set half precision for numpy arrays#87
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lsantuari wants to merge 2 commits into
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arnikz
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Jan 15, 2021
| last_t = time() | ||
| i = 1 | ||
| padding = np.zeros(shape=(padding_len, n_channels), dtype=np.float32) | ||
| padding = np.zeros(shape=(padding_len, n_channels), dtype=np.half) |
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Is this precision sufficient? I would keep the former.
>>> np.finfo(np.float32).precision
6
>>> np.finfo(np.half).precision
3
``
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From the result on the test data it seems to be sufficient, but I need to try it on the real data.
| reference_sequence = twobit.TwoBitFile(itwobit) | ||
| snv_list = ['BQ', 'SNV', 'MAPQ'] | ||
| snv_array = np.zeros(shape=(stop_pos, len(snv_list)), dtype=np.float32) | ||
| snv_array = np.zeros(shape=(stop_pos, len(snv_list)), dtype=np.half) |
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Btw aren't all channel values counts only?
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It reduces the file size for numpy arrays by setting half precision.