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v0.1.3

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@shz9 shz9 released this 03 Jun 01:06
· 14 commits to master since this release

Changed

  • Updated the logic for detect_outliers in phenotype transforms to actually reflect the function
    name (before it was returning true for inliers...).
  • Updated quantize and dequantize to minimize data copying as much as possible.
  • Updated LDMatrix.load_rows() method to minimize data copying.
  • Fixed bug in LDMatrix.n_neighbors implementation.
  • Updated dask version in requirements.txt to avoid installing dask-expr.

Added

  • Added get_peak_memory_usage to system_utils to inspect peak memory usage of a process.
  • Placeholder method to perform QC on SumstatsTable objects (needs to be implemented still).
  • New attached dataset for long-range LD regions.
  • New method in SumstatsTable to impute rsID (if missing).
  • Preliminary support for matching with CHR+POS in SumstatsTable (still needs more work).
  • LDMatrix updates:
    • New method to filter long-range LD regions.
    • New method to prune LD matrix.
  • New algorithm for symmetrizing upper triangular and block diagonal LD matrices.
    • Much faster and more memory efficient than using scipy.
    • New LDMatrix class has efficient data loading in .load_data method.
    • We still retain load_rows because it is useful for loading a subset of rows.