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Add option to change gramtools kmer length in var call pipeline #34

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martinghunt opened this issue Apr 23, 2018 · 2 comments
Open

Add option to change gramtools kmer length in var call pipeline #34

martinghunt opened this issue Apr 23, 2018 · 2 comments
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@martinghunt
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Ideas for what this could be called:

--map_seed <integer between 1 and 20> gramtools stores a mapping from seeds/kmers in the graph to suffix-array intervals, to accelerate quasimapping (purely performance, identical results). Longer seeds cost more RAM but accelerate quasimapping.

--sa_index_cache ...same text here...

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cc-ing everyone

@ffranr ffranr removed their assignment Oct 11, 2019
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@martinghunt @ffranr @iqbal-lab