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Break up tiles into smaller chunks #106

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jimrybarski opened this issue Jun 15, 2017 · 0 comments
Open

Break up tiles into smaller chunks #106

jimrybarski opened this issue Jun 15, 2017 · 0 comments
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@jimrybarski
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Splitting FastQ tiles into multiple chunks would speed up alignments significantly. When pixels are .2666 microns/pixel, the FastQ tiles will be padded to 4096x4096 for the FFT, while .21666 microns/pixel will be padded to 8192x8192. The latter will cause alignments to take over a day, while the former takes at least 8 hours.

We get a factor of four speedup each time we reduce the maximum tile size by a power of 2. It's not reasonable to aim for 1024, but we should be able to get to 2048 easily with just four subtiles.

Subtiles should be overlapping. This ensures that even if an image aligns to multiple subtiles, it will align best to the one where it's fully saturated with FastQ points.

@jimrybarski jimrybarski self-assigned this Jun 15, 2017
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