---
name: "update-sort-bed-migrate-candidates"
section: "1"
platform: "linux"
package: "bedops"
version: "2.4.41+dfsg-1"
release: "Debian 12 (Bookworm)"
platforms: ["linux"]
url: "https://new.carta.tech/update-sort-bed-migrate-candidates"
---

# update-sort-bed-migrate-candidates(1)

manual page for update-sort-bed-migrate-candidates 2.4.41+dfsg

## NAME

update-sort-bed-migrate-candidates - manual page for update-sort-bed-migrate-candidates 2.4.41+dfsg

## DESCRIPTION

update-sort-bed-migrate-candidates

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  citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract version:  2.4.41 authors:  Alex Reynolds and Shane Neph

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  `$ 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\> \[ **--non-recursive-search** \]

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  The "update-sort-bed-migrate-candidates" utility recursively locates BED and Starch files in the specified parent directory and tests if they require re-sorting to conform to the updated, post-v2.4.20 "sort-bed" order.

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  Files with the extensions starch, bstarch, gstarch, bed, or bed\[g\|G\]raph in the parent directory are tested. Files without these extensions are ignored.

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  If the "--non-recursive-search" option is added, this utility will only search within the specified parent directory, and go no deeper.

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

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  1\. Using "--write-list", files that require re-sorting can have their paths

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  written to standard output, which can be written to a file to be processed later on, as desired.

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  2\. Using "--resort-immediately", qualifying files can be resorted immediately

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  after all candidates are found, through a local, serial application of 'sort-bed'.

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  3\. Using "--resort-in-parallel-via-slurm", candidate files can be migrated by

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  applying the 'update-sort-bed-slurm' script to resort in parallel on a computational cluster managed with a SLURM job scheduler.

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  Note that one of these three options must be chosen, to perform the stated action, and only one option can be selected.

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  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.

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  Use the "--bedops-root-dir" option to specify the directory containing the BEDOPS toolkit binaries to be used for migration. You can provide more specific paths to individual binaries, using the following options:

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  Add the "--bedextract-path", "--sort-bed-path", "--unstarch-path", "--starch-path", "--starchcat-path", "--update-sort-bed-slurm", and/or "--update-sort-bed-starch-slurm" options 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:

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  1\. Add the "--dry-run" option to "--resort-immediately" or the

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  "--resort-in-parallel-via-slurm" options to see the behavior before any filesystem actions are performed. Remove "--dry-run" to perform the specified work.

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  2\. If you use the resort-via-SLURM option, consider using "--slurm-memory",

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  "--slurm-partition", "--slurm-workdir", "--slurm-output", and "--slurm-error" options to match the setup of your particular cluster environment and inputs.

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  3\. Add "--debug" option to log debug statements to get more detail about

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  internal operation of update process.

## 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

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  **info update-sort-bed-migrate-candidates**

should give you access to the complete manual.