Happy 2015!

 

The website migrated to a new internal URL. There might be a few borked links, but I will try and go over everything in the next few day’s.

 

Cheers!

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Some updates

Updates on both the main library and the python wrapper!

A small parsing error for the Wig parser and some minor reformating of code. Should fix problems with certain type of fixed step wigs. Having had to write a C++ parser for BW files for another project, I am currently working on integrating BigWig and BigBed support into the file parser. The beta version should appear in the developpement branch some time in the next couple of weeks.

The python wrapper had a few more important changes. There was an important memory leak that is now solved and the file types have been centralised to avoid having to call multiple import lines when working with the uBasicNGS datatype.

Enjoy the end of the summer!

 

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Small updates

Cheers everyone

It’s been much more quiet then planned on the developement side, both Charles and I have been somewhat swamped by other academic projects that appeared post publication. However if you get the developpement version, there have been some bug fixes, including a somewhat annoying one in the Wig file parser. The python wrapper has been moderately improved with some streamlining of the modules and a few memory leak/bug fixes.

I cannot promise rapid progress during the spring, but bugs are plugged when found and hopefully some developpement will show itself soon!

 

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Published!

NGS++ has been officially accepted at Oxford Bioinformatics ( advance access link  )!

We would like to thank the reviewers and editor for their time and effort during the process. Reviewing a code library is arguably one of the most laborious tasks that can be imagined (directly after writing unit tests for said library) and  several improvements to NGS++ are direct results of their input.

We are very appreciative of the time they have taken. We would also like to thank everyone who gave feedback during our developpement or who served as guinea pigs for the installation procedure. Special thanks goes to Phillipe Boissoneault for the website framework,  Élaine Beaulieu for reviewing the website and Sébastien Boisvert for feedback on the manuscript and website.

A post with our future plans will be up in a few days. Until then, good coding!

 

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New python bindings for NGS++

We are happy to now offer a Python  2.7 wrapper for the NGS++ library. While a work in progress, it is now stable and mature enough that we believe it can be of use to developpers. The binding is written using ctypes and allows access to several functionalities of the library via Python.

Complete instructions on how to install the wrapper can be found here while a list of the wrapped functionalities can be found here. Note that while it should be stable, this wrapper is still a work in progress and  any bug reports or suggested enhancements are welcome

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Library update

Good morning!

There have been various  updates to the library in the past few day’s, including several small bug fixes, a minor interface change ( all functions with the word “length” are now typed correctly ), minor improvements to the parsing of a file format and so on. As such, it is recommended to starting using the latest version on the gitHub.

We will also be changing our developpement structure. Where previously we worked on a private github then copied the build to the public one, we will be opening a developpement branch directly on the public server. This will make it easier to stay up to date with the versions and reduce repo duplication. This branch will be popping up in the next few day’s and while you are free to use it, there are no guarantees for it’s stability at any particular moment ( we do try to keep the developpement version stable, but bugs happen! )

 

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Small update

Small update on the GitHub, mostly minor code changes to remove some warnings. Every use of std::to_string and similar functions has been replaced by equivalents from our utility namespace. This will facilitate building the library in Windows with TDM-GCC ( that does not currently support these functions)  and in-pair with this change, the Windows 7 installation guide has been updated. Note that Windows is still not officially supported.

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New repository in our GitHub!

We added a new repository in our github: NGSplusplus-Examples.

This repository will contain examples of small programs we used to solve small bioinformatic tasks.

All the program comes with no guarantee and may require the installation of extra dependencies.

Nonetheless, it will provide many concrete examples that demonstrate some of the functionalities of NGS++.

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New version live!

And it is up!

We have pushed a substantial update to the public gitHub, far to many changes, small and big to list in detail. Going forward we hope to move to a more incremental update schedule that will make it easier to included a detailed changelog. But in general, this new version should be more stabler, better commented and offer some extra functionalities. More file formats for the Parser!

Of particular note is that BAM read support is now integrated in the library, courtesy of the excellent BamTools API. For linear loading, simply calling a parser with “BAM” as its file type will do the trick, for indexed loading and such, you will need to go through a uTagsExperiment object and play around a bit with a BamReader object. All in the documentation! As a side-effect of this, the library now requires zlib to build and link correctly.

Otherwise, we have included extra samples to give some ideas of how to do some common tasks and extended our documentation. At this point, community feedback is essential to grow the library in the right direction so please contact us with any bugs or request via our Contact page!

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Welcome!

Welcome to the new NGS++ website. We have moved the majority of our documentation to an online format; this should be much more accessible then our previous large PDF files. The website is not 100% complete yet so look forward to additional content and some interface changes!

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