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Test long read giraffe for short reads #4378
Commits on May 21, 2024
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Merge pull request #4303 from xchang1/fix-lr-params
Fix command line downsmapling parameters to match what they're doing
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Set chainier R10 parameters and swap count and length presets for HiF…
…i to follow swapped parameters
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Commits on Jun 6, 2024
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Adopt R10 parameters with lower fragment gap cost and no fragment sco…
…re fraction filter to control softclips
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Make chain middle DP limit large and configurable, and allow sorting …
…by chain and not base-level score
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Commits on Jun 11, 2024
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Merge branch 'exact-name' into lr-giraffe
Make -c be --correctly-mapped and -e be --exact-name like in the main branch.
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I think this makes it track full length gapless extensions through th…
…e funnel properly
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Merge remote-tracking branch 'origin/master' into lr-giraffe
Combine two implementations of alignment edit sequence validation.
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Use libvgio that doesn't multithread decompression and make sure we a…
…ctually get our own htslib
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Try getting all values at once but it doesnt work so Im going to try …
…going beck to the payload
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Find minimizer hit count by walking through minimziers ordered by rea…
…d instead of score
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Revert "Find minimizer hit count by walking through minimziers ordere…
…d by read instead of score" This reverts commit ee5b6b6.
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Revert "Add hacky way of dealing with multicomponent chains"
This reverts commit 02a3369.
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Revert "Only store zipcodes in a separate file"
This reverts commit 116dc01.
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Use unpacked zipcode for getting snarl values and fix but I missed fi…
…nding the minimum distance
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Revert "Make map from node id to net handle"
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