bamkit

🦀 bamkit: a simple program for bam file manipulation

install

```bash cargo install bamkit

or

git clone https://github.com/sharkLoc/bamkit.git cd bamkit cargo b --release

mv target/release/bamkit to anywhere you want

```

usage:

``` bamkit: a simple program for bam file manipulation

Usage: bamkit

Commands: view sam bam conversion region get target region from bam file flags bam file flag value show insert insert size plot for bam file help Print this message or the help of the given subcommand(s)

Options: -h, --help Print help information -V, --version Print version information

```

view :

``` bamkit view -h sam bam conversion

Usage: bamkit view [OPTIONS] [INPUT]

Arguments: [INPUT] input bam[sam] file

Options: -H, --Header show sam file header only -b, --bam output is bam -o, --out output file name or write to stdout -h, --help Print help information ```

region :

``` bamkit region -h get target region from bam file

Usage: bamkit region [OPTIONS] --bam

Arguments: bam[sam] file target postion, eg, chr1:100-300

Options: -b, --bam input sorted and indexed bam file -s, --sam output is sam -o, --out output file name or write to stdout, default bam format -h, --help Print help information ```

insert :

``` bamkit insert -h insert size plot for bam file

Usage: bamkit insert [OPTIONS] --name [BAM]

Arguments: [BAM] input bam[sam] file

Options: -m, --max max insert szie length [default: 1000] -n, --name the html format plot file name -h, --help Print help information ```

eg: bamkit insert test.bam -n insertPlot

flags :

``` bamkit flags -h bam file flag value show

Usage: bamkit flags

Arguments: specify bam[sam] flag value

Options: -h, --help Print help information ```

eg: bamkit flags 163

* any bugs please report issues *💖