🦀 bamkit: a simple program for bam file manipulation
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 bamkit: a simple program for bam file manipulation
Usage: bamkit <COMMAND>
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
sample sample sequences by number or fraktion
help Print this message or the help of the given subcommand(s)
Options:
-h, --help Print help information
-V, --version Print version information
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 <OUT> output file name or write to stdout
-h, --help Print help information
bamkit region -h
get target region from bam file
Usage: bamkit region [OPTIONS] --bam <BAM> <REG>
Arguments:
<REG> bam[sam] file target postion, eg, chr1:100-300
Options:
-b, --bam <BAM> input sorted and indexed bam file
-s, --sam output is sam
-o, --out <OUT> output file name or write to stdout, default bam format
-h, --help Print help information
bamkit insert -h
insert size plot for bam file
Usage: bamkit insert [OPTIONS] --name <NAME> [BAM]
Arguments:
[BAM] input bam[sam] file
Options:
-m, --max <MAX> max insert szie length [default: 1000]
-n, --name <NAME> the html format plot file name
-h, --help Print help information
eg: bamkit insert test.bam -n insertPlot
bamkit flags -h
bam file flag value show
Usage: bamkit flags <FLAG>
Arguments:
<FLAG> specify bam[sam] flag value
Options:
-h, --help Print help information
eg: bamkit flags 163
bamkit sample -h
sample sequences by number or fraktion
Usage: bamkit sample [OPTIONS] [BAM]
Arguments:
[BAM] input bam[sam] file
Options:
-s, --seed <SEED> set rand seed [default: 69]
-n, --num <NUM> sample by number, use with -r on large bam file
-f, --frak <FRAK> sample by fraktion, use with -r on large bam file
-r, --rdc reduce much memory but cost more time
-o, --out <OUT> output bam file name or write to stdout
** any bugs please report issues **💖