Noisy Pneumatic Mnemonic

    samflags

    1.0.0 • Public • Published

    samflags

    Samflags is a command line utility to decode SAM flags (e.g. 1804) into plain English text.

    Basically, it turns 1804 into this:

    • Read unmapped
    • Mate unmapped
    • Not primary alignment
    • Read fails platform/vendor quality checks
    • Read is PCR or optical duplicate

    It also exposes a library that can decode SAM flags for you if you want to use it in your own application.

    It was inspired by websites like the following that do the same thing:

    I use them quite frequently, and wanted to have a command line utility to use instead.

    Installation

    This is a standard NodeJS package. It requires you to have NodeJS and npm installed.

    If you have npm installed, you can install samflags as a command-line utility by using the following command.

    $ npm install -g samflags

    If you want to use it in your own project as a library, do this instead...

    $ npm install samflags
    const samflags = require('samflags');

    Command-line Usage

    After installation, you can use samflags like this.

    $ samflags parse --help
     
      Usage: parse|p [options] <flags...>
     
      parse the given SAM flags into human readable strings
     
     
      Options:
     
        -h, --help  output usage information
     
     
      Example:
     
        $ samflags parse 1548
          Checking 1548...
           - Read unmapped (4)
           - Mate unmapped (8)
           - Read fails platform/vendor quality checks (512)
           - Read is PCR or optical duplicate (1024)

    Library Usage

    A simple example library usage.

    const samflags = require('samflags');
    const samflagsParse = samflags.parse;
     
    let flags = samflagsParse.getFlagNumbers(516); // flags == [0x4, 0x200]
     
    let flagStrings = samflagsParse.getFlagStrings(516); // flagStrings == ['Read unmapped', 'Read fails platform/vendor quality checks']

    Install

    npm i samflags

    DownloadsWeekly Downloads

    2

    Version

    1.0.0

    License

    MIT

    Last publish

    Collaborators

    • cbp44