!wget -c ftp://hgdownload.cse.ucsc.edu/goldenPath/galGal4/bigZips/galGal4.fa.masked.gz

!bwa index galGal4.fa.masked.gz

!samtools faidx galGal4.fa.masked.gz

!bwa mem galGal4.fa.masked.gz reads.fastq > reads.fastq.sam

!samtools import galGal4.fa.masked.gz.fai reads.fastq.sam reads.fastq.bam
!samtools sort reads.fastq.bam reads.fastq.sorted
!samtools index reads.fastq.sorted.bam

!samtools view -c -f 4 reads.fastq.sorted.bam

!samtools view -c reads.fastq.sorted.bam

!pip install bioinfo

!bioinfo -h

!bioinfo bam_coverage galGal4.fa.masked reads.fastq.sorted.bam 200 reads.fastq --mapq=30

from bioinfo import bam_coverage

## same call, using the module.
bam_coverage("galGal4.fa.masked", "reads.fastq.sorted.bam", 200, "reads.fastq", 30)

!wget -c https://github.com/luizirber/bioinfo/blob/master/bioinfo/bam_coverage.py

!python bam_coverage.py galGal4.fa.masked reads.fastq.sorted.bam 200 reads.fastq 45