Use CGG website.
Rework safeSAM2BAM into new bam_cleanup tool.

This merges all steps assosiated with processing "raw" SAM records produced
by e.g. BWA to a sorted BAM, including tagging, sorting, cleaning of
inproperly tagged (unmapped) reads, and quality / flag-based filtering into
a single command, simplifying setup of BWA / Bowtie2 nodes.
Test-cases for bugs in BWA.

Adding a small set of test-cases for BWA, which document a few previous and
extant bugs in BWA (mainly 0.7.x). These are included in part to enable me
to track when these bugs are fixed in BWA.