Metadata-Version: 2.1
Name: seqalign
Version: 0.1.2
Summary: Manage sequence alignments
Home-page: https://github.com/anthony-aylward/seqalign.git
Author: Anthony Aylward
Author-email: anthony.aylward@protonmail.com
License: UNKNOWN
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Description-Content-Type: text/markdown
Requires-Dist: biopython
Requires-Dist: pyhg19
Requires-Dist: tempfifo
Requires-Dist: cutadapt

# seqalign

Manage sequence alignments

## Installation

```sh
pip3 install seqalign
```
or
```sh
pip3 install --user seqalign
```

## Examples

```python
with SequenceAlignment(<path to input BAM or FASTQ file>) as sa:
    sa.cleans_up_bam = False
    sa.remove_supplementary_alignments()
    sa.samtools_sort(memory_limit=10)
    sa.samtools_index()
    sa.write(<path to output BAM file>)
```

## Notes

The `input_file` argument to `SequenceAlignment()` should be a string for
single-end reads or for data that is already aligned. For raw paired-end reads,
it should be a tuple containing two strings giving the paths to the two
FASTA / FASTQ files.


