Version 0.5.0 released

Changes:

• We are now also using read mapping qualities. This is achieved by joining base-call (P_bq) and mapping qualities (P_mq): P_joined = P_mq + (1-P_mq)*P_bq
• Now using GNU autotools for compilation and installation (./configure && make install)
• Now including a modified version of samtools mpileup
• Now including helper scripts to create a stringent, recalibrated mapping (bwa_unique.sh and base_qual_calib_wrapper.sh)
• Fixed mixup between --bonf options auto-ign-zero-cov and auto. The former is now default
• Added script lofreq_alnoffset.py which makes comparison of SNV calls made on different coordinate systems / against different reference sequences easier