23andMe doesn't do genome sequencing per se... they use a SNP array. It's basically a collection of DNA probes that each hybridize with a specific genetic variant. According to a forum I read, they don't have a probe for this specific CRY1 variant. So if your friend doesn't have the variant listed in their 23andMe tab-delimited list of variants, that doesn't mean they don't carry it.
You said you're interested in writing a program to look for this in the raw tab-delimited data. It would be totally doable! Just grep the tsv for the rs ID of interest. In this case it will be rs184039278. If doing more exploratory stuff, you'll probably want to connect variants with annotations. SNPedia has a database of descriptions of what the variants do. Biostars is a decent, dedicated resource for help with stuff like this.
I‘m a scientist diagnosed with delayed sleep phase disorder (DSPD). I studied the related protein CRY2 for part of my PhD (ironically not why I joined the lab), and now I’m doing human genomics research. It’s encouraging that this recently described heritable mutation causing familial DSPD is getting more attention. Most normal chronotypes (non-night owls) don’t even know DSPD is a thing. The Facebook groups for DSPD are full of truly emotional stories about how hard life with DSPD is. They are also full of people connecting over relief and validation that we’re neither freaks nor consciously at fault for our late schedules.
Unfortunately, accessible genetic testing is probably a long way away. It looks like 23andMe won’t tell you if you have this mutation; the variant rs184039278 that causes CRY1 Δ11 disappointingly isn’t part of their panel. Whole exome sequencing might work, or might not, depending on the capture kit. But if you suspect you have DSPD, my advice is to see a sleep doctor as soon as possible to get a diagnosis. You’ll get prescribed a morning light box like I did. Your brain will get tricked into thinking it’s later than it actually is. It’s not a cure, but life and the 9-5 should get a little bit easier.
I also wrote a post on the TidalCycles blog. It covers my microtonal tuning and composing process. https://tidalcycles.org/blog/blog_topic_relyt_r_xuixo