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Commit 55b750c4 authored by Blaise Li's avatar Blaise Li
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Updated README, that was a copy of another one.

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# 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)
```
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