BAM outputs are now sorted and indexed by default.
Variant BAM slice reads are now checked for direction. If reads are aligned reverse, their sequence is reverse complimented before being written to FASTQ
Most main module names have been renamed with snake_case (Pylint C0103)
Merged all module_v2 with module_v1 (e.g. vase2.py and vase.py)
VcfBamScanner changed to sample_mapper, but still includes old VcfBamScanner class.
Last remaining VBS function added to SampleMapper
Refactoring for guard clauses
Refactored vaselogger initialization
Refactored config file check
Linting and style fixes
Bugfixes:
Fixes issue #85 by checking for reverse reads, then reverse complementing them. Qualities are also reversed.
Fixes issue #88, which was caused by incorrect reference to unsorted BAM output file.
Fixes issue #89, which was caused by setting object equal to function with no return.
Changes:
Bugfixes: