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mirror of https://github.com/pcvolkmer/fastq-tools.git synced 2025-09-13 05:02:53 +00:00

feat: generate GRZ metadata for file

This commit is contained in:
2025-08-14 23:25:53 +02:00
parent 9cc7762af2
commit d719fed150
7 changed files with 413 additions and 23 deletions

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@@ -10,12 +10,13 @@ This application provides the following subcommands
Usage: fastq-tools [OPTIONS] <COMMAND>
Commands:
info Show information about input
scramble Scramble input data
help Print this message or the help of the given subcommand(s)
info Show information about input
grz-metadata Show GRZ metadata
scramble Scramble input data
help Print this message or the help of the given subcommand(s)
Options:
-i, --input <INPUT_FILE> Input file (optional)
-i, --input <INPUT_FILE> Input file
-d, --decompress Decompress input as gzip compressed data
-h, --help Print help
-V, --version Print version
@@ -44,6 +45,24 @@ This will result in output like
![Info subcommand](docs/info_subcommand.jpg)
### GRZ Metadata
To generate GRZ metadata for a file use:
```shell
fastq-tools --decompress --input file_fastq.gz grz-metadata
```
The use of the `--input` argument is required for this sub command.
If the file is an uncompressed FASTQ file, you can omit the `--decompress` option.
![GRZ Metadata subcommand](docs/grz-metadata_subcommand.jpg)
Supported file types are:
* fastq (full support)
* bam, bed, vcf (limited support)
### Scramble
To scramble compressed FASTQ files use: