Ekka is coming
Some changes from npscarf command:
(1) adding bwa index step for contigs file by default since many users forget this step
(2) option --format to specify the format of input is mandatory since, again, many users forget to include this and leading to failure of algorithm.
Please run npscarf --help for further details.
For npBarcode:
(1) give users more control by adding parameters --threshold, --distance
Update: re-compile with Java 1.8.0_144 (previous one class was mistakenly compiled with Java 9)