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Long Read Giraffe #4323

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Commits on Jul 10, 2024

  1. Use libvgio that doesn't multithread decompression and make sure we a… 

    …ctually get our own htslib
    @adamnovak
    adamnovak committed Jul 10, 2024
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  2. Use payload less for old short read code path

    @xchang1
    xchang1 committed Jul 10, 2024
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  3. Use the distance index a bit less

    @xchang1
    xchang1 committed Jul 10, 2024
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  4. Stop making new decoders

    @xchang1
    xchang1 committed Jul 10, 2024
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  5. Get parent depth from zipcodes but idk if its any faster

    @xchang1
    xchang1 committed Jul 10, 2024
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  6. Save chain component

    @xchang1
    xchang1 committed Jul 10, 2024
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  7. Make docs build not have untracked files laying around in submodules

    @adamnovak
    adamnovak committed Jul 10, 2024
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  8. Add code reference

    @adamnovak
    adamnovak committed Jul 10, 2024
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  9. Make crash code actually include stringstream

    @adamnovak
    adamnovak committed Jul 10, 2024
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Commits on Jul 11, 2024

  1. Cache more stuff in the seed from the zipcodes

    @xchang1
    xchang1 committed Jul 11, 2024
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Commits on Jul 12, 2024

  1. Try getting all values at once but it doesnt work so Im going to try … 

    …going beck to the payload
    @xchang1
    xchang1 committed Jul 12, 2024
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Commits on Jul 13, 2024

  1. Get all cache values from zipcodes once

    @xchang1
    xchang1 committed Jul 13, 2024
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  2. Dont use distance index for getting is_root_snarl

    @xchang1
    xchang1 committed Jul 13, 2024
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  3. Add the zipcode to the clustering problems and use to get parents

    @xchang1
    xchang1 committed Jul 13, 2024
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  4. Acually use zipcode to get handle

    @xchang1
    xchang1 committed Jul 13, 2024
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  5. Stop expecting the parent of a snarl to be a root

    @xchang1
    xchang1 committed Jul 13, 2024
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  6. Use zipcodes for getting chain parent

    @xchang1
    xchang1 committed Jul 13, 2024
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Commits on Jul 14, 2024

  1. Use zipcodes for distances

    @xchang1
    xchang1 committed Jul 14, 2024
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  2. Add distance check

    @xchang1
    xchang1 committed Jul 14, 2024
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Commits on Jul 15, 2024

  1. Don't copy seed to cluster

    @xchang1
    xchang1 committed Jul 15, 2024
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  2. Fix is_root_snarl

    @xchang1
    xchang1 committed Jul 15, 2024
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  3. Reserve space in some vectors

    @xchang1
    xchang1 committed Jul 15, 2024
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  4. Take out unused map

    @xchang1
    xchang1 committed Jul 15, 2024
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  5. Take out another unused hash set

    @xchang1
    xchang1 committed Jul 15, 2024
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  6. Reserve more and fix indenting

    @xchang1
    xchang1 committed Jul 15, 2024
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Commits on Jul 16, 2024

  1. Reserve memory for zipcode

    @xchang1
    xchang1 committed Jul 16, 2024
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  2. Reserve memory for decoders

    @xchang1
    xchang1 committed Jul 16, 2024
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  3. Use zipcode for snarl length

    @xchang1
    xchang1 committed Jul 16, 2024
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  4. Reserve more memory

    @xchang1
    xchang1 committed Jul 16, 2024
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Commits on Jul 17, 2024

  1. Add cluster checking

    @xchang1
    xchang1 committed Jul 17, 2024
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  2. Find minimizer hit count by walking through minimziers ordered by rea… 

    …d instead of score
    @xchang1
    xchang1 committed Jul 17, 2024
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  3. Revert "Find minimizer hit count by walking through minimziers ordere… 

    …d by read instead of score"

This reverts commit ee5b6b6.
    @xchang1
    xchang1 committed Jul 17, 2024
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Commits on Jul 18, 2024

