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https://github.com/dhslab/methfast

Simple c program for manipulating bed-like methylation files

https://github.com/dhslab/methfast

Science Score: 26.0%

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Repository

Simple c program for manipulating bed-like methylation files

Basic Info
  • Host: GitHub
  • Owner: dhslab
  • License: mit
  • Language: C
  • Default Branch: main
  • Size: 298 KB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 2
Created over 1 year ago · Last pushed 9 months ago
Metadata Files
Readme License

README.md

Introduction

methfast is a program for extracting methylation values from a bed-like file for a target bed file. It can accept gzipped or plain text files and by default assumes the format for the bed file with methylation is like this:

chrom start end methylation coverage

Other formats can be used by specifying the column numbers for the methylation and coverage values.

methfast is written in C using Heng Li's cgranges library to perform overlap queries between methylation and bed intervals.

Dependencies and Installation

methfast can be compiled via:

gcc methfast.c cgranges.c -o methfast -lz -lm

Usage

methfast [-f ] [-c ] [-m ] [-u ]

Options: -f column number for methylation fraction (default is 4) -c column number for total coverage (default is 5) -m column number for methylated coverage (no default) -u column number for unmethylated coverage (no default)

Test data

A small test dataset is included, which can be tested via:

methfast meth.bed.gz regions.bed

https://github.com/samtools/htslib

https://github.com/lh3/cgranges/

Owner

  • Name: Code and Software from David Spencer's lab
  • Login: dhslab
  • Kind: organization
  • Email: dspencerlab@gmail.com
  • Location: United States of America

GitHub Events

Total
  • Release event: 1
  • Push event: 9
  • Pull request event: 9
  • Create event: 2
Last Year
  • Release event: 1
  • Push event: 9
  • Pull request event: 9
  • Create event: 2

Dependencies

Dockerfile docker
  • ubuntu focal-20221130 build