Speed up consensus iteration

[andreas-wilm]

Use plain consensus rules for variant calling in consensus update. This will be much faster and we can live with a few FP / FN, since a final LoFreq call is done eventually anyway

[andreas-wilm]

The following as taken from http://samtools.github.io/bcftools/howtos/consensus-sequence.html, with --ploidy 1 added to call should work:

bcftools mpileup -Ou -f reference.fa alignments.bam | bcftools call -mv -Oz -o calls.vcf.gz
tabix calls.vcf.gz
cat reference.fa | bcftools consensus calls.vcf.gz > consensus.fa