  1. Add hacky way of dealing with multicomponent chains

    @xchang1
    xchang1 committed Jul 18, 2024
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Commits on Jul 19, 2024

  1. Revert "Add hacky way of dealing with multicomponent chains" 

    This reverts commit 02a3369.
    @xchang1
    xchang1 committed Jul 19, 2024
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  2. Merge commit '094b956' into lr-giraffe

    @adamnovak
    adamnovak committed Jul 19, 2024
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  3. Merge commit '755a634' into lr-giraffe

    @adamnovak
    adamnovak committed Jul 19, 2024
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  4. Merge commit 'dfac868' into lr-giraffe

    @adamnovak
    adamnovak committed Jul 19, 2024
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  5. Merge remote-tracking branch 'origin/master' into lr-giraffe

    @adamnovak
    adamnovak committed Jul 19, 2024
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  6. Merge commit 'b55be13' into lr-giraffe

    @adamnovak
    adamnovak committed Jul 19, 2024
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  7. Merge remote-tracking branch 'origin/unlimited-anchors' into lr-giraffe

    @adamnovak
    adamnovak committed Jul 19, 2024
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  8. Make a string identifier for a snarl tree node

    @xchang1
    xchang1 committed Jul 19, 2024
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Commits on Jul 21, 2024

  1. Fix zipcode identifiers

    @xchang1
    xchang1 committed Jul 21, 2024
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Commits on Jul 22, 2024

  1. Add chain component to zipcodes

    @xchang1
    xchang1 committed Jul 22, 2024
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  2. Use zipcodes to get chain component for nodes

    @xchang1
    xchang1 committed Jul 22, 2024
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  3. Add get_chain_component to zipcodes

    @xchang1
    xchang1 committed Jul 22, 2024
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  4. Get chain component from zipcodes for payload

    @xchang1
    xchang1 committed Jul 22, 2024
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  5. Use zipcode chain component

    @xchang1
    xchang1 committed Jul 22, 2024
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  6. Add failing unit test

    @xchang1
    xchang1 committed Jul 22, 2024
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  7. Get chain component for irregular snarls

    @xchang1
    xchang1 committed Jul 22, 2024
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  8. Fix debug code

    @xchang1
    xchang1 committed Jul 22, 2024
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Commits on Jul 23, 2024

  1. Add chain component count to chains zipcodes

    @xchang1
    xchang1 committed Jul 23, 2024
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  2. Add unit test for looping zipcodes and fix bugs

    @xchang1
    xchang1 committed Jul 23, 2024
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  3. Use zipcodes for chain component in clustering

    @xchang1
    xchang1 committed Jul 23, 2024
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Commits on Jul 24, 2024

  1. Use regular snarls to skip finding distances

    @xchang1
    xchang1 committed Jul 24, 2024
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  2. Add external connectivity to zipcodes

    @xchang1
    xchang1 committed Jul 24, 2024
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  3. Take out end_in net_handle_t

    @xchang1
    xchang1 committed Jul 24, 2024
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  4. Fix payload with new values

    @xchang1
    xchang1 committed Jul 24, 2024
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  5. Add external connectivity for root nodes

    @xchang1
    xchang1 committed Jul 24, 2024
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  6. Use zipcode for external connectivity

    @xchang1
    xchang1 committed Jul 24, 2024
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  7. Don't use distance index for ordering children in chains

    @xchang1
    xchang1 committed Jul 24, 2024
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  8. Fix orientation for simple snarls since we took them out

    @xchang1
    xchang1 committed Jul 24, 2024
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  9. Start taking out net_handle_t's from the payload

    @xchang1
    xchang1 committed Jul 24, 2024
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  10. Take out grandparent handle

    @xchang1
    xchang1 committed Jul 24, 2024
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Commits on Jul 25, 2024

  1. Add net identifier strings but don't actually use them

    @xchang1
    xchang1 committed Jul 25, 2024
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  2. Use net identifiers as keys for all the lookups

    @xchang1
    xchang1 committed Jul 25, 2024
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  3. Mostly take out finding net handles until they're needed

