There is no truncating performed in the SAM file construction. This quickly leads to the inability to convert bbMAP's native SAM output to BAM. The query name the full read name supplied by Polyester during RNASeq dataset construction, which is far beyond the SAM specification of 256 characters maximum. Trying to convert with samtools (or with bbMAP's own BAM output flag) will result in errors.
Is there a way to convert the SAM to BAM with bbMap?