+ [util/bwa] switched to forked bwa repo at bioinf
- [util/bwa] upgrade to a fix for skipping unmapped alignments
- [proovread] removed samfilter call from bwa/gmapper-ls
+ [Sam::Seq,proovread,bam2cns] added fallback-phred for qual-less alignments, removed now obsolete samfilter for blasr
- [proovread] multithreaded samtools view calls