replaced sorting of bowtie2 output
fix
version
keep all files sorted during progressive mapping
fix
check out of memory status
fixed pv calls
changed order of clone_id and read_group_id in internal naming system;
this will cause crashes if using old files
added conversion scripts from old naming to new naming
version
tails removed earlier
major change of internal read naming scheme, now sq&qv are kept in
SAM fields, using soft clipping