Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Long Read Giraffe #4323

Open
wants to merge 1,242 commits into
base: master
Choose a base branch
from
Open

Long Read Giraffe #4323

wants to merge 1,242 commits into from
This pull request is big! We’re only showing the most recent 250 commits.

Commits on Jun 26, 2024

  1. Adopt HiFi parameters that look competitive with minimap2 on the 10k … 

    …read set
    @adamnovak
    adamnovak committed Jun 26, 2024
    1 Configuration menu
    Copy the full SHA
    ef2a138 View commit details
    Browse the repository at this point in the history

Commits on Jun 27, 2024

  1. Stop applying a score scale *and* a score window to HiFi reads

    @adamnovak
    adamnovak committed Jun 27, 2024
    1 Configuration menu
    Copy the full SHA
    1b52afe View commit details
    Browse the repository at this point in the history

Commits on Jun 28, 2024

  1. Add debugging code to find and dump problems for adjacent indels

    @adamnovak
    adamnovak committed Jun 28, 2024
    Configuration menu
    Copy the full SHA
    ac748fa View commit details
    Browse the repository at this point in the history

  2. Report offending alignment better

    @adamnovak
    adamnovak committed Jun 28, 2024
    Configuration menu
    Copy the full SHA
    c380167 View commit details
    Browse the repository at this point in the history

  3. Remove old check function and add test

    @adamnovak
    adamnovak committed Jun 28, 2024
    Configuration menu
    Copy the full SHA
    74ed7bf View commit details
    Browse the repository at this point in the history

  4. Check for validity around simplify

    @adamnovak
    adamnovak committed Jun 28, 2024
    Configuration menu
    Copy the full SHA
    5c91a96 View commit details
    Browse the repository at this point in the history

  5. Isolate problem in a small unit test

    @adamnovak
    adamnovak committed Jun 28, 2024
    Configuration menu
    Copy the full SHA
    5d15bed View commit details
    Browse the repository at this point in the history

  6. Stop using generic mapping cutter and just move insertions

    @adamnovak
    adamnovak committed Jun 28, 2024
    Configuration menu
    Copy the full SHA
    0555273 View commit details
    Browse the repository at this point in the history

  7. Quiet debugging

    @adamnovak
    adamnovak committed Jun 28, 2024
    2 Configuration menu
    Copy the full SHA
    3277498 View commit details
    Browse the repository at this point in the history

Commits on Jul 1, 2024

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

    @adamnovak
    adamnovak committed Jul 1, 2024
    Configuration menu
    Copy the full SHA
    d8803f0 View commit details
    Browse the repository at this point in the history

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

    @adamnovak
    adamnovak committed Jul 1, 2024
    Configuration menu
    Copy the full SHA
    22c6e69 View commit details
    Browse the repository at this point in the history

  3. Fix Mac build

    @adamnovak
    adamnovak committed Jul 1, 2024
    1 Configuration menu
    Copy the full SHA
    3a1cd38 View commit details
    Browse the repository at this point in the history

  4. Fix compatibility with Mac sed by using a nonempty backup extension

    @adamnovak
    adamnovak committed Jul 1, 2024
    Configuration menu
    Copy the full SHA
    accbe34 View commit details
    Browse the repository at this point in the history

  5. Add in offset even when the alignment starts past the end of the anch… 

    …or node
    @adamnovak
    adamnovak committed Jul 1, 2024
    1 Configuration menu
    Copy the full SHA
    88c3ff6 View commit details
    Browse the repository at this point in the history

Commits on Jul 3, 2024

  1. Add --max-graph-scale/-g option to surject and make giving up scale w… 

    …ith read size
    @adamnovak
    adamnovak committed Jul 3, 2024
    1 Configuration menu
    Copy the full SHA
    a6dfc43 View commit details
    Browse the repository at this point in the history

Commits on Jul 9, 2024

  1. Check zipcode tree distances in snarls properly

    @xchang1
    xchang1 committed Jul 9, 2024
    Configuration menu
    Copy the full SHA
    01ac6ee View commit details
    Browse the repository at this point in the history

  2. Turn off random tests

    @xchang1
    xchang1 committed Jul 9, 2024
    Configuration menu
    Copy the full SHA
    dd468e8 View commit details
    Browse the repository at this point in the history

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

    @xchang1
    xchang1 committed Jul 9, 2024
    1 Configuration menu
    Copy the full SHA
    0d6723d View commit details
    Browse the repository at this point in the history

  4. Update to current libbdsg

    @adamnovak
    adamnovak committed Jul 9, 2024
    Configuration menu
    Copy the full SHA
    fcdff75 View commit details
    Browse the repository at this point in the history

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

    Combine two implementations of alignment edit sequence validation.
    @adamnovak
    adamnovak committed Jul 9, 2024
    Configuration menu
    Copy the full SHA
    8d0878a View commit details
    Browse the repository at this point in the history

  6. Make crashes know what subcommand we tried to run

    @adamnovak
    adamnovak committed Jul 9, 2024
    Configuration menu
    Copy the full SHA
    b0ece9b View commit details
    Browse the repository at this point in the history

  7. Prefer to link vg's own built htslib dylib over the system one on Mac

    @adamnovak
    adamnovak committed Jul 9, 2024
    Configuration menu
    Copy the full SHA
    4d149ed View commit details
    Browse the repository at this point in the history

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

    @adamnovak
    adamnovak committed Jul 9, 2024
    Configuration menu
    Copy the full SHA
    6d7f4b6 View commit details
    Browse the repository at this point in the history

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
    Configuration menu
    Copy the full SHA
    a3b296e View commit details
    Browse the repository at this point in the history

  2. Use payload less for old short read code path

    @xchang1
    xchang1 committed Jul 10, 2024
    Configuration menu
    Copy the full SHA
    93c3f7a View commit details
    Browse the repository at this point in the history

  3. Use the distance index a bit less

    @xchang1
    xchang1 committed Jul 10, 2024
    Configuration menu
    Copy the full SHA
    783e452 View commit details
    Browse the repository at this point in the history

  4. Stop making new decoders

    @xchang1
    xchang1 committed Jul 10, 2024
    Configuration menu
    Copy the full SHA
    425c4cf View commit details
    Browse the repository at this point in the history

  5. Get parent depth from zipcodes but idk if its any faster

    @xchang1
    xchang1 committed Jul 10, 2024
    Configuration menu
    Copy the full SHA
    6e8f889 View commit details
    Browse the repository at this point in the history

  6. Save chain component

    @xchang1
    xchang1 committed Jul 10, 2024
    Configuration menu
    Copy the full SHA
    7fc2f1f View commit details
    Browse the repository at this point in the history

  7. Make docs build not have untracked files laying around in submodules

    @adamnovak
    adamnovak committed Jul 10, 2024
    Configuration menu
    Copy the full SHA
    4620f16 View commit details
    Browse the repository at this point in the history

