Patch picard summary

changing some summaries for picard metrics

See merge request !163

Feature vcffilter trio filters

Added some more filter options

See merge request !162

zcat fix for mapping pipeline

This fix makes sure that the pipeline first performs a zcat on gzipped fastq files.

See merge request !161

Fix mpileup to vcf

Fix MpileupToVcf to handle multi-nuclitides char better.

Also some refactoring in mapping and flexiprep. R2 should now be a Option[File], also for #133

See merge request !160

Feature improved bammetrics

see #127

See merge request !158

Fix flag handling and add some logging

See merge request !159

Patch rscript

See merge request !156