    @xchang1
    xchang1 committed Jul 25, 2024
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  4. Fix identifiers but its not working

    @xchang1
    xchang1 committed Jul 25, 2024
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Commits on Jul 26, 2024

  1. Fix parent

    @xchang1
    xchang1 committed Jul 26, 2024
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  2. Fix getting the node identifier

    @xchang1
    xchang1 committed Jul 26, 2024
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  3. Fix getting handle to trivial chain

    @xchang1
    xchang1 committed Jul 26, 2024
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  4. Include chain component in identifier

    @xchang1
    xchang1 committed Jul 26, 2024
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  5. Fix getting net handle for child of root snarl

    @xchang1
    xchang1 committed Jul 26, 2024
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Commits on Jul 27, 2024

  1. Fix clustering the root snarl

    @xchang1
    xchang1 committed Jul 27, 2024
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Commits on Jul 29, 2024

  1. Get chain sorting values for snarls earlier and sort properly for two… 

    … seeds
    @xchang1
    xchang1 committed Jul 29, 2024
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  2. Get parent from children

    @xchang1
    xchang1 committed Jul 29, 2024
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  3. Take out distance index when not used

    @xchang1
    xchang1 committed Jul 29, 2024
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  4. Take the distance index out of more functions that don't use it

    @xchang1
    xchang1 committed Jul 29, 2024
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  5. Use distance index for chain values less

    @xchang1
    xchang1 committed Jul 29, 2024
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  6. turn off debug

    @xchang1
    xchang1 committed Jul 29, 2024
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Commits on Jul 30, 2024

  1. Get identifier at the same time as payload

    @xchang1
    xchang1 committed Jul 30, 2024
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  2. Merge remote-tracking branch 'upstream/master' into lr-giraffe

    @adamnovak
    adamnovak committed Jul 30, 2024
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Commits on Jul 31, 2024

  1. Undo using identifier strings as keys and fix some bugs

    @xchang1
    xchang1 committed Jul 31, 2024
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  2. Put zipcode and decoder together

    @xchang1
    xchang1 committed Jul 31, 2024
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  3. Fix unit tests

    @xchang1
    xchang1 committed Jul 31, 2024
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  4. Fix reserving decoder length

    @xchang1
    xchang1 committed Jul 31, 2024
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  5. Add an int vector that uses a minimal bit width for storing stuff

    @xchang1
    xchang1 committed Jul 31, 2024
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  6. Merge branch 'read-quietly' into lr-giraffe

    @adamnovak
    adamnovak committed Jul 31, 2024
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Commits on Aug 1, 2024

  1. Use new int vectors for zipcodes but it doesn't work yet

    @xchang1
    xchang1 committed Aug 1, 2024
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  2. Merge remote-tracking branch 'origin/low-cplx-context' into lr-giraffe

    @adamnovak
    adamnovak committed Aug 1, 2024
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Commits on Aug 2, 2024

  1. Fix zipcodes

    @xchang1
    xchang1 committed Aug 2, 2024
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Commits on Aug 3, 2024

  1. Revert using minint vectors

    @xchang1
    xchang1 committed Aug 3, 2024
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  2. Make decoder use fewer bits

    @xchang1
    xchang1 committed Aug 3, 2024
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  3. Only store zipcodes in a separate file

    @xchang1
    xchang1 committed Aug 3, 2024
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  4. Serialize zipcode and decoder

    @xchang1
    xchang1 committed Aug 3, 2024
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  5. Revert "Serialize zipcode and decoder" 

    This reverts commit eace413.
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    xchang1 committed Aug 3, 2024
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  6. Revert "Only store zipcodes in a separate file" 

    This reverts commit 116dc01.
    @xchang1
    xchang1 committed Aug 3, 2024
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  7. Undo putting zipcode and decoder together

    @xchang1
    xchang1 committed Aug 3, 2024
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  8. Fix typo

    @xchang1
    xchang1 committed Aug 3, 2024
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  9. Use distance index less for chain values