  8. Add code reference

    @adamnovak
    adamnovak committed Jul 10, 2024
    Configuration menu
    Copy the full SHA
    da73e20 View commit details
    Browse the repository at this point in the history

  9. Make crash code actually include stringstream

    @adamnovak
    adamnovak committed Jul 10, 2024
    1 Configuration menu
    Copy the full SHA
    89e74ac View commit details
    Browse the repository at this point in the history

Commits on Jul 11, 2024

  1. Cache more stuff in the seed from the zipcodes

    @xchang1
    xchang1 committed Jul 11, 2024
    Configuration menu
    Copy the full SHA
    45d4987 View commit details
    Browse the repository at this point in the history

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
    Configuration menu
    Copy the full SHA
    d8c6e18 View commit details
    Browse the repository at this point in the history

Commits on Jul 13, 2024

  1. Get all cache values from zipcodes once

    @xchang1
    xchang1 committed Jul 13, 2024
    Configuration menu
    Copy the full SHA
    0244761 View commit details
    Browse the repository at this point in the history

  2. Dont use distance index for getting is_root_snarl

    @xchang1
    xchang1 committed Jul 13, 2024
    Configuration menu
    Copy the full SHA
    729c322 View commit details
    Browse the repository at this point in the history

  3. Add the zipcode to the clustering problems and use to get parents

    @xchang1
    xchang1 committed Jul 13, 2024
    Configuration menu
    Copy the full SHA
    33b7e87 View commit details
    Browse the repository at this point in the history

  4. Acually use zipcode to get handle

    @xchang1
    xchang1 committed Jul 13, 2024
    Configuration menu
    Copy the full SHA
    412dcec View commit details
    Browse the repository at this point in the history

  5. Stop expecting the parent of a snarl to be a root

    @xchang1
    xchang1 committed Jul 13, 2024
    Configuration menu
    Copy the full SHA
    2bdcb1a View commit details
    Browse the repository at this point in the history

  6. Use zipcodes for getting chain parent

    @xchang1
    xchang1 committed Jul 13, 2024
    Configuration menu
    Copy the full SHA
    ea7a0ed View commit details
    Browse the repository at this point in the history

Commits on Jul 14, 2024

  1. Use zipcodes for distances

    @xchang1
    xchang1 committed Jul 14, 2024
    Configuration menu
    Copy the full SHA
    6a693ad View commit details
    Browse the repository at this point in the history

  2. Add distance check

    @xchang1
    xchang1 committed Jul 14, 2024
    Configuration menu
    Copy the full SHA
    536c7d7 View commit details
    Browse the repository at this point in the history

Commits on Jul 15, 2024

  1. Don't copy seed to cluster

    @xchang1
    xchang1 committed Jul 15, 2024
    Configuration menu
    Copy the full SHA
    7fa624d View commit details
    Browse the repository at this point in the history

  2. Fix is_root_snarl

    @xchang1
    xchang1 committed Jul 15, 2024
    Configuration menu
    Copy the full SHA
    83d1ffa View commit details
    Browse the repository at this point in the history

  3. Reserve space in some vectors

    @xchang1
    xchang1 committed Jul 15, 2024
    Configuration menu
    Copy the full SHA
    f79ad09 View commit details
    Browse the repository at this point in the history

  4. Take out unused map

    @xchang1
    xchang1 committed Jul 15, 2024
    Configuration menu
    Copy the full SHA
    276d60b View commit details
    Browse the repository at this point in the history

  5. Take out another unused hash set

    @xchang1
    xchang1 committed Jul 15, 2024
    Configuration menu
    Copy the full SHA
    5e4fea4 View commit details
    Browse the repository at this point in the history

  6. Reserve more and fix indenting

    @xchang1
    xchang1 committed Jul 15, 2024
    Configuration menu
    Copy the full SHA
    acff6f6 View commit details
    Browse the repository at this point in the history

Commits on Jul 16, 2024

  1. Reserve memory for zipcode

    @xchang1
    xchang1 committed Jul 16, 2024
    Configuration menu
    Copy the full SHA
    310beb7 View commit details
    Browse the repository at this point in the history

  2. Reserve memory for decoders

    @xchang1
    xchang1 committed Jul 16, 2024
    Configuration menu
    Copy the full SHA
    73477be View commit details
    Browse the repository at this point in the history

  3. Use zipcode for snarl length

    @xchang1
    xchang1 committed Jul 16, 2024
    Configuration menu
    Copy the full SHA
    f5d0c4b View commit details
    Browse the repository at this point in the history

  4. Reserve more memory

    @xchang1
    xchang1 committed Jul 16, 2024
    Configuration menu
    Copy the full SHA
    a2dc51f View commit details
    Browse the repository at this point in the history

Commits on Jul 17, 2024

  1. Add cluster checking

    @xchang1
    xchang1 committed Jul 17, 2024
    Configuration menu
    Copy the full SHA
    c912afb View commit details
    Browse the repository at this point in the history

  2. Find minimizer hit count by walking through minimziers ordered by rea… 

    …d instead of score
    @xchang1
    xchang1 committed Jul 17, 2024
    Configuration menu
    Copy the full SHA
    ee5b6b6 View commit details
    Browse the repository at this point in the history

  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
    Configuration menu
    Copy the full SHA
    a7bb77c View commit details
    Browse the repository at this point in the history

Commits on Jul 18, 2024

  1. Add hacky way of dealing with multicomponent chains

    @xchang1
    xchang1 committed Jul 18, 2024
    Configuration menu
    Copy the full SHA
    02a3369 View commit details
    Browse the repository at this point in the history

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
    Configuration menu
    Copy the full SHA
    a410321 View commit details
    Browse the repository at this point in the history

  2. Merge commit '094b956' into lr-giraffe

    @adamnovak
    adamnovak committed Jul 19, 2024
    Configuration menu
    Copy the full SHA
    3b536dd View commit details
    Browse the repository at this point in the history

  3. Merge commit '755a634' into lr-giraffe

    @adamnovak
    adamnovak committed Jul 19, 2024
    Configuration menu
    Copy the full SHA
    381001c View commit details
    Browse the repository at this point in the history

  4. Merge commit 'dfac868' into lr-giraffe

    @adamnovak
    adamnovak committed Jul 19, 2024
    Configuration menu
    Copy the full SHA
    11fc884 View commit details
    Browse the repository at this point in the history

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

    @adamnovak
    adamnovak committed Jul 19, 2024
    Configuration menu
    Copy the full SHA
    adc6476 View commit details
    Browse the repository at this point in the history

  6. Merge commit 'b55be13' into lr-giraffe

    @adamnovak
    adamnovak committed Jul 19, 2024
    Configuration menu
    Copy the full SHA
    e9aac7e View commit details
    Browse the repository at this point in the history

