Add HiC heatmap for combined haps

[christinawu2008]

Description of feature

feature requirement
Phasing assessment is required for phased assemblies. A heatmap generated from combined haps can assist with this checking. This is required for red assemblies also, AWS testing.
Steps

1. Combining two haplotypes with chr orders following Chr1_A, Chr1_B, Chr2_A, Chr2_B, etc..
2. Mapping HiC with allowing multi-mapping reads
3. Generating heatmap

[GallVp]

Roadmap

• There are no sequence labels on the HiC contact map #147
• (Nice to have) Add a parameter to include/exclude multi mapping reads in the SAMBLASTER module
• Add a parameter to create a single (or multiple?) merged HiC contact map
• Add an option to use haphic refsort for sorting. If ref is missing, use the first assembly from the merge group as the reference.