Commits

Branch selector

 master

User selector

All users

Datepicker

All time

Commit History

Commits on Jun 17, 2022

• Merge pull request #2 from jackwadden/remove_subprocess

  Show description for d16c591
  jackwadden

  authored
  d16c591

Commits on Jun 7, 2022

• Major updates to improve speed and add online mode. This version of LAMPrey was used for all online end-to-end runs for the final paper submission.

  jackwadden

  committed
  3537ac5

Commits on Oct 8, 2021

• Added prototype online monitoring code that takes a fast5 directory where squiggles are dumped, copies them locally, basecalls them, and then processes them.

  jackwadden

  committed
  e2ae325

Commits on Sep 28, 2021

• Adding prototype watchdog functionality for true real-time analysis.

  jackwadden

  committed
  414e74f

Commits on Sep 27, 2021

• Slight modifications to high_confidence mode (renamed to confidence_level) to allow for parameterized concatemer filtering for VAF computation.

  jackwadden

  committed
  ea82330

Commits on Jul 27, 2021

• Fixed bug where searching left would break if the final correct primer sequence was identified but was not the last primer.

  jackwadden

  committed
  cd61a59

Commits on Jul 7, 2021

• Fixed issue where I wasn't revcomping reverse target sub-reads before alignment.

  jackwadden

  committed
  00319eb

• First prototype completely removing subprocess calls. Led to a ~10x speedup.

  jackwadden

  committed
  f3a6ca2

Commits on Jul 6, 2021

• Still mucking around. Biopython is just a wrapper for subprocess, so that was a dead end.

  jackwadden

  committed
  ba1dd6a

Commits on Jun 28, 2021

• First working candidate with removal of minimap2 dependency.

  jackwadden

  committed
  b7b9e4f

• First ripout of subprocess.

  jackwadden

  committed
  72ef10f

• Merge branch 'swaccel' of https://github.com/jackwadden/lamprey into swaccel

  jackwadden

  committed
  a6c21fb

• Checkpoint of skbio integration.

  jackwadden

  committed
  bb113df

• Merge branch 'master' of https://github.com/jackwadden/lamprey into swaccel

