Develop#164
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In `read_simulator.utils`, `apply_mutations` passed the genomic coordinates instead of the relative location of the mutation in the simulated read to `update_quality_array`, causing wrong or no quality scores to be updated. This commit corrects it by passing the relative location.
When QUAL is missing in user VCF files, replace it with 42. (Address #161)
Handling missing QUAL in user VCF files
Fix genomic coordinate incorrectly used as array index in quality array update
fixed default output folder name
…f using subscripts
Feature/integrate parallel into sim
Feature/fix options
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