whatshap stats - Calculate all length statistics on split blocks #412
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marcelm
reviewed
Nov 11, 2022
whatshap/cli/stats.py
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| """Return DetailedStats""" | ||
| block_sizes = sorted(len(block) for block in self.blocks) | ||
| n_singletons = sum(1 for size in block_sizes if size == 1) | ||
| block_sizes = [size for size in block_sizes if size > 1] | ||
| block_lengths = sorted(block.span() for block in self.blocks if len(block) > 1) | ||
| # Block length stats calculated from split interleaved blocks to avoid inflating values | ||
| block_lengths = sorted([block.span() for block in self.split_blocks if len(block) > 1]) |
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Can this remain a generator expression (without the [ and ])?
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Yes, sorted returns a list so this is definitely redundant.
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I forgot: This also needs a documentation update and an entry in the changelog. In the docs, I think it makes sense to move the sentence about "interleaved blocks are cut" to the paragraph "The numbers in the following columns describe these blocks." https://whatshap.readthedocs.io/en/latest/guide.html#whatshap-stats |
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Thanks! |
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fix #400
Fixes inflated stats for block lengths in
whatshap statsif there are overlapping blocks, also see #384.I tested on chromosome
SUPER_3(116801625 bp) in the VCF referenced in issue #400 where there were a lot of overlapping blocks.Before
After
As you can see there is a drastic reduction in
Sum of lengths,Average block lengthandLongest block.This PR also a removes an additional call to
PhasingStats.get(now renamedPhasingStats.get_detailed_stats) when using the flag--tsv.