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I'm normally a C# / .net developer, but a new project is going to be working with Next Generation Sequencing BAM and VCF files. I will need to read these files, make some changes, and save them. As far as I can tell, there's not much in the way of existing .net libraries for working with these files.
What programming languages are typically used in this field, and have libraries supporting these files?
Python with pysam and pyvcf libraries.
Or use shell with samtools, sambamba, vcflib, vcftools, bcftools and many other command line utilities. You can install many of them with bioconda.
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Is it really necessary ? like loops , list etc ... Is using those feature really necessary in a project ?
Yes,Mixins,Variables,Extend,Nesting,PartialImport are necessary . But are other functions , loops ,list really used on daily basis on projects?
__I AM A BEGINEER (Noobie)
As projects has different requirements differs the used tools which are used to build a project. So, the answer to your question is no. The different features are not allways needed alltogether in all project. But all the named features are basic and common used features to that language.
And as you don't know what features are needed for the next project: if you want to code in SASS (or become a good coder) you should know all the features and have basic knowledge about how they work and how to use them. But as you are a beginner: that comes with time when you have to use the different features with every project you realise.
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I'm about to setup a new project in Go. I came across the term vendoring. Is this standard or an obsolete concept. I'm coming from a nodejs world and this feels like copying the nod_modules folder to a separate directory or am I confusing the whole purpose of this?
It's not technically obsolete, but most cases should use go modules instead.
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To learn go I am trying to build an open source library, I like the language but since I am still a bit new I can't find good direction on how to automate building, testing and releasing.
I had the idea to use Makefiles etc.. am I in the right direction or there is better tools to do that.
Best,
Khaled
Here some useful links
Here you have a link for best practice for coding
https://peter.bourgon.org/go-best-practices-2016/
https://golang.org/doc/code.html
Working with packages, useful links.
http://thenewstack.io/understanding-golang-packages/
https://www.goinggo.net/2013/07/how-packages-work-in-go-language.html
I recommend to review the open source libraries to get an idea.(there are tons of them)
https://github.com/urfave/cli
https://github.com/boltdb/raw
https://github.com/matryer/try
To automate your project. I recommend to see projects like Drone
https://github.com/drone/drone
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Make is a very handy and capable feature for developing and more specifically compiling software. What process does it actually use to determine which files get recompiled when necessary (touched files) vs skipping over files which have not been touched?
It checks the modification dates of prerequisites and compares them to the modification dates of targets. If any prerequisites is newer, that target is rebuilt.
There are some special cases (phony targets, for example), but that's pretty much all there is to it.
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Say, we have ABC.exe and CDE.exe
I want to bundle these 2 installation files into a single un-attended installation file [XYZ.exe].
And when I run the XYZ.exe it should install the above applications.
Any ideas how this can be achieved ?
You need a Bootstrapper.
Try dotNetInstaller if you need some logic in the bootstrapper, I haven't used it myself but it's often recommended on the WiX mailing list as a good free bootstrapper.
I think what you want is a self-extracting archive.