    @xchang1
    xchang1 committed Aug 3, 2024
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Commits on Aug 5, 2024

  1. Put decoder back with zipcode

    @xchang1
    xchang1 committed Aug 5, 2024
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  2. Serialize decoder

    @xchang1
    xchang1 committed Aug 5, 2024
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  3. Actually serialize the decoder

    @xchang1
    xchang1 committed Aug 5, 2024
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  4. Put decoder into zipcode payload

    @xchang1
    xchang1 committed Aug 5, 2024
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  5. Actually serialize the decoder

    @xchang1
    xchang1 committed Aug 5, 2024
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Commits on Aug 6, 2024

  1. Add an unpacked zipcode but it doesn't compile yet

    @xchang1
    xchang1 committed Aug 6, 2024
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  2. Get everything to compile

    @xchang1
    xchang1 committed Aug 6, 2024
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  3. Add unit tests and fix bug for unpacked zip codes

    @xchang1
    xchang1 committed Aug 6, 2024
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Commits on Aug 7, 2024

  1. Merge remote-tracking branch 'origin/master' into lr-giraffe

    @adamnovak
    adamnovak committed Aug 7, 2024
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  2. Use the unpacked zipcode for clustering instead of the old payload

    @xchang1
    xchang1 committed Aug 7, 2024
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Commits on Aug 8, 2024

  1. Use the length of the last chain component as the length of a multico… 

    …mponent chain
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  2. Use unpacked zipcode in SnarlTreeNodeProblem instead of zipcode

    @xchang1
    xchang1 committed Aug 8, 2024
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Commits on Aug 9, 2024

  1. Reserve memory for unpacked zipcode

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    xchang1 committed Aug 9, 2024
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  2. Reserve memory

    @xchang1
    xchang1 committed Aug 9, 2024
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  3. Take out chain component

    @xchang1
    xchang1 committed Aug 9, 2024
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  4. Fix bug getting best distanecs

    @xchang1
    xchang1 committed Aug 9, 2024
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  5. Make vg filter see empty list annotations as not there

    @adamnovak
    adamnovak committed Aug 9, 2024
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  6. Merge remote-tracking branch 'origin/master' into lr-giraffe

    @adamnovak
    adamnovak committed Aug 9, 2024
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  7. Merge remote-tracking branch 'origin/left-align-better' into lr-giraffe

    @adamnovak
    adamnovak committed Aug 9, 2024
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Commits on Aug 10, 2024

  1. Get the length of a cyclic chain

    @xchang1
    xchang1 committed Aug 10, 2024
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  2. Turn off debug

    @xchang1
    xchang1 committed Aug 10, 2024
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  3. Get values from unpacked zipcode for children of problems

    @xchang1
    xchang1 committed Aug 10, 2024
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Commits on Aug 11, 2024

  1. Take out unused chain component ints

    @xchang1
    xchang1 committed Aug 11, 2024
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Commits on Aug 12, 2024

  1. Reserve memory when getting zipcodes from payload

    @xchang1
    xchang1 committed Aug 12, 2024
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  2. Remove unused ints and reserve memory for unpacked zipcode

    @xchang1
    xchang1 committed Aug 12, 2024
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  3. Reserve less memory because it made it slower

    @xchang1
    xchang1 committed Aug 12, 2024
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Commits on Aug 13, 2024

  1. Undo unpacking zipcode to get back to 020cbb

    @xchang1
    xchang1 committed Aug 13, 2024
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  2. Fix bug getting minimum distances

    @xchang1
    xchang1 committed Aug 13, 2024
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  3. Get chains last component length and get chain length from zipcode

    @xchang1
    xchang1 committed Aug 13, 2024
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  4. Make a decoded code type (but not for roots) and use it for building … 

    …the zipcode
    @xchang1
    xchang1 committed Aug 13, 2024
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  5. Add getters and setters for unpacked codes

    @xchang1
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  6. Move build info headers from phony targets to top-level shell invocat… 

