Bug fixes :
- fix crash in Smith Waterman code for reads shorter than 30 bp
- fix multiple crashes in rescue scanning code for short reads
- fix ineligible alignments / fix alignment with impossible coordinates past the end of chromosome
- fix issue in unclipped bonus score adjustment in SW
- fix crash when input bam is not name sorted ( now detects if bam is not name-sorted and outputs correct error message)
New feature :
- now allows "process substitution" input of uncompressed fastq format
Code Optimization :
Up to 30 % runtime reduction
Misc
- now using C++17 standard (requires gcc >= 7.1 to compile)