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Use np.int8 for indicator matrix in generateMatrix (8x memory reduction, closes #28) #29

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Use np.int8 for indicator matrix in generateMatrix (8x memory reduction, closes #28) #29

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6 changes: 5 additions & 1 deletion AMULET.py
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Original file line number Diff line number Diff line change
Expand Up @@ -44,7 +44,11 @@ def generateMatrix(data, cellids, unionoverlaps):

regioninfo = dict()

matrix = np.zeros((len(unionoverlaps), len(cellids)))
# Indicator matrix only ever stores 0/1 (peak-in-cell), so int8 is
# sufficient and 8x smaller than the float64 default. This is the
# binding memory constraint for high-per-cell-coverage assays
# (e.g. 10x Chromium multiome at 25K+ cells/library). See #28.
matrix = np.zeros((len(unionoverlaps), len(cellids)), dtype=np.int8)
for i in range(len(data)):
curchr = data[i,0]
curstart = data[i,1]
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