UPDATE-SORT-B...TE-CANDIDATES(1)

✨ NAME ✨

okay so bestie, this is the manual page for update-sort-bed-migrate-candidates, which lives in the User Commands part of the manual (section 1, so you already know it's a runnable thing 💅). It's version 2.4.42+dfsg and it is, and I cannot stress this enough, the little utility you want when your BED files are stuck in the old sort order. 🦋

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🌸 DESCRIPTION 🌸

update-sort-bed-migrate-candidates

citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract version: 2.4.42 authors: Alex Reynolds and Shane Neph

Here's the whole shape of it, fr fr:

$ update-sort-bed-migrate-candidates [ --dry-run ] [ --debug ]

[ --write-list |
--resort-immediately | --resort-in-parallel-via-slurm

[ --slurm-memory <MB> ]
[ --slurm-partition <SLURM partition> ] [ --slurm-workdir
<working directory> ] [ --slurm-output <SLURM output directory> ]
[ --slurm-error <SLURM error directory> ]

]      [ --bedops-root-dir <bedops directory> ] [ --bedextract-path
<path> ] [ --sort-bed-path <path> ] [ --unstarch-path <path> ] [
--starch-path <path> ] [ --starchcat-path <path> ] [
--update-sort-bed-slurm-path <path> ] [
--update-sort-bed-starch-slurm-path <path> ] --parent-dir <parent
directory> [ --non-recursive-search ]

So what does it actually do, you ask? The update-sort-bed-migrate-candidates utility goes recursively snooping through the parent directory you hand it, hunts down all the BED and Starch files, and vibe-checks whether each one needs re-sorting to conform to the updated, post-v2.4.20 sort-bed order. 🔥

Which files get tested? Files in the parent directory with the extensions starch, bstarch, gstarch, bed, or bed[g|G]raph. Files without those extensions? Ignored, not even a glance, no cap. 🙈

If you add the --non-recursive-search option, this utility will only search within the specified parent directory and go no deeper. Shallow queen behavior, respectfully. 👑

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🎀 the three (exclusive) migration actions 🎀

This utility offers one of three (exclusive) actions for migration:

1. Using --write-list, files that require re-sorting can have their paths written to standard output, which can be written to a file to be processed later on, as desired. 📝
2. Using --resort-immediately, qualifying files can be resorted immediately after all candidates are found, through a local, serial application of sort-bed.
3. Using --resort-in-parallel-via-slurm, candidate files can be migrated by applying the update-sort-bed-slurm script to resort in parallel on a computational cluster managed with a SLURM job scheduler. 🚀

Note that one of these three options must be chosen, to perform the stated action, and only one option can be selected. Exclusive. Pick your fighter, not all three. 😭

When using --resort-immediately or --resort-in-parallel-via-slurm, the resorted files will have the name of the original BED or Starch file. The original files will have their old name, with the .backup extension. So nothing gets lost, your old data is just chilling in the .backup lane. 💖

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🧚 pointing it at your toolkit 🧚

Use the --bedops-root-dir option to specify the directory containing the BEDOPS toolkit binaries to be used for migration.

You can also provide more specific paths to individual binaries, using the following options:

• --bedextract-path
• --sort-bed-path
• --unstarch-path
• --starch-path
• --starchcat-path
• --update-sort-bed-slurm
• --update-sort-bed-starch-slurm

Add any and/or all of these to specify custom paths to versions of these tools, if desired. These values will be passed along to downstream helper scripts that use them. 🫶

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💜 Suggestions 💜

1. Add the --dry-run option to --resort-immediately or the --resort-in-parallel-via-slurm options to see the behavior before any filesystem actions are performed. Remove --dry-run to perform the specified work. Look before you leap, bestie. 👀
2. If you use the resort-via-SLURM option, consider using --slurm-memory, --slurm-partition, --slurm-workdir, --slurm-output, and --slurm-error options to match the setup of your particular cluster environment and inputs. Customize it to your cluster's whole deal. ✨
3. Add --debug option to log debug statements to get more detail about internal operation of update process. For when you need the tea. 🍓

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🌈 SEE ALSO 🌈

The full documentation for update-sort-bed-migrate-candidates is maintained as a Texinfo manual. If the info and update-sort-bed-migrate-candidates programs are properly installed at your site, the command

info update-sort-bed-migrate-candidates

should give you access to the complete manual. Go read the full lore, iykyk. 📖

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and that's the whole page, bestie 💖 this beauty comes from the source/version line update-sort-bed-migrate-candid... and it was dated August 2025, filed under UPDATE-SORT-B...TE-CANDIDATES(1). Slay, periodt. 👑🌸