diff --git a/README.md b/README.md index b92ab5834db028504de44cfff59ae9b6c1acaf4c..1af164bd799596db32ec313a620b9f6d45eead93 100644 --- a/README.md +++ b/README.md @@ -1,13 +1,32 @@ -# Utilities to generate stats and graphs from reads. - -This is a very preliminary version, with very few utilities. +# Utilities to collapse reads in bam files to their 5' end. ## Installing -Get the source using `git clone git@gitlab.pasteur.fr:bli/libreads.git`, `cd` into it and run `python3 -m pip install .` +Get the source using `git clone git@gitlab.pasteur.fr:bli/bam25prime.git`, `cd` into it and run `python3 -m pip install .` It might also work directly: - python3 -m pip install git+ssh://git@gitlab.pasteur.fr/bli/libreads.git + python3 -m pip install git+ssh://git@gitlab.pasteur.fr/bli/bam25prime.git + +## Usage + +This package provides a `bam25prime`. +Its help can be obtained using option `-h` or `--help`. + +``` +$ bam25prime --help +usage: bam25prime [-h] -b BAMFILE -o OUT_BED + +When executed, this module collapses reads in a bam file to their 5-prime end +(reducing them to length 1) and writes the result in bed format. +optional arguments: + -h, --help show this help message and exit + -b BAMFILE, --bamfile BAMFILE + Sorted and indexed bam file containing the aligned + reads. (default: None) + -o OUT_BED, --out_bed OUT_BED + Bed file in which the results should be written. + (default: None) +```