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SooLee authored Dec 1, 2017
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# pairix

[![Codacy Badge](https://api.codacy.com/project/badge/Grade/6e73d29f423f49ff9293f60b25b4778a)](https://www.codacy.com/app/SooLee/pairix?utm_source=github.com&utm_medium=referral&utm_content=4dn-dcic/pairix&utm_campaign=badger)

* Pairix is a tool for indexing and querying on a block-compressed text file containing pairs of genomic coordinates.
* Pairix is a stand-alone C program that was written on top of tabix (https://github.com/samtools/tabix) as a tool for the 4DN-standard pairs file format describing Hi-C data: [pairs_format_specification.md](pairs_format_specification.md)
* However, Pairix can be used as a generic tool for indexing and querying any bgzipped text file containing genomic coordinates, for either 2D- or 1D- indexing and querying.
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# In order to use utils, add util path to PATH
# In order to use bam2pairs, add util/bam2pairs to PATH
# eg: PATH=~/git/pairix/bin/:~/git/pairix/util:~/git/pairix/util/bam2pairs:$PATH
```
Alternatively, `conda install pairix` can be used to install both Pairix and Pypairix together. This requires Anaconda or Miniconda.
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### Usage for pairix
#### Compression
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