Plot ancestry karyograms

[mike-w-wilson]

• Get plotting script: https://github.com/armartin/ancestry_pipeline (Step 2.1 in ancestry_pipeline repo)
• Fig 1, supplementary material for Tractor paper

[mike-w-wilson]

These have been run periodically throughout the project to investigate local ancestry inference performance. Attached are the simulated dat karyotypes

Elizabeths script was updated to include only a single chromosome in the output for now: plot_karyogram1.py. The bash script plot_painted_karyogram.sh was also updated. A bug was found in both collapse_ancestry1.py and plot_karyogram1.py. The plot_karyogram1.py bug rescues the collapse ancestry. Collapse_ancestry1.py has a fence post problem where the last window in a file is not being added for the ancestry in the bed file. This creates gaps on the right side of the ancestry windows in the karyograms. Plot ancestry rescues this by grabbing the incorrect field, bp, and plotting the rectangles from a cM position to the bp position instead of cM to cM. This fills in the gap as the anc rectangle extend off the plotted areas.