Try using C++ bam-errorrate for bwamem alignments

BamQC now tries to use an in-development C++ rewrite of bam-errorrate
for bwamem alignments. Previously it would skip bam-errorrate when the
aligner was bwamem.
update microarray cnv calling
change cnv dir structure
add files to manifest
update microarray cnv results
add checks to glob results
update microarray cnvs

Use the CNV calls from the HMM algorithm, they seem to work better in
terms of determining local sequence context than naively calling CN from
LRR and then segmenting.
small tweak to makecircos test
format awk command
fix cnv diff
update clinseq cnv dir
add plot cnv convergence tool
update clin-seq blessed build
modify check for mrkdup file
update number of tests
add minimum test