I've been lurking on devrant a while now, I figure it's time to add my first rant.

Little background and setting a frame of reference for the rant: I'm currently a software engineer in the bioinformatics field. I have a computer science background whereas a vast majority of those around me, especially other devs, are people with little to no formal computer background - mostly biology in some form or another. Now, this said, a lot of the other devs are excellent developers, but some are as bad as you could imagine.

I started at a new company in April. About a month after joining a dev who worked there left, and I inherited the pipeline he maintained. Primarily 3 perl scripts (yes, perl, welcome to bioinformatics, especially when it comes to legacy code like is seen in this pipeline) that mostly copied and generated some files and reports in different places. No biggie, until I really dove in.

This dev, which I barely feel he deserves to be called, is a biology major turned computer developer. He was hired at this company and learned to program on the job. That being said, I give him a bit of a pass as I'm sure he did not have had an adequate support structure to teach him any better, but still, some of this is BS.

One final note: not all of the code, especially a lot of the stupid logic, in this pipeline was developed by this other dev. A lot of it he adopted himself. However, he did nothing about it either, so I put fault on him.

Now, let's start.
1. perl - yay bioinformatics
2. Redundant code. Like, you literally copied 200+ lines of code into a function to change 3 lines in that code for a different condition, and added if(condition) {function();} else {existing code;}?? Seriously??
3. Whitesmiths indentation style.. why? Just, why? Fuck off with that. Where did you learn that and why do you insist on using it??
4. Mixing of whitesmiths and more common K&R indentation.
5. Fucked indentation. Code either not indented and even some code indented THE WRONG WAY
6. 10+ indentation levels. This, not "terrible" normally, but imagine this with the last 3 points. Cannot follow the code at freaking all.
7. Stupid logic. Like, for example, check if a string has a comma in it. If it does, split the string on the comma and push everything to an array. If not, just push the string to the array.... You, you know you can just split the string on the comma and push it, right?? If there is no comma it will be an array containing the original string.. Why the fuck did you think you needed to add a condition for that??
8. Functions that are called to set values in global variables, arrays, and hashes.. function has like 5 lines in it and is called in 2 locations. Just keep that code in place!
9. 50+ global variables/hashes/arrays in one of the scripts with no clear way to tell how/when values are set nor what they are used for.
10. Non-descriptive names for everything
11. Next to no comments in the code. What comments there are are barely useful.
12. No documentation

There's more, but this is all I can think to identify right now. All together these issues have made this pipeline the pinnacle of all the garbage that I've had to work on.

Attaching some screenshots of just a tiny fraction of the code to show some of the crap I'm talking about.