4dn-dcic / rpairix Goto Github PK
View Code? Open in Web Editor NEWR binder for pairix - 2D/1D genomic indexing and querying on bgzipped text file
License: MIT License
R binder for pairix - 2D/1D genomic indexing and querying on bgzipped text file
License: MIT License
2000000 easily handled.
If you query for '10:1-200000|20' when chromosome names are 'chr10' not '10', it produces core dump. Do a safe exit.
indexer function. index on bgzipped file.
also bgzip?
@SooLee Just noticing this in successful Travis builds:
Error in file(con, "r") : cannot open the connection
Calls: <Anonymous> -> package_coverage -> add_hooks -> readLines -> file
In addition: Warning messages:
1: In utils::install.packages(repos = NULL, lib = tmp_lib, pkg$path, :
installation of package ‘/home/travis/build/4dn-dcic/Rpairix’ had non-zero exit status
2: In file(con, "r") :
cannot open file '/tmp/RtmpcY81mB/R_LIBS323bc6cc5bc/Rpairix/R/Rpairix': No such file or directory
Execution halted
I'll look into this at some point
px_query("samples/SRR1171591.variants.snp.vqsr.p.vcf.gz","chr10:1-20000000|chr20",6000000)
*** caught segfault ***
address 0x20, cause 'memory not mapped'
Exit smoothly.
take a vector of coordinates for px_query
Add 1D query for for 2d files
A declarative, efficient, and flexible JavaScript library for building user interfaces.
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google ❤️ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.