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        "author": "Marcus D. R. Klarqvist",
        "author_email": "mk819@cam.ac.uk",
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        "classifiers": [
            "Development Status :: 4 - Beta",
            "Intended Audience :: Science/Research",
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            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "# pyflagstats\n\n[![PyPI version](https://badge.fury.io/py/pyflagstats.svg)](https://badge.fury.io/py/pyflagstats)\n\nGiven a stream of k-bit words, we seek to sum the bit values at indexes 0, 1, 2,\n..., k-1 across multiple words by computing k distinct sums. If the k-bit words\nare one-hot encoded then the sums corresponds to their frequencies.\n\nThis multiple-sum problem is a generalization of the population-count problem\nwhere we count the total number of set bits in independent machine words. We\nrefer to this new problem as the positional population-count problem.\n\nUsing SIMD (Single Instruction, Multiple Data) instructions from recent Intel\nprocessors, we describe algorithms for computing the 16-bit position population\ncount using about one eighth (0.125) of a CPU cycle per 16-bit word. Our best\napproach is about 140-fold faster than competitive code using only non-SIMD\ninstructions in terms of CPU cycles.\n\nThis package contains native Python bindings for the applying the efficient\npositional population count operator to computing summary statistics for the SAM\nFLAG field\n\n## Intallation\n\nInstall with\n```bash\npip3 install .\n```\n\nor locally with\n```bash\npython3 setup.py build_ext --inplace\n```\n\nUninstall with\n```bash\npip3 uninstall pyflagstats\n```\n\n## Example\n\n```python\nimport numpy as np\nimport pyflagstats as fs\n\n# Compute summary statistics for 100 million random FLAG fields.\n# Completes in around 1 second.\nfs.flagstats(np.random.randint(0,8192,100000000,dtype=\"uint16\"))\n```\n\nreturns (for example)\n\n```\n{'passed': array([ 624787,  312748, 2500089,  312384,  312314,  312678,  312045,\n        311845, 2499502, 4999279, 2497500, 1248979,  389744,  156194,\n        156029,       0], dtype=uint32), 'failed': array([ 625143,  312906, 2498840,  312818,  312129,  312802,  311869,\n        312105, 2501477, 5000721, 2499178, 1249105,  390962,  155828,\n        156018,       0], dtype=uint32)}\n```",
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        "name": "pyflagstats",
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        "summary": "Efficient subroutines for computing summary statistics for the SAM FLAG field",
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