added test for alignment_info.py #227
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andrewprzh
requested changes
Aug 24, 2024
src/alignment_info.py
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| @@ -10,6 +10,8 @@ | |||
| from .common import get_read_blocks | |||
| from .polya_verification import shift_polya, shift_polyt | |||
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| REGION_TO_CHECK_LEN = 12 | |||
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Agree with moving to constants, but I'd also put it back into AlignmentInfo as a global field (AlignmentInfo.REGION_TO_CHECK_LEN)
src/common.py
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| @classmethod | ||
| def get_match_events(cls): | ||
| return [cls.match, cls.seq_match, cls.seq_mismatch] |
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I think using set might be faster as we use for in checks.
I don't really know what is faster for small collections
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Simple tests show that even for collections of size 2 checking element in set works a bit faster than in list, from size 3 difference is noticeable
So, yeah, let's switch to set, idk why I used lists before :)
src/common.py
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| @classmethod | ||
| def get_ins_del_match_events(cls): | ||
| return [cls.match, cls.insertion, cls.deletion, cls.seq_match, cls.seq_mismatch] |
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I think using set will be faster as we use for in checks
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andrewprzh
approved these changes
Aug 26, 2024
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also removed unused code, change the order of expected/actual in number of asserts