  7. Merge remote-tracking branch 'origin/unlimited-anchors' into lr-giraffe

    @adamnovak
    adamnovak committed Jul 19, 2024
    1 Configuration menu
    Copy the full SHA
    e551487 View commit details
    Browse the repository at this point in the history

  8. Make a string identifier for a snarl tree node

    @xchang1
    xchang1 committed Jul 19, 2024
    Configuration menu
    Copy the full SHA
    eb1e302 View commit details
    Browse the repository at this point in the history

Commits on Jul 21, 2024

  1. Fix zipcode identifiers

    @xchang1
    xchang1 committed Jul 21, 2024
    Configuration menu
    Copy the full SHA
    b177d07 View commit details
    Browse the repository at this point in the history

Commits on Jul 22, 2024

  1. Add chain component to zipcodes

    @xchang1
    xchang1 committed Jul 22, 2024
    Configuration menu
    Copy the full SHA
    636abe8 View commit details
    Browse the repository at this point in the history

  2. Use zipcodes to get chain component for nodes

    @xchang1
    xchang1 committed Jul 22, 2024
    Configuration menu
    Copy the full SHA
    a4da073 View commit details
    Browse the repository at this point in the history

  3. Add get_chain_component to zipcodes

    @xchang1
    xchang1 committed Jul 22, 2024
    Configuration menu
    Copy the full SHA
    6e287f5 View commit details
    Browse the repository at this point in the history

  4. Get chain component from zipcodes for payload

    @xchang1
    xchang1 committed Jul 22, 2024
    Configuration menu
    Copy the full SHA
    6565acb View commit details
    Browse the repository at this point in the history

  5. Use zipcode chain component

    @xchang1
    xchang1 committed Jul 22, 2024
    Configuration menu
    Copy the full SHA
    c476d12 View commit details
    Browse the repository at this point in the history

  6. Add failing unit test

    @xchang1
    xchang1 committed Jul 22, 2024
    Configuration menu
    Copy the full SHA
    9e2153f View commit details
    Browse the repository at this point in the history

  7. Get chain component for irregular snarls

    @xchang1
    xchang1 committed Jul 22, 2024
    Configuration menu
    Copy the full SHA
    2c49a23 View commit details
    Browse the repository at this point in the history

  8. Fix debug code

    @xchang1
    xchang1 committed Jul 22, 2024
    Configuration menu
    Copy the full SHA
    ce9b0ad View commit details
    Browse the repository at this point in the history

Commits on Jul 23, 2024

  1. Add chain component count to chains zipcodes

    @xchang1
    xchang1 committed Jul 23, 2024
    Configuration menu
    Copy the full SHA
    da5f891 View commit details
    Browse the repository at this point in the history

  2. Add unit test for looping zipcodes and fix bugs

    @xchang1
    xchang1 committed Jul 23, 2024
    Configuration menu
    Copy the full SHA
    3b4855e View commit details
    Browse the repository at this point in the history

  3. Use zipcodes for chain component in clustering

    @xchang1
    xchang1 committed Jul 23, 2024
    Configuration menu
    Copy the full SHA
    d135aab View commit details
    Browse the repository at this point in the history

Commits on Jul 24, 2024

  1. Use regular snarls to skip finding distances

    @xchang1
    xchang1 committed Jul 24, 2024
    Configuration menu
    Copy the full SHA
    ddef07f View commit details
    Browse the repository at this point in the history

  2. Add external connectivity to zipcodes

    @xchang1
    xchang1 committed Jul 24, 2024
    Configuration menu
    Copy the full SHA
    9761748 View commit details
    Browse the repository at this point in the history

  3. Take out end_in net_handle_t

    @xchang1
    xchang1 committed Jul 24, 2024
    Configuration menu
    Copy the full SHA
    74d4122 View commit details
    Browse the repository at this point in the history

  4. Fix payload with new values

    @xchang1
    xchang1 committed Jul 24, 2024
    Configuration menu
    Copy the full SHA
    804c44d View commit details
    Browse the repository at this point in the history

  5. Add external connectivity for root nodes

    @xchang1
    xchang1 committed Jul 24, 2024
    Configuration menu
    Copy the full SHA
    18b4e7e View commit details
    Browse the repository at this point in the history

  6. Use zipcode for external connectivity

    @xchang1
    xchang1 committed Jul 24, 2024
    Configuration menu
    Copy the full SHA
    56fbd52 View commit details
    Browse the repository at this point in the history

  7. Don't use distance index for ordering children in chains

    @xchang1
    xchang1 committed Jul 24, 2024
    Configuration menu
    Copy the full SHA
    f2bd83a View commit details
    Browse the repository at this point in the history

  8. Fix orientation for simple snarls since we took them out

    @xchang1
    xchang1 committed Jul 24, 2024
    Configuration menu
    Copy the full SHA
    07de5de View commit details
    Browse the repository at this point in the history

  9. Start taking out net_handle_t's from the payload

    @xchang1
    xchang1 committed Jul 24, 2024
    Configuration menu
    Copy the full SHA
    5203413 View commit details
    Browse the repository at this point in the history

  10. Take out grandparent handle

    @xchang1
    xchang1 committed Jul 24, 2024
    Configuration menu
    Copy the full SHA
    461de64 View commit details
    Browse the repository at this point in the history

Commits on Jul 25, 2024

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

    @xchang1
    xchang1 committed Jul 25, 2024
    Configuration menu
    Copy the full SHA
    8655513 View commit details
    Browse the repository at this point in the history

  2. Use net identifiers as keys for all the lookups

    @xchang1
    xchang1 committed Jul 25, 2024
    Configuration menu
    Copy the full SHA
    5170df0 View commit details
    Browse the repository at this point in the history

  3. Mostly take out finding net handles until they're needed

    @xchang1
    xchang1 committed Jul 25, 2024
    Configuration menu
    Copy the full SHA
    e541b48 View commit details
    Browse the repository at this point in the history

  4. Fix identifiers but its not working

    @xchang1
    xchang1 committed Jul 25, 2024
    Configuration menu
    Copy the full SHA
    985ea32 View commit details
    Browse the repository at this point in the history

Commits on Jul 26, 2024

  1. Fix parent

    @xchang1
    xchang1 committed Jul 26, 2024
    Configuration menu
    Copy the full SHA
    9b36204 View commit details
    Browse the repository at this point in the history

  2. Fix getting the node identifier

    @xchang1
    xchang1 committed Jul 26, 2024
    Configuration menu
    Copy the full SHA
    d23653a View commit details
    Browse the repository at this point in the history

  3. Fix getting handle to trivial chain

    @xchang1
    xchang1 committed Jul 26, 2024
    Configuration menu
    Copy the full SHA
    6e09743 View commit details
    Browse the repository at this point in the history

