Comments (2)
apregier
commented on September 24, 2024
Another possible approach - similar to unix sort, you could write out temp sorted partitions.
from svtools.
ernfrid
commented on September 24, 2024
This addressed by #17 which implements an external merge sort.
Memory usage for a 1000 person, 800,000 line cohort is now ~6GB and merging completes in ~30 minutes of wall clock. In testing on a 5000 person cohort, ~5000 lines per file, merging completes in ~3:40h with ~5G of RAM.
from svtools.
Related Issues (20)
- Syntax error msg
- Does svtools support to mapping BEDPE to human genes?
- Genotyping skips insertions (INS)
- vcftobedpe complains about no END field in LUMPY BNDs. HOT 1
- Python 3.6
- No module named 'l_bp' HOT 1
- svtools vcfpaste error HOT 2
- pip install fails HOT 2
- what is the difference between lmerge sum and prod algorithm ?
- Installation still fails due to conflicting pandas version
- lmerge divide zero error HOT 2
- lsort Index error HOT 3
- Are lmerge same as l_merge.py scripts included in LUMPY?
- possible bug in TRA conversion
- MEI annotations and list index out of range while classifying deletions
- Not able to convert vcf to bedpe (Manta output)
- svtools copynumber error *** Break *** segmentation violation
- bedpetovcf does not work with vcftobedpe output as input HOT 1
- ValueError: max() arg is an empty sequence
- svtools afreq KeyError: 'SQ' in
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 svtools.