formatting and clippy changes

update usage

Merge pull request #40 from wdecoster/json-output

Json + tsv output

bugfix! on how mean length and identity are calculated

and one optimization and some updates

Merge pull request #35 from wdecoster:number_of_reads

add number of reads in addition to number of alignments

filter out secondary reads before counting all_counts

should address #33

filter out secondary reads before counting all_counts

should address #33

filter out secondary reads before counting all_counts

should address #33

filter out secondary reads before counting all_counts

should address #33

updates