  4. Include chain component in identifier

    @xchang1
    xchang1 committed Jul 26, 2024
    Configuration menu
    Copy the full SHA
    e433831 View commit details
    Browse the repository at this point in the history

  5. Fix getting net handle for child of root snarl

    @xchang1
    xchang1 committed Jul 26, 2024
    Configuration menu
    Copy the full SHA
    fd9a049 View commit details
    Browse the repository at this point in the history

Commits on Jul 27, 2024

  1. Fix clustering the root snarl

    @xchang1
    xchang1 committed Jul 27, 2024
    Configuration menu
    Copy the full SHA
    27f47cf View commit details
    Browse the repository at this point in the history

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
    Configuration menu
    Copy the full SHA
    7e74771 View commit details
    Browse the repository at this point in the history

  2. Get parent from children

    @xchang1
    xchang1 committed Jul 29, 2024
    Configuration menu
    Copy the full SHA
    a4eadd3 View commit details
    Browse the repository at this point in the history

  3. Take out distance index when not used

    @xchang1
    xchang1 committed Jul 29, 2024
    Configuration menu
    Copy the full SHA
    bc642aa View commit details
    Browse the repository at this point in the history

  4. Take the distance index out of more functions that don't use it

    @xchang1
    xchang1 committed Jul 29, 2024
    Configuration menu
    Copy the full SHA
    1a32937 View commit details
    Browse the repository at this point in the history

  5. Use distance index for chain values less

    @xchang1
    xchang1 committed Jul 29, 2024
    Configuration menu
    Copy the full SHA
    2a77f66 View commit details
    Browse the repository at this point in the history

  6. turn off debug

    @xchang1
    xchang1 committed Jul 29, 2024
    Configuration menu
    Copy the full SHA
    d2fc0a3 View commit details
    Browse the repository at this point in the history

Commits on Jul 30, 2024

  1. Get identifier at the same time as payload

    @xchang1
    xchang1 committed Jul 30, 2024
    Configuration menu
    Copy the full SHA
    82f714e View commit details
    Browse the repository at this point in the history

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

    @adamnovak
    adamnovak committed Jul 30, 2024
    Configuration menu
    Copy the full SHA
    0adfea0 View commit details
    Browse the repository at this point in the history

Commits on Jul 31, 2024

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

    @xchang1
    xchang1 committed Jul 31, 2024
    Configuration menu
    Copy the full SHA
    aa87f36 View commit details
    Browse the repository at this point in the history

  2. Put zipcode and decoder together

    @xchang1
    xchang1 committed Jul 31, 2024
    Configuration menu
    Copy the full SHA
    b9a2010 View commit details
    Browse the repository at this point in the history

  3. Fix unit tests

    @xchang1
    xchang1 committed Jul 31, 2024
    Configuration menu
    Copy the full SHA
    a18edec View commit details
    Browse the repository at this point in the history

  4. Fix reserving decoder length

    @xchang1
    xchang1 committed Jul 31, 2024
    Configuration menu
    Copy the full SHA
    831f231 View commit details
    Browse the repository at this point in the history

  5. Add an int vector that uses a minimal bit width for storing stuff

    @xchang1
    xchang1 committed Jul 31, 2024
    Configuration menu
    Copy the full SHA
    2923cde View commit details
    Browse the repository at this point in the history

  6. Merge branch 'read-quietly' into lr-giraffe

    @adamnovak
    adamnovak committed Jul 31, 2024
    1 Configuration menu
    Copy the full SHA
    2bbd62b View commit details
    Browse the repository at this point in the history

Commits on Aug 1, 2024

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

    @xchang1
    xchang1 committed Aug 1, 2024
    Configuration menu
    Copy the full SHA
    595cafb View commit details
    Browse the repository at this point in the history

  2. Merge remote-tracking branch 'origin/low-cplx-context' into lr-giraffe

    @adamnovak
    adamnovak committed Aug 1, 2024
    1 Configuration menu
    Copy the full SHA
    c5385a3 View commit details
    Browse the repository at this point in the history

Commits on Aug 2, 2024

  1. Fix zipcodes

    @xchang1
    xchang1 committed Aug 2, 2024
    Configuration menu
    Copy the full SHA
    de6c76f View commit details
    Browse the repository at this point in the history

Commits on Aug 3, 2024

  1. Revert using minint vectors

    @xchang1
    xchang1 committed Aug 3, 2024
    Configuration menu
    Copy the full SHA
    7aa1fe7 View commit details
    Browse the repository at this point in the history

  2. Make decoder use fewer bits

    @xchang1
    xchang1 committed Aug 3, 2024
    Configuration menu
    Copy the full SHA
    39ed6c8 View commit details
    Browse the repository at this point in the history

  3. Only store zipcodes in a separate file

    @xchang1
    xchang1 committed Aug 3, 2024
    Configuration menu
    Copy the full SHA
    116dc01 View commit details
    Browse the repository at this point in the history

  4. Serialize zipcode and decoder

    @xchang1
    xchang1 committed Aug 3, 2024
    Configuration menu
    Copy the full SHA
    eace413 View commit details
    Browse the repository at this point in the history

  5. Revert "Serialize zipcode and decoder" 

    This reverts commit eace413.
    @xchang1
    xchang1 committed Aug 3, 2024
    Configuration menu
    Copy the full SHA
    a9dffbe View commit details
    Browse the repository at this point in the history

  6. Revert "Only store zipcodes in a separate file" 

    This reverts commit 116dc01.
    @xchang1
    xchang1 committed Aug 3, 2024
    Configuration menu
    Copy the full SHA
    05480d0 View commit details
    Browse the repository at this point in the history

  7. Undo putting zipcode and decoder together

    @xchang1
    xchang1 committed Aug 3, 2024
    Configuration menu
    Copy the full SHA
    0207c82 View commit details
    Browse the repository at this point in the history

  8. Fix typo

    @xchang1
    xchang1 committed Aug 3, 2024
    Configuration menu
    Copy the full SHA
    69d48f0 View commit details
    Browse the repository at this point in the history

  9. Use distance index less for chain values

    @xchang1
    xchang1 committed Aug 3, 2024
    Configuration menu
    Copy the full SHA
    e12b23a View commit details
    Browse the repository at this point in the history

Commits on Aug 5, 2024

  1. Put decoder back with zipcode

    @xchang1
    xchang1 committed Aug 5, 2024
    Configuration menu
    Copy the full SHA
    f4f10f3 View commit details
    Browse the repository at this point in the history

  2. Serialize decoder

    @xchang1
    xchang1 committed Aug 5, 2024
    Configuration menu
    Copy the full SHA
    d72d232 View commit details
    Browse the repository at this point in the history

  3. Actually serialize the decoder

    @xchang1
    xchang1 committed Aug 5, 2024
    Configuration menu
    Copy the full SHA
    c4a2e48 View commit details
    Browse the repository at this point in the history

