https://github.com/multimeric/bamcmp

Checks that two alignment files have exactly the same contents
https://github.com/multimeric/bamcmp

alignment-files bioinformatics

Last synced: 12 months ago
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Checks that two alignment files have exactly the same contents

• Host: GitHub
• URL: https://github.com/multimeric/bamcmp
• Owner: multimeric
• License: gpl-3.0
• Created: 2018-12-01T07:12:56.000Z (over 7 years ago)
• Default Branch: master
• Last Pushed: 2018-12-03T04:17:08.000Z (over 7 years ago)
• Last Synced: 2025-03-21T05:23:29.858Z (about 1 year ago)
• Topics: alignment-files, bioinformatics
• Language: Python
• Homepage:
• Size: 19.5 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# BamCmp

`bamcmp` is a command-line tool for comparing two alignment files that contain the same alignment data. For example, 

 two alignments that are in BAM and SAM format, or BAM and CRAM format.

## Installation

To install the command, first ensure you have Python 3.7 or above installed. Then, run:

```bash

python3 -m pip install git+https://github.com/TMiguelT/BamCmp

```

## Usage

Once you install this package, you will have the `bamcmp` command available. 

The full command line interface, including additional flags, is listed here:

```

usage: bamcmp [-h] [--reference REFERENCE] [--ignore-tags] [--sort-tags]

              bam_a bam_b

positional arguments:

  bam_a

  bam_b

optional arguments:

  -h, --help            show this help message and exit

  --reference REFERENCE

                        Path to reference fasta file, needed for CRAM

                        alignments

  --ignore-tags         Ignore the optional tags section for each segment

  --sort-tags           Sort tag dictionary before comparing, meaning that

                        alignments with differently ordered tags will still be

                        considered identical

```