added bases_in and bases_out status to read/write fasta/fastq
fixed test for bases_in status in read_fasta
fixed test for bases_in status in read_fastq
fixed test for bases_out status in write_fasta
fixed test for bases_out status in write_fastq
added fasta/fastq_in/out status and tests
refactored bases_in/out to residues_in/out
Merge branch 'status-improvement' into develop
refactored fasta/fastq_in/out to sequecnes_in/out in stats
assemble_pairs working pending testing
added stats to assemble_pairs
added documantation to assemble_pairs command
finished tests for assemble_pairs command
Merge branch 'assemble-pairs' into develop
done porting trim_seq and do tests
Merge branch 'trim-seq' into develop
added options_required_single method
added remove_adaptor command
removed old documentation from remove_adaptor
renamed remove_adaptor to clip_primer