  4. Put decoder into zipcode payload

    @xchang1
    xchang1 committed Aug 5, 2024
    Configuration menu
    Copy the full SHA
    7fd62d2 View commit details
    Browse the repository at this point in the history

  5. Actually serialize the decoder

    @xchang1
    xchang1 committed Aug 5, 2024
    Configuration menu
    Copy the full SHA
    020cbb4 View commit details
    Browse the repository at this point in the history

Commits on Aug 6, 2024

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

    @xchang1
    xchang1 committed Aug 6, 2024
    Configuration menu
    Copy the full SHA
    06a6b04 View commit details
    Browse the repository at this point in the history

  2. Get everything to compile

    @xchang1
    xchang1 committed Aug 6, 2024
    Configuration menu
    Copy the full SHA
    d5a9e4d View commit details
    Browse the repository at this point in the history

  3. Add unit tests and fix bug for unpacked zip codes

    @xchang1
    xchang1 committed Aug 6, 2024
    Configuration menu
    Copy the full SHA
    dfde735 View commit details
    Browse the repository at this point in the history

Commits on Aug 7, 2024

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

    @adamnovak
    adamnovak committed Aug 7, 2024
    Configuration menu
    Copy the full SHA
    1ecc8ae View commit details
    Browse the repository at this point in the history

  2. Use the unpacked zipcode for clustering instead of the old payload

    @xchang1
    xchang1 committed Aug 7, 2024
    Configuration menu
    Copy the full SHA
    7cc9f4c View commit details
    Browse the repository at this point in the history

Commits on Aug 8, 2024

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

    …mponent chain
    @xchang1
    xchang1 committed Aug 8, 2024
    Configuration menu
    Copy the full SHA
    2c955f9 View commit details
    Browse the repository at this point in the history

  2. Use unpacked zipcode in SnarlTreeNodeProblem instead of zipcode

    @xchang1
    xchang1 committed Aug 8, 2024
    Configuration menu
    Copy the full SHA
    cf6b5be View commit details
    Browse the repository at this point in the history

Commits on Aug 9, 2024

  1. Reserve memory for unpacked zipcode

    @xchang1
    xchang1 committed Aug 9, 2024
    Configuration menu
    Copy the full SHA
    e5fe8b6 View commit details
    Browse the repository at this point in the history

  2. Reserve memory

    @xchang1
    xchang1 committed Aug 9, 2024
    Configuration menu
    Copy the full SHA
    8ccb110 View commit details
    Browse the repository at this point in the history

  3. Take out chain component

    @xchang1
    xchang1 committed Aug 9, 2024
    Configuration menu
    Copy the full SHA
    a73b80e View commit details
    Browse the repository at this point in the history

  4. Fix bug getting best distanecs

    @xchang1
    xchang1 committed Aug 9, 2024
    Configuration menu
    Copy the full SHA
    4286171 View commit details
    Browse the repository at this point in the history

  5. Make vg filter see empty list annotations as not there

    @adamnovak
    adamnovak committed Aug 9, 2024
    1 Configuration menu
    Copy the full SHA
    434a861 View commit details
    Browse the repository at this point in the history

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

    @adamnovak
    adamnovak committed Aug 9, 2024
    Configuration menu
    Copy the full SHA
    007df92 View commit details
    Browse the repository at this point in the history

  7. Merge remote-tracking branch 'origin/left-align-better' into lr-giraffe

    @adamnovak
    adamnovak committed Aug 9, 2024
    1 Configuration menu
    Copy the full SHA
    dbc77d7 View commit details
    Browse the repository at this point in the history

Commits on Aug 10, 2024

  1. Get the length of a cyclic chain

    @xchang1
    xchang1 committed Aug 10, 2024
    Configuration menu
    Copy the full SHA
    5beb1be View commit details
    Browse the repository at this point in the history

  2. Turn off debug

    @xchang1
    xchang1 committed Aug 10, 2024
    Configuration menu
    Copy the full SHA
    a0cbb23 View commit details
    Browse the repository at this point in the history

  3. Get values from unpacked zipcode for children of problems

    @xchang1
    xchang1 committed Aug 10, 2024
    Configuration menu
    Copy the full SHA
    d7e2553 View commit details
    Browse the repository at this point in the history

Commits on Aug 11, 2024

  1. Take out unused chain component ints

    @xchang1
    xchang1 committed Aug 11, 2024
    Configuration menu
    Copy the full SHA
    98a5518 View commit details
    Browse the repository at this point in the history

Commits on Aug 12, 2024

  1. Reserve memory when getting zipcodes from payload

    @xchang1
    xchang1 committed Aug 12, 2024
    Configuration menu
    Copy the full SHA
    f5ad687 View commit details
    Browse the repository at this point in the history

  2. Remove unused ints and reserve memory for unpacked zipcode

    @xchang1
    xchang1 committed Aug 12, 2024
    Configuration menu
    Copy the full SHA
    d02f4f7 View commit details
    Browse the repository at this point in the history

  3. Reserve less memory because it made it slower

    @xchang1
    xchang1 committed Aug 12, 2024
    Configuration menu
    Copy the full SHA
    2762b05 View commit details
    Browse the repository at this point in the history

Commits on Aug 13, 2024

  1. Undo unpacking zipcode to get back to 020cbb

    @xchang1
    xchang1 committed Aug 13, 2024
    Configuration menu
    Copy the full SHA
    f5e5638 View commit details
    Browse the repository at this point in the history

  2. Fix bug getting minimum distances

    @xchang1
    xchang1 committed Aug 13, 2024
    Configuration menu
    Copy the full SHA
    c172816 View commit details
    Browse the repository at this point in the history

  3. Get chains last component length and get chain length from zipcode

    @xchang1
    xchang1 committed Aug 13, 2024
    Configuration menu
    Copy the full SHA
    aff0cc6 View commit details
    Browse the repository at this point in the history

  4. Make a decoded code type (but not for roots) and use it for building … 

    …the zipcode
    @xchang1
    xchang1 committed Aug 13, 2024
    Configuration menu
    Copy the full SHA
    7ed8f6e View commit details
    Browse the repository at this point in the history

  5. Add getters and setters for unpacked codes

    @xchang1
    xchang1 committed Aug 13, 2024
    Configuration menu
    Copy the full SHA
    a600bbc View commit details
    Browse the repository at this point in the history

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

    …ions
    @adamnovak
    adamnovak committed Aug 13, 2024
    Configuration menu
    Copy the full SHA
    4b994b6 View commit details
    Browse the repository at this point in the history

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

    @adamnovak
    adamnovak committed Aug 13, 2024
    Configuration menu
    Copy the full SHA
    cc418dc View commit details
    Browse the repository at this point in the history

  8. Remove extra tabs

    @adamnovak
    adamnovak committed Aug 13, 2024
    Configuration menu
    Copy the full SHA
    aaf3cb9 View commit details
    Browse the repository at this point in the history

