trace_to_matrix

Reliability status: development

Notes on default outputs

By default, trace_to_matrix now skips the all-pairs PWD KDE histogram figure because this calculation is often the slowest step for datasets with many barcodes. The default run still produces the single-cell PWD matrix, unique barcode list, N-matrix, Hi-M contact matrix, PWD median plot, PWD KDE plot, and N-matrix plot.

To also calculate and save *_Matrix_PWDhistograms.png, opt in explicitly:

trace_to_matrix --input traces.ecsv --plot_histograms

For larger datasets, you can combine histogram generation with per-trace parallel matrix construction:

trace_to_matrix --input traces.ecsv --n_jobs 6 --plot_histograms