No way to override '-T 0' in bwa mem

[keiranmraine]

Hi,

Just a note but the current implementation prevents anyone from discarding alignments with very low AS scores as -T 0 is a fixed append.

Seqware-BWA-Workflow/src/main/java/com/github/seqware/WorkflowClient.java

Line 318 in 64d5e6c

.addArgument(this.parameters("mem") == null ? " " : this.parameters("mem")).addArgument("-p -T 0")