    …ions
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    adamnovak committed Aug 13, 2024
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  7. Merge branch 'update-version-fast' into lr-giraffe

    @adamnovak
    adamnovak committed Aug 13, 2024
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  8. Remove extra tabs

    @adamnovak
    adamnovak committed Aug 13, 2024
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  9. Add functions for interpreting one level of the zipcode

    @xchang1
    xchang1 committed Aug 13, 2024
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  10. Add unit tests for unpacked codes

    @xchang1
    xchang1 committed Aug 13, 2024
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  11. Merge remote-tracking branch 'origin/left-align-better' into lr-giraffe

    @adamnovak
    adamnovak committed Aug 13, 2024
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  12. Cut direct, broken static flag to version header dependency

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    adamnovak committed Aug 13, 2024
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Commits on Aug 14, 2024

  1. Use chain_minimum_length in zipcode

    @xchang1
    xchang1 committed Aug 14, 2024
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  2. Make unacking const

    @xchang1
    xchang1 committed Aug 14, 2024
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  3. Used unpacked zipcode for getting chain values

    @xchang1
    xchang1 committed Aug 14, 2024
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  4. Use unpacked zipcode for getting snarl values and fix but I missed fi… 

    …nding the minimum distance
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    xchang1 committed Aug 14, 2024
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  5. Get parent with distance index if its faster

    @xchang1
    xchang1 committed Aug 14, 2024
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  6. Make a map from connected component number to net handle

    @xchang1
    xchang1 committed Aug 14, 2024
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  7. Make map from node id to net handle

    @xchang1
    xchang1 committed Aug 14, 2024
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  8. Revert "Make map from node id to net handle" 

    This reverts commit a4410a9.
    @xchang1
    xchang1 committed Aug 14, 2024
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  9. Reserve memory for children

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    xchang1 committed Aug 14, 2024
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  10. Revert "Reserve memory for children" 

    This reverts commit 17120fb.
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  11. Set up Docker build and CI to get the version build right

    @adamnovak
    adamnovak committed Aug 14, 2024
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  12. Remove wayward tabs

    @adamnovak
    adamnovak committed Aug 14, 2024
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  13. Report errors better for vg inject failures

    @adamnovak
    adamnovak committed Aug 14, 2024
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Commits on Aug 15, 2024

  1. Merge remote-tracking branch 'upstream/lr-giraffe' into lr-giraffe

    @xchang1
    xchang1 committed Aug 15, 2024
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Commits on Aug 16, 2024

  1. Merge branch 'update-version-fast' into lr-giraffe

    @adamnovak
    adamnovak committed Aug 16, 2024
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Commits on Aug 19, 2024

  1. Merge remote-tracking branch 'upstream/master' into lr-giraffe

    @adamnovak
    adamnovak committed Aug 19, 2024
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  2. Implement consistent orientation around WFA connections

    @adamnovak
    adamnovak committed Aug 19, 2024
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  3. Implement consistent orientation for align_sequence_between with a wr… 

    …apper.
    @adamnovak
    adamnovak committed Aug 19, 2024
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  4. Fix build errors in implementation

    @adamnovak
    adamnovak committed Aug 19, 2024
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  5. Add test for non-WFA orientation fix

    @adamnovak
    adamnovak committed Aug 19, 2024
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  6. Add testing for connect_consistently

    @adamnovak
    adamnovak committed Aug 19, 2024
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Commits on Aug 21, 2024

  1. Merge remote-tracking branch 'upstream/lr-giraffe' into lr-giraffe

    @xchang1
    xchang1 committed Aug 21, 2024
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Commits on Aug 22, 2024

  1. Use bitfields for child_info_t and add chain component

    @xchang1
    xchang1 committed Aug 22, 2024
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  2. Check chain component when making zipcode trees

    @xchang1
    xchang1 committed Aug 22, 2024
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  3. Add unit test for multicomponent chain

    @xchang1
    xchang1 committed Aug 22, 2024
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  4. Merge remote-tracking branch 'upstream/master' into HEAD

