Add missing EAGER1 functionality

[jfy133]

Is your feature request related to a problem? Please describe.

'EAGER2' should (within reason) reach functional parity with EAGER1.

The options are

• FastQC
• Adapter Removal/Merging [Drop Clip&Merge as not maintained and slower]
• Quality Filtering [Remove as can be done with AdapterRemoval when turn off merging and large overlap]
• Mapping
• BAM filtering
• Complexity Estimation
• Remove Duplicates
• Mt2NucRatio
• PMDTools
• Contamination Estimation [Replace Schmutzi with ANGSD system]
• Damage Calculation
• SNP Calling
• SNP Filtering [No evidence ever used this - drop for steamlinging]
• VCF2Genome
• Report

[jfy133]

Mt2NucRatio: #304

[jfy133]

VCF2Genome: #305