  9. Add functions for interpreting one level of the zipcode

    @xchang1
    xchang1 committed Aug 13, 2024
    Configuration menu
    Copy the full SHA
    3cbd7be View commit details
    Browse the repository at this point in the history

  10. Add unit tests for unpacked codes

    @xchang1
    xchang1 committed Aug 13, 2024
    Configuration menu
    Copy the full SHA
    72025a0 View commit details
    Browse the repository at this point in the history

  11. Merge remote-tracking branch 'origin/left-align-better' into lr-giraffe

    @adamnovak
    adamnovak committed Aug 13, 2024
    Configuration menu
    Copy the full SHA
    e00dd49 View commit details
    Browse the repository at this point in the history

  12. Cut direct, broken static flag to version header dependency

    @adamnovak
    adamnovak committed Aug 13, 2024
    Configuration menu
    Copy the full SHA
    ae6b91a View commit details
    Browse the repository at this point in the history

Commits on Aug 14, 2024

  1. Use chain_minimum_length in zipcode

    @xchang1
    xchang1 committed Aug 14, 2024
    Configuration menu
    Copy the full SHA
    096000a View commit details
    Browse the repository at this point in the history

  2. Make unacking const

    @xchang1
    xchang1 committed Aug 14, 2024
    Configuration menu
    Copy the full SHA
    0356878 View commit details
    Browse the repository at this point in the history

  3. Used unpacked zipcode for getting chain values

    @xchang1
    xchang1 committed Aug 14, 2024
    Configuration menu
    Copy the full SHA
    dca72e7 View commit details
    Browse the repository at this point in the history

  4. Use unpacked zipcode for getting snarl values and fix but I missed fi… 

    …nding the minimum distance
    @xchang1
    xchang1 committed Aug 14, 2024
    Configuration menu
    Copy the full SHA
    01e7b4d View commit details
    Browse the repository at this point in the history

  5. Get parent with distance index if its faster

    @xchang1
    xchang1 committed Aug 14, 2024
    Configuration menu
    Copy the full SHA
    62f6c38 View commit details
    Browse the repository at this point in the history

  6. Make a map from connected component number to net handle

    @xchang1
    xchang1 committed Aug 14, 2024
    Configuration menu
    Copy the full SHA
    b0c0234 View commit details
    Browse the repository at this point in the history

  7. Make map from node id to net handle

    @xchang1
    xchang1 committed Aug 14, 2024
    Configuration menu
    Copy the full SHA
    a4410a9 View commit details
    Browse the repository at this point in the history

  8. Revert "Make map from node id to net handle" 

    This reverts commit a4410a9.
    @xchang1
    xchang1 committed Aug 14, 2024
    Configuration menu
    Copy the full SHA
    45cba14 View commit details
    Browse the repository at this point in the history

  9. Reserve memory for children

    @xchang1
    xchang1 committed Aug 14, 2024
    Configuration menu
    Copy the full SHA
    17120fb View commit details
    Browse the repository at this point in the history

  10. Revert "Reserve memory for children" 

    This reverts commit 17120fb.
    @xchang1
    xchang1 committed Aug 14, 2024
    Configuration menu
    Copy the full SHA
    b0f1f70 View commit details
    Browse the repository at this point in the history

  11. Set up Docker build and CI to get the version build right

    @adamnovak
    adamnovak committed Aug 14, 2024
    Configuration menu
    Copy the full SHA
    083f2b3 View commit details
    Browse the repository at this point in the history

  12. Remove wayward tabs

    @adamnovak
    adamnovak committed Aug 14, 2024
    Configuration menu
    Copy the full SHA
    1248b0f View commit details
    Browse the repository at this point in the history

  13. Report errors better for vg inject failures

    @adamnovak
    adamnovak committed Aug 14, 2024
    Configuration menu
    Copy the full SHA
    08218c6 View commit details
    Browse the repository at this point in the history

Commits on Aug 15, 2024

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

    @xchang1
    xchang1 committed Aug 15, 2024
    Configuration menu
    Copy the full SHA
    35ae926 View commit details
    Browse the repository at this point in the history

Commits on Aug 16, 2024

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

    @adamnovak
    adamnovak committed Aug 16, 2024
    1 Configuration menu
    Copy the full SHA
    0e7d66f View commit details
    Browse the repository at this point in the history

Commits on Aug 19, 2024

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

    @adamnovak
    adamnovak committed Aug 19, 2024
    Configuration menu
    Copy the full SHA
    370f8fa View commit details
    Browse the repository at this point in the history

  2. Implement consistent orientation around WFA connections

    @adamnovak
    adamnovak committed Aug 19, 2024
    Configuration menu
    Copy the full SHA
    748169d View commit details
    Browse the repository at this point in the history

  3. Implement consistent orientation for align_sequence_between with a wr… 

    …apper.
    @adamnovak
    adamnovak committed Aug 19, 2024
    Configuration menu
    Copy the full SHA
    4e871f9 View commit details
    Browse the repository at this point in the history

  4. Fix build errors in implementation

    @adamnovak
    adamnovak committed Aug 19, 2024
    Configuration menu
    Copy the full SHA
    3a6022f View commit details
    Browse the repository at this point in the history

  5. Add test for non-WFA orientation fix

    @adamnovak
    adamnovak committed Aug 19, 2024
    Configuration menu
    Copy the full SHA
    eef142d View commit details
    Browse the repository at this point in the history

  6. Add testing for connect_consistently

    @adamnovak
    adamnovak committed Aug 19, 2024
    Configuration menu
    Copy the full SHA
    b99200a View commit details
    Browse the repository at this point in the history

Commits on Aug 21, 2024

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

    @xchang1
    xchang1 committed Aug 21, 2024
    Configuration menu
    Copy the full SHA
    f36ebdd View commit details
    Browse the repository at this point in the history

Commits on Aug 22, 2024

  1. Use bitfields for child_info_t and add chain component

    @xchang1
    xchang1 committed Aug 22, 2024
    Configuration menu
    Copy the full SHA
    ff6fa27 View commit details
    Browse the repository at this point in the history

  2. Check chain component when making zipcode trees

    @xchang1
    xchang1 committed Aug 22, 2024
    Configuration menu
    Copy the full SHA
    247aaef View commit details
    Browse the repository at this point in the history

  3. Add unit test for multicomponent chain

    @xchang1
    xchang1 committed Aug 22, 2024
    Configuration menu
    Copy the full SHA
    cb1f600 View commit details
    Browse the repository at this point in the history

  4. Merge remote-tracking branch 'upstream/master' into HEAD

    @xchang1
    xchang1 committed Aug 22, 2024
    Configuration menu
    Copy the full SHA
    292bdd4 View commit details
    Browse the repository at this point in the history

