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Use optimized indexing parameters
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See #407
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@marcelm
marcelm committed Mar 20, 2024
1 parent 6fd4c5d commit 4c10938
Showing 1 changed file with 8 additions and 7 deletions.
15 changes: 8 additions & 7 deletions src/indexparameters.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -35,13 +35,14 @@ struct Profile {
static auto max{std::numeric_limits<int>::max()};

static std::vector<Profile> profiles = {
Profile{ 50, 90, 20, -4, -3, 2},
Profile{100, 110, 20, -4, -2, 2},
Profile{125, 135, 20, -4, -1, 4},
Profile{150, 175, 20, -4, 1, 7},
Profile{250, 275, 20, -4, 4, 13},
Profile{300, 375, 22, -4, 2, 12},
Profile{400, max, 23, -6, 2, 12},
Profile{ 50, 70, 16, -4, -2, 0},
Profile{ 75, 90, 20, -4, -3, -1},
Profile{100, 110, 16, -4, 1, 3},
Profile{125, 135, 20, -4, 1, 4},
Profile{150, 175, 20, -4, 2, 5},
Profile{250, 275, 24, -4, 4, 12},
Profile{300, 375, 24, -4, 5, 13},
Profile{400, max, 25, -6, 7, 13},
};

/* Create an IndexParameters instance based on a given read length.
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1 comment on commit 4c10938

@ksahlin
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Is there a bug in the parameter setting for canonical read length 100? A k of 16 seems too low. Maybe it is causing the drop we see at read lengths 100? (See attached fig)

percentage_aligned_plot.pdf

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