[FIX] Adjusting samcat, bs_tools, and mason2 to fixed SAM/BAM.

Hash of hotfix was 2fae0b1d3270fc9bcb1cfa3b0c55b5c61d5e6ddb.
Merge pull request #573 from holtgrewe/hotfix/apps-to-new-sam-bam

[FIX] Adjusting samcat, bs_tools, and mason2 to fixed SAM/BAM.