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

    @adamnovak
    adamnovak committed Aug 22, 2024
    1 Configuration menu
    Copy the full SHA
    bd8ded6 View commit details
    Browse the repository at this point in the history

Commits on Aug 29, 2024

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

    @adamnovak
    adamnovak committed Aug 29, 2024
    Configuration menu
    Copy the full SHA
    ad62378 View commit details
    Browse the repository at this point in the history

  2. Fetch out edit

    @adamnovak
    adamnovak committed Aug 29, 2024
    1 Configuration menu
    Copy the full SHA
    3bf557e View commit details
    Browse the repository at this point in the history

  3. Add missing continue

    @adamnovak
    adamnovak committed Aug 29, 2024
    1 Configuration menu
    Copy the full SHA
    d4b77fb View commit details
    Browse the repository at this point in the history

Commits on Sep 3, 2024

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

    @xchang1
    xchang1 committed Sep 3, 2024
    Configuration menu
    Copy the full SHA
    7ecf940 View commit details
    Browse the repository at this point in the history

  2. Fix empty top-level snarl zip trees

    @xchang1
    xchang1 committed Sep 3, 2024
    Configuration menu
    Copy the full SHA
    fab3f5e View commit details
    Browse the repository at this point in the history

  3. Turn off debug

    @xchang1
    xchang1 committed Sep 3, 2024
    Configuration menu
    Copy the full SHA
    f0e8389 View commit details
    Browse the repository at this point in the history

  4. Remove any empty snarl

    @xchang1
    xchang1 committed Sep 3, 2024
    Configuration menu
    Copy the full SHA
    a7ba479 View commit details
    Browse the repository at this point in the history

Commits on Sep 4, 2024

  1. Check if previous_index is 0

    @xchang1
    xchang1 committed Sep 4, 2024
    Configuration menu
    Copy the full SHA
    1b5387f View commit details
    Browse the repository at this point in the history

Commits on Sep 9, 2024

  1. Check orientation of seeds

    @xchang1
    xchang1 committed Sep 9, 2024
    1 Configuration menu
    Copy the full SHA
    1bef104 View commit details
    Browse the repository at this point in the history

  2. Add stuff to go around a looping chain but I haven't tested it yet

    @xchang1
    xchang1 committed Sep 9, 2024
    Configuration menu
    Copy the full SHA
    a325238 View commit details
    Browse the repository at this point in the history

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
    Configuration menu
    Copy the full SHA
    20fa2d2 View commit details
    Browse the repository at this point in the history

  2. Don't count nodes that loop

    @xchang1
    xchang1 committed Sep 10, 2024
    Configuration menu
    Copy the full SHA
    dafb61b View commit details
    Browse the repository at this point in the history

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

    @adamnovak
    adamnovak committed Sep 10, 2024
    1 Configuration menu
    Copy the full SHA
    beec239 View commit details
    Browse the repository at this point in the history

Commits on Sep 12, 2024

  1. Take out looping chains in zipcode trees

    @xchang1
    xchang1 committed Sep 12, 2024
    Configuration menu
    Copy the full SHA
    cd1ffce View commit details
    Browse the repository at this point in the history

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

    @xchang1
    xchang1 committed Sep 12, 2024
    Configuration menu
    Copy the full SHA
    92628c9 View commit details
    Browse the repository at this point in the history

Commits on Sep 16, 2024

  1. Use more bits for distance index indices

    @xchang1
    xchang1 committed Sep 16, 2024
    Configuration menu
    Copy the full SHA
    cffccc9 View commit details
    Browse the repository at this point in the history

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
    Configuration menu
    Copy the full SHA
    2b9ac09 View commit details
    Browse the repository at this point in the history

  2. Add dp limit to be the same as the dozeu limit

    @xchang1
    xchang1 committed Sep 18, 2024
    Configuration menu
    Copy the full SHA
    3d118f3 View commit details
    Browse the repository at this point in the history

  3. Get cell count estimate right

    @xchang1
    xchang1 committed Sep 18, 2024
    Configuration menu
    Copy the full SHA
    c1f7cf5 View commit details
    Browse the repository at this point in the history

  4. Get sequence properly

    @xchang1
    xchang1 committed Sep 18, 2024
    Configuration menu
    Copy the full SHA
    61df098 View commit details
    Browse the repository at this point in the history

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

    @adamnovak
    adamnovak committed Sep 18, 2024
    Configuration menu
    Copy the full SHA
    068d88c View commit details
    Browse the repository at this point in the history

  6. Revert trying to stop banded global aligner when the problem is too big

    @xchang1
    xchang1 committed Sep 18, 2024
    Configuration menu
    Copy the full SHA
    c667c6a View commit details
    Browse the repository at this point in the history

  7. Revert "Try bailing on banded global alignment between seeds if it's … 

    …going to use too much memory"

This reverts commit 2b9ac09.
    @xchang1
    xchang1 committed Sep 18, 2024
    Configuration menu
    Copy the full SHA
    0850aa2 View commit details
    Browse the repository at this point in the history

  8. Apply --max-dp-cells to BandedGlobalAligner and set to 100M for R10 a… 

    …nd HiFi
    @adamnovak
    adamnovak committed Sep 18, 2024
    1 Configuration menu
    Copy the full SHA
    b2b2ea9 View commit details
    Browse the repository at this point in the history

Commits on Sep 22, 2024

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

    @xchang1
    xchang1 committed Sep 22, 2024
    Configuration menu
    Copy the full SHA
    42f2915 View commit details
    Browse the repository at this point in the history

  2. Lower default max-dp-cells

    @xchang1
    xchang1 committed Sep 22, 2024
    1 Configuration menu
    Copy the full SHA
    5041ff4 View commit details
    Browse the repository at this point in the history

Commits on Sep 24, 2024

  1. Actually use fragment-min-score

    @xchang1
    xchang1 committed Sep 24, 2024
    Configuration menu
    Copy the full SHA
    062ba7a View commit details
    Browse the repository at this point in the history

  2. Bump max-dp-cells back up

    @xchang1
    xchang1 committed Sep 24, 2024
    1 Configuration menu
    Copy the full SHA
    839e934 View commit details
    Browse the repository at this point in the history

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
    @xchang1
    xchang1 committed Oct 18, 2024
    1 Configuration menu
    Copy the full SHA
    4aee9f3 View commit details
    Browse the repository at this point in the history

  2. Break off most of main() from the x86-64-supporting preflight code

    @adamnovak
    adamnovak committed Oct 18, 2024
    Configuration menu
    Copy the full SHA
    b05d3e3 View commit details
    Browse the repository at this point in the history

  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.
    @adamnovak
    adamnovak committed Oct 18, 2024
    Configuration menu
    Copy the full SHA
    8459d7b View commit details
    Browse the repository at this point in the history

Commits on Oct 21, 2024

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

    …dependence
    @adamnovak
    adamnovak committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    527f4a4 View commit details
    Browse the repository at this point in the history