    @xchang1
    xchang1 committed Aug 22, 2024
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  5. Merge remote-tracking branch 'upstream/lr-giraffe' into lr-giraffe

    @adamnovak
    adamnovak committed Aug 22, 2024
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Commits on Aug 29, 2024

  1. Add handling for softclips off the edge of contigs in inject

    @adamnovak
    adamnovak committed Aug 29, 2024
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  2. Fetch out edit

    @adamnovak
    adamnovak committed Aug 29, 2024
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  3. Add missing continue

    @adamnovak
    adamnovak committed Aug 29, 2024
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Commits on Sep 3, 2024

  1. Merge remote-tracking branch 'upstream/lr-giraffe' into lr-giraffe

    @xchang1
    xchang1 committed Sep 3, 2024
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  2. Fix empty top-level snarl zip trees

    @xchang1
    xchang1 committed Sep 3, 2024
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  3. Turn off debug

    @xchang1
    xchang1 committed Sep 3, 2024
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  4. Remove any empty snarl

    @xchang1
    xchang1 committed Sep 3, 2024
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Commits on Sep 4, 2024

  1. Check if previous_index is 0

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    xchang1 committed Sep 4, 2024
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Commits on Sep 9, 2024

  1. Check orientation of seeds

    @xchang1
    xchang1 committed Sep 9, 2024
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  2. Add stuff to go around a looping chain but I haven't tested it yet

    @xchang1
    xchang1 committed Sep 9, 2024
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Commits on Sep 10, 2024

  1. Add unit test for looping chains and fix sorting nodes in multicompon… 

    …ent chains
    @xchang1
    xchang1 committed Sep 10, 2024
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  2. Don't count nodes that loop

    @xchang1
    xchang1 committed Sep 10, 2024
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  3. Merge remote-tracking branch 'origin/master' into lr-giraffe

    @adamnovak
    adamnovak committed Sep 10, 2024
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Commits on Sep 12, 2024

  1. Take out looping chains in zipcode trees

    @xchang1
    xchang1 committed Sep 12, 2024
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  2. Merge remote-tracking branch 'upstream/lr-giraffe' into lr-giraffe

    @xchang1
    xchang1 committed Sep 12, 2024
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Commits on Sep 16, 2024

  1. Use more bits for distance index indices

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    xchang1 committed Sep 16, 2024
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Commits on Sep 18, 2024

  1. Try bailing on banded global alignment between seeds if it's going to… 

    … use too much memory
    @xchang1
    xchang1 committed Sep 18, 2024
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  2. Add dp limit to be the same as the dozeu limit

    @xchang1
    xchang1 committed Sep 18, 2024
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  3. Get cell count estimate right

    @xchang1
    xchang1 committed Sep 18, 2024
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  4. Get sequence properly

    @xchang1
    xchang1 committed Sep 18, 2024
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  5. Merge remote-tracking branch 'origin/master' into lr-giraffe

    @adamnovak
    adamnovak committed Sep 18, 2024
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  6. Revert trying to stop banded global aligner when the problem is too big

    @xchang1
    xchang1 committed Sep 18, 2024
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  7. Revert "Try bailing on banded global alignment between seeds if it's … 

    …going to use too much memory"

This reverts commit 2b9ac09.
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    xchang1 committed Sep 18, 2024
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  8. Apply --max-dp-cells to BandedGlobalAligner and set to 100M for R10 a… 

    …nd HiFi
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    adamnovak committed Sep 18, 2024
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Commits on Sep 22, 2024

  1. Merge remote-tracking branch 'upstream/lr-giraffe' into lr-giraffe

    @xchang1
    xchang1 committed Sep 22, 2024
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  2. Lower default max-dp-cells

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    xchang1 committed Sep 22, 2024
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Commits on Sep 24, 2024

  1. Actually use fragment-min-score

    @xchang1
    xchang1 committed Sep 24, 2024
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  2. Bump max-dp-cells back up

    @xchang1
    xchang1 committed Sep 24, 2024
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Commits on Oct 18, 2024

  1. Increase max-dp-cells. Works for r10 reads on non-d9 hprc graph but I… 

    … didn't check the collapsed graphs
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    xchang1 committed Oct 18, 2024
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  2. Break off most of main() from the x86-64-supporting preflight code

    @adamnovak
    adamnovak committed Oct 18, 2024
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  3. Partially revert "fix build on Ubuntu 24.04.1 / GCC 13.2.0" 

    This partially reverts commit fa824c1.

