initial information commit

# pyTSOfilter

python script to filter TSO artifact reads from aligned bam files

Current version: v.0.1.2

Important note: Only zUMIs-processed bam files are compatible. Assignment of UMI-reads to genes must be performed in stranded mode during zUMIs processing.

## Requirements

- pysam

- regex

## Usage

```

usage: pyTSOfilter.py [-h] --bam FILENAME --out FILENAME --fa FILENAME [--p P]

                      [--n_mismatch N_MISMATCH] [--ggg]

optional arguments:

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

  --bam FILENAME        Path to input BAM file

  --out FILENAME        Path to output bam file

  --fa FILENAME         Path to genome reference fasta

  --p P                 Number of processes to use

  --n_mismatch N_MISMATCH

                        Number of mismatches allowed when matching TSO

  --ggg                 Require template-switching Gs as part of sequence match

```