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[docs] add docs for
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yangli committed Sep 24, 2022
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10 changes: 6 additions & 4 deletions document/boss-fqsp.md
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- [3. Performance](#performance)
- [4. Current Issues](#current-issues)


## Aim

`boss-fqsp` is used to split one fastq file into two fastq files. The format of the input fastq file is as follows:
Expand All @@ -27,7 +26,10 @@ Every four lines are belong to one end of paired reads.

## Usage

`boss-fqsp -h` will show the help message.

```console
$ boss-fqsp -h
fqsp - A program to split ncbi fq files into forward and reverse files.
Usage:
boss-fqsp [OPTION...] [input.fq|.fq.gz]
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The performance is tested simply by `time` command. It is not a benchmark.
The slowest part is the gzip decompression and compression.

| File Size | Line Number | Format | Time |
| File Size | Line Number | Format | Time |
|:----------|-------------|--------|-------|
| 2.2G | 420'010'288 | fq.gz | 18m |
| 28G | 420'010'288 | fq | 4m14s |
| 2.2G | 420'010'288 | fq.gz | 18m |
| 28G | 420'010'288 | fq | 4m14s |

## Current Issues
26 changes: 25 additions & 1 deletion document/boss-squeue.md
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## Aim

`boss-squeue` is used to get the status of jobs in the HPC. It is a wrapper of `squeue` command. Hence, it is necessary
to install `slurm` first.

## Usage

`boss-squeue -h` will show the help message.

## Usage
```console
$ boss-squeue -h
squeue - A program to get the status of jobs in the queue.
Usage:
boss-squeue [OPTION...]

-h, --help Show help
-v, --version Print the current version number
-m, --me Check Your own jobs' status
-d, --debug Enable debug mode
```

* Example 1

![img.png](imgs/boss-squeue-ex1.png)

* Example 2

![img.png](imgs/boss-squeue-ex2.png)

## Performance

The performance is tested simply by `time` command. It is not a benchmark.

| Command | Time |
|:--------------------|-----:|
| `boss-squeue` | 0.7s |
| `boss-squeue --me` | 0.5s |

## Current Issues
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