two or more files and merge them as you go.
from libbigwig.
So overall, I'd need to get the list of chroms for both files, merge them, iterate all intervals with bwOverlappingIntervalsIterator
, and merge those intervals? And how would I merge those intervals?
Sorry for bothering, I'm a noob in regards to genomics data so I'm not even sure what those intervals represent :/
from libbigwig.
You might look into https://github.com/Ensembl/WiggleTools
from libbigwig.
Thanks @cmdcolin! But I went a different way, I forked kent tools and re-used the code of bigWigMerge
to create bigWigMergePlus
: a tool to directly merge bigWig files into another bigWig. It contains also a few more features that were needed in the case of our project, such as outputting the standard deviation. Release is here: https://github.com/c3g/kent/releases/tag/bigWigMergePlus_2.0.0
from libbigwig.
FYI I think this is also basically what bigWigCat
does
https://github.com/ENCODE-DCC/kentUtils/tree/master/src/utils/bigWigCat
from libbigwig.
I think bigWigCat
is meant for when the intervals in the files don't overlap. I'd suggest sticking to wiggletools, which uses this library.
from libbigwig.
Related Issues (20)
- Clarification over large buffer sizes sought HOT 2
- Slow loading a remote BigWig file HOT 9
- URL with Temporary Redirect HOT 16
- Segmentation fault with sparse data HOT 7
- cache for reading bigwig and bigbed remote files? HOT 1
- Rename io.h to BigWig_io.h HOT 2
- Segmentation fault in url_fread HOT 9
- parameter values HOT 8
- Optionally check new entries for consistency/sanity
- high memory usage during indexing
- Problem with compilation due to curl.h
- Support for extraIndex fields in BigBed files HOT 5
- Trouble with files on Amazon S3 HOT 5
- Search improvement ? HOT 1
- Time for a new release? HOT 1
- Test failures on other architectures HOT 2
- Online docs rendered incorrectly
- Please publish in the README how to run tests HOT 1
- usr/bin/ld: cannot find -lz when installing libBigWig 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 libbigwig.