Long Read Giraffe #4323
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Long Read Giraffe #4323
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Fix command line downsmapling parameters to match what they're doing
…i to follow swapped parameters
…re fraction filter to control softclips
…by chain and not base-level score
Make -c be --correctly-mapped and -e be --exact-name like in the main branch.
…e funnel properly
This reverts commit 17120fb.
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Changelog Entry
To be copied to the draft changelog by merger:
vg giraffenow has--parameter-preset hifiand--parameter_preset r10for using a new chaining-based algorithm to map long reads.--parameter-preset sruses the new algorithm for single-ended short reads; the old--parameter-preset defaultand--parameter-preset fastremain available with the old non-chaining algorithm.giraffe-facts.pyscript now knows how to read GAM files internally and no longer needs JSON preprocessing.Description
This adds the much-anticipated Long Read Giraffe to mainline vg.