add scripts to utils to merge FASTQ and BAM files
add bamtools in case other tool fail and get script in utils
add docs

Update configuration.rst

fix typos

Update configuration.rst

fix command format

Update configuration.rst

getting correct command format
move code to pipeline/fastq.py and handle mix up of fastq/fastq.gz samples
change var names, and remove old code
add paired fastq files  support
add documentation
add sra processing. download and convert to fastq
fix move command
merge branches