Include chrY in the makefile template; was too used to not having this chrom in equcab20 ....
Reworking genotyping to allow parallelization.
Minor tweaks to makefile template.
Better handling of unmapped, secondary, suppl. reads in validation step.
Support setting readgroup in 'paleomix cleanup'.
Tweak makefile template.
Add support for BWA mem/bwasw.
Fix missing file dependencies.
Include filters in VCF header; use ':' instead of '=' to sep. values.
Fix wrong comment in summary file.
Update adapters in example makefiles.
Always use 'paleomix' as the process name.
Handle 32bit JREs; dont try to set -Xmx.
Avoid keeping too many sequences in memory at once.
Update tests with new arg. order.