srf_list(1)

💖 srf_list(1) — the SRF peeker 💖

okay bestie, welcome to srf_list, part of the Staden io_lib family. she's the one you call when you wanna see what's inside an SRF file. nosy? yes. iconic? also yes. 🦋

✨ NAME ✨

srf_list — lists and/or counts the contents of an SRF file 💅

🌸 SYNOPSIS 🌸

srf_list [options] srf_archive ...

🎀 DESCRIPTION 🎀

so basically, srf_list lists the filenames held inside one or more SRF containers. that's her whole thing. she opens the box and reads out the names. 🫶

but like… sometimes you don't wanna read every name out loud, you just wanna know how many there are. in that case you pass the -c option and she'll count instead of list. lowkey a glow-up tbh. ✨

heads up bestie: when you're in count-only mode and there's an index present, it will be used to figure out the number of entries in the index — and hence the sequences in the SRF file. sneaky efficient. 💅

but the index cannot be used when you're listing the filenames, because the index itself doesn't contain the full filenames. the way that the index is out here gatekeeping the actual names… 😭 so fr fr, no index shortcut for listing.

also note: it is not possible to count sequences matching certain patterns or with specific flags set. if that's what you're after, srf_info is the more general purpose tool that may cover it. she's the versatile one. 👑

⭐ OPTIONS ⭐

• -c — counts sequences instead of listing them. and bestie, if an index exists this may be substantially faster than listing. speed. 🏎️✨
• -v — verbose mode. instead of just dumping the total at the end, you get summary count information per file. the details, the receipts, the whole vibe. 📋
• -l — long format. when listing sequence names, this also gives you info on the position in the archive, the size of the sequence specific data block, and the size of the shared data block header. it's giving thorough. 💅

🔥 EXAMPLES 🔥

wanna count the total number of sequences across several SRF files? say less:

srf_list -c *.srf

wanna produce a "fofn" (file of filenames) for an SRF file? chef's kiss:

srf_list foo.srf > foo.fofn

👑 AUTHOR 👑

James Bonfield, Wellcome Trust Sanger Institute — the legend, the main character, the one who wrote this. 🫶

and that's a wrap, bestie! 🎀 this lil guide was brought to you by Staden io_lib, dated September 29, and it lives right there in the srf_list(1) section of your manual. go peek inside an SRF file, you deserve it. 💖 no cap.