pip install blat
pip install samtools
pip install bedtools
pip install pysam
pip install pyfastx
pip install os
pip install pandas
pip install collections
pip install heapq
pip install operator

$ python3 appli_debut_launcher.py -fp your_chr_position -o output_folder -b your_bam_file.bam -r refrence_genome.fa -fq1 your_fastq.R1.fastq -fq2 your_fastq.R2.fastq

$ python3 appli_debut_launcher.py - h

usage: appli_debut_launcher.py [-h] [-sp span] [-mq map_qua] [-bsp min_block_size] [-mbs span] [-nbp nb_pos] -fp filter_position -o output -b BAM -r ref -fq1 fastq1 -fq2 fastq2

Detect long INDELs in a BAM file an return a informations about the INDEL and the Variant Allele Frequency (VAF).

optional arguments:
  -h, --help            show this help message and exit
  -sp span, --span span
                        Position span to filter BAM (default: 200)
  -mq map_qua, --map_quality map_qua
                        Minimum mapping quality for the filtering part (default: 10)
  -bsp min_block_size, --blocks_span min_block_size
                        Block span to map the break point (default: 15)
  -mbs span, --min_len_blocks_size span
                        Min blocks size length acceptable (default: 5)
  -nbp nb_pos, --nb_pos_analyse nb_pos
                        Number of position to analyse (default: 1)
  -fp filter_position, --filter_pos filter_position
                        Position to filter the BAM file
  -o output, --output_folder output
                        PPath to the output folder
  -b BAM, --bam BAM     Path to the bam file
  -r ref, --reference ref
                        Path to the reference genome
  -fq1 fastq1, --fastq1 fastq1
                        Path to the fastq sample
  -fq2 fastq2, --fastq2 fastq2
                        Path to the fastq sample

python -m pytest unit_test_lic.py