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)