  2. Remove extra debugging

    @adamnovak
    adamnovak committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    ef939ee View commit details
    Browse the repository at this point in the history

  3. Change short tail pruning to only require being one tail and not both

    @adamnovak
    adamnovak committed Oct 21, 2024
    Configuration menu
    Copy the full SHA
    09d2e7e View commit details
    Browse the repository at this point in the history

  4. Add a test for surjection orientation independence

    @adamnovak
    adamnovak committed Oct 21, 2024
    1 Configuration menu
    Copy the full SHA
    1ff1009 View commit details
    Browse the repository at this point in the history

Commits on Oct 24, 2024

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

    @adamnovak
    adamnovak committed Oct 24, 2024
    Configuration menu
    Copy the full SHA
    c25f9ed View commit details
    Browse the repository at this point in the history

  2. Add simple local slide check to anchor pruning

    @adamnovak
    adamnovak committed Oct 24, 2024
    1 Configuration menu
    Copy the full SHA
    1221a0c View commit details
    Browse the repository at this point in the history

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
    Configuration menu
    Copy the full SHA
    04e267c View commit details
    Browse the repository at this point in the history

  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
    1 Configuration menu
    Copy the full SHA
    1863c9e View commit details
    Browse the repository at this point in the history

  3. Merge pull request #4425 from vgteam/lr-giraffe-missinsert 

    Lr giraffe missinsert
    @xchang1
    xchang1 authored Oct 25, 2024
    1 Configuration menu
    Copy the full SHA
    de2f21c View commit details
    Browse the repository at this point in the history

  4. Add --max-slide option to surject to control duplicate anchor sequenc… 

    …e finding
    @adamnovak
    adamnovak committed Oct 25, 2024
    Configuration menu
    Copy the full SHA
    af6ce11 View commit details
    Browse the repository at this point in the history

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

    @adamnovak
    adamnovak committed Oct 25, 2024
    Configuration menu
    Copy the full SHA
    092568c View commit details
    Browse the repository at this point in the history

  6. Add timing to surject and std:: to move

    @adamnovak
    adamnovak committed Oct 25, 2024
    1 Configuration menu
    Copy the full SHA
    afb393f View commit details
    Browse the repository at this point in the history

Commits on Oct 26, 2024

  1. Turn off debug output

    @xchang1
    xchang1 committed Oct 26, 2024
    Configuration menu
    Copy the full SHA
    ace49a2 View commit details
    Browse the repository at this point in the history

  2. Merge pull request #4427 from xchang1/lr-giraffe-missinsert 

    Turn off debug output
    @xchang1
    xchang1 authored Oct 26, 2024
    1 Configuration menu
    Copy the full SHA
    821623a View commit details
    Browse the repository at this point in the history

Commits on Oct 28, 2024

  1. Switch to sort_shuffling_ties for sorting minimizers

    @xchang1
    xchang1 committed Oct 28, 2024
    Configuration menu
    Copy the full SHA
    adeed1c View commit details
    Browse the repository at this point in the history

  2. Keep picking seeds until the agglomerations cover most of the read

    @xchang1
    xchang1 committed Oct 28, 2024
    Configuration menu
    Copy the full SHA
    d70b6bd View commit details
    Browse the repository at this point in the history

Commits on Oct 29, 2024

  1. Add a target read coverage for minimizers

    @xchang1
    xchang1 committed Oct 29, 2024
    Configuration menu
    Copy the full SHA
    69fc8d4 View commit details
    Browse the repository at this point in the history

  2. Only keep seeds if there is no coverage in their agglomeratoin

    @xchang1
    xchang1 committed Oct 29, 2024
    Configuration menu
    Copy the full SHA
    08257c0 View commit details
    Browse the repository at this point in the history

  3. Remember the coverage of reads taken before the minimizer count cutoff

    @xchang1
    xchang1 committed Oct 29, 2024
    Configuration menu
    Copy the full SHA
    b3578c9 View commit details
    Browse the repository at this point in the history

  4. Remember to count the bases of seeds

    @xchang1
    xchang1 committed Oct 29, 2024
    Configuration menu
    Copy the full SHA
    998ca50 View commit details
    Browse the repository at this point in the history

  5. Use a constant flank size instead of agglomeration

    @xchang1
    xchang1 committed Oct 29, 2024
    Configuration menu
    Copy the full SHA
    f3836d5 View commit details
    Browse the repository at this point in the history

  6. Fix adding coverage

    @xchang1
    xchang1 committed Oct 29, 2024
    Configuration menu
    Copy the full SHA
    73ef8e8 View commit details
    Browse the repository at this point in the history

Commits on Oct 30, 2024

  1. Fix counting overlapping bases

    @xchang1
    xchang1 committed Oct 30, 2024
    Configuration menu
    Copy the full SHA
    ff0e63d View commit details
    Browse the repository at this point in the history

  2. Take out target coverage and increase flank

    @xchang1
    xchang1 committed Oct 30, 2024
    Configuration menu
    Copy the full SHA
    44e1dc2 View commit details
    Browse the repository at this point in the history

  3. Make minimizer flank coverage a command line option

    @xchang1
    xchang1 committed Oct 30, 2024
    Configuration menu
    Copy the full SHA
    345163b View commit details
    Browse the repository at this point in the history

  4. Make limiting the max_middle_gap an option

    @xchang1
    xchang1 committed Oct 30, 2024
    Configuration menu
    Copy the full SHA
    d0e7490 View commit details
    Browse the repository at this point in the history

Commits on Oct 31, 2024

  1. Add new defaults

    @xchang1
    xchang1 committed Oct 31, 2024
    Configuration menu
    Copy the full SHA
    30a8319 View commit details
    Browse the repository at this point in the history

Commits on Nov 1, 2024

  1. Make sorting minimizers check key

    @xchang1
    xchang1 committed Nov 1, 2024
    Configuration menu
    Copy the full SHA
    329e434 View commit details
    Browse the repository at this point in the history

Commits on Nov 4, 2024

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

    …ond the cap
    @xchang1
    xchang1 committed Nov 4, 2024
    Configuration menu
    Copy the full SHA
    9f569ed View commit details
    Browse the repository at this point in the history

  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
    @xchang1
    xchang1 authored Nov 4, 2024
    1 Configuration menu
    Copy the full SHA
    e667000 View commit details
    Browse the repository at this point in the history

Commits on Nov 5, 2024

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

    @xchang1
    xchang1 committed Nov 5, 2024
    1 Configuration menu
    Copy the full SHA
    8e0373a View commit details
    Browse the repository at this point in the history

Commits on Nov 8, 2024

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

    @adamnovak
    adamnovak committed Nov 8, 2024
    1 Configuration menu
    Copy the full SHA
    a14a8d5 View commit details
    Browse the repository at this point in the history