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Fix processing of MR batches at chromosome breaks

Patrick Hüther requested to merge perlscript_patches into master

This contains 3 patches that are currently out of sync between this and the nextflow version of the pipeline

  1. The fix for processing the MRbatches at chromosome breaks 951598b7

  2. Support for consensus files produced by methlypy 793ee12f

  3. Removed scipy dependency from pv2qv.py script by replacing the scipy functions with their numpy equivalents (scipy throws deprecation warnings that it will drop those in a future release) ec5d20fb

Edited by Patrick Hüther

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