We don't need to avoid string operations if we don't build all of main for the
lowest common denominator architecture.
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Commits on Oct 21, 2024

  1. Make padded window size parity match anchor parity for orientation in… 

    …dependence
    @adamnovak
    adamnovak committed Oct 21, 2024
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  2. Remove extra debugging

    @adamnovak
    adamnovak committed Oct 21, 2024
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  3. Change short tail pruning to only require being one tail and not both

    @adamnovak
    adamnovak committed Oct 21, 2024
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  4. Add a test for surjection orientation independence

    @adamnovak
    adamnovak committed Oct 21, 2024
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Commits on Oct 24, 2024

  1. Add a script to cut GAM records to node ranges

    @adamnovak
    adamnovak committed Oct 24, 2024
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  2. Add simple local slide check to anchor pruning

    @adamnovak
    adamnovak committed Oct 24, 2024
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Commits on Oct 25, 2024

  1. Increase search length to include gap length when finding the dagifie… 

    …d graph for aligning to
    @xchang1
    xchang1 committed Oct 25, 2024
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  2. Add the max_gap_length earlier to match what the other calls to align… 

    …_sequence_between_consistently do
    @xchang1
    xchang1 committed Oct 25, 2024
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  3. Merge pull request #4425 from vgteam/lr-giraffe-missinsert 

    Lr giraffe missinsert
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    xchang1 authored Oct 25, 2024
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  4. Add --max-slide option to surject to control duplicate anchor sequenc… 

    …e finding
    @adamnovak
    adamnovak committed Oct 25, 2024
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  5. Merge remote-tracking branch 'origin/lr-giraffe' into lr-giraffe

    @adamnovak
    adamnovak committed Oct 25, 2024
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  6. Add timing to surject and std:: to move

    @adamnovak
    adamnovak committed Oct 25, 2024
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Commits on Oct 26, 2024

  1. Turn off debug output

    @xchang1
    xchang1 committed Oct 26, 2024
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  2. Merge pull request #4427 from xchang1/lr-giraffe-missinsert 

    Turn off debug output
    @xchang1
    xchang1 authored Oct 26, 2024
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Commits on Oct 28, 2024

  1. Switch to sort_shuffling_ties for sorting minimizers

    @xchang1
    xchang1 committed Oct 28, 2024
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  2. Keep picking seeds until the agglomerations cover most of the read

    @xchang1
    xchang1 committed Oct 28, 2024
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Commits on Oct 29, 2024

  1. Add a target read coverage for minimizers

    @xchang1
    xchang1 committed Oct 29, 2024
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  2. Only keep seeds if there is no coverage in their agglomeratoin

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    xchang1 committed Oct 29, 2024
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  3. Remember the coverage of reads taken before the minimizer count cutoff

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    xchang1 committed Oct 29, 2024
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  4. Remember to count the bases of seeds

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    xchang1 committed Oct 29, 2024
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  5. Use a constant flank size instead of agglomeration

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    xchang1 committed Oct 29, 2024
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  6. Fix adding coverage

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    xchang1 committed Oct 29, 2024
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Commits on Oct 30, 2024

  1. Fix counting overlapping bases

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    xchang1 committed Oct 30, 2024
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  2. Take out target coverage and increase flank

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    xchang1 committed Oct 30, 2024
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  3. Make minimizer flank coverage a command line option

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    xchang1 committed Oct 30, 2024
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  4. Make limiting the max_middle_gap an option

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    xchang1 committed Oct 30, 2024
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Commits on Oct 31, 2024

  1. Add new defaults

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    xchang1 committed Oct 31, 2024
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Commits on Nov 1, 2024

  1. Make sorting minimizers check key

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    xchang1 committed Nov 1, 2024
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Commits on Nov 4, 2024

  1. Limit the number of hits that a minimizer can have when adding it bey… 

    …ond the cap
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    xchang1 committed Nov 4, 2024
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  2. Merge pull request #4429 from xchang1/lr-giraffe-seedsort 

    Shuffle tied minimizers when sorting and keep extra minimizers to fill gaps in read coverage
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    xchang1 authored Nov 4, 2024
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Commits on Nov 5, 2024

  1. Only keep extra minimizers if they're as good as the ones we kept

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    xchang1 committed Nov 5, 2024
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Commits on Nov 7, 2024

  1. Add flag for minimizer repetitiveness and an hmm repetitiveness finder

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    xchang1 committed Nov 7, 2024
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Commits on Nov 8, 2024

  1. Add skippability to anchors and skip skippable anchors when aligning … 

    …chains if it doesn't make a big gap
    @xchang1
    xchang1 committed Nov 8, 2024
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  2. Fix bug looking off the end of a vector

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    xchang1 committed Nov 8, 2024
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  3. Don't skip minimizers if there's no gap

    @xchang1
    xchang1 committed Nov 8, 2024
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  4. Fix bug

    @xchang1
    xchang1 committed Nov 8, 2024
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  5. Fix which score gets used

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    xchang1 committed Nov 8, 2024
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  6. Set neighbors of a repetitive minimizers as being repetitive

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    xchang1 committed Nov 8, 2024
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  7. Merge remote-tracking branch 'upstream/master' into HEAD

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    adamnovak committed Nov 8, 2024
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Commits on Nov 9, 2024

  1. Only skip minimizers if there is a gap

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    xchang1 committed Nov 9, 2024
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Commits on Nov 11, 2024

  1. Fix adding distances and add a parameter for how much graph distance … 

    …we can skip
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    xchang1 committed Nov 11, 2024
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Commits on Nov 12, 2024

  1. Make it the default to not take out seeds

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    xchang1 committed Nov 12, 2024
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  2. Merge pull request #4441 from xchang1/skip-minimizers 

    Skip minimizers
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    xchang1 authored Nov 12, 2024
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  3. Add a way for gamcompare to ignore truth contigs

    @adamnovak
    adamnovak committed Nov 12, 2024
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  4. Don't add reads with all positions dropped to truth table

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    adamnovak committed Nov 12, 2024
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Commits on Nov 14, 2024

  1. Add unit test for nested multicomponent chain

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    xchang1 committed Nov 14, 2024
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  2. Make the zip code tree maker use the prefix sum values in the orienta… 

    …tion of the chain instead of the tree itself
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    xchang1 committed Nov 14, 2024
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Commits on Nov 15, 2024

  1. Flip runs of a cyclic snarl to take into account the new order of the… 

    … prefix sum
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    xchang1 committed Nov 15, 2024
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  2. Add unit tests for what I thought would fail but looks like the bug I… 

    … thought I made won't happen
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    xchang1 committed Nov 15, 2024
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Commits on Nov 19, 2024

  1. Get the prefix sum to the right side of a snarl in a chain

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    xchang1 committed Nov 19, 2024
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  2. Fix getting snarl offsets in children of cyclic snarls to match the o… 

    …ld version
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    xchang1 committed Nov 19, 2024
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  3. Get snarl offsets as a range in the child of a cyclic snarl

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    xchang1 committed Nov 19, 2024
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Commits on Nov 20, 2024

  1. Fix bug getting the grandchild of a snarl

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    xchang1 committed Nov 20, 2024
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  2. Merge remote-tracking branch 'upstream/lr-giraffe' into ziptree-bug

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    xchang1 committed Nov 20, 2024
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Commits on Nov 24, 2024

  1. Merge pull request #4453 from xchang1/ziptree-bug 

    Ziptree bug
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    xchang1 authored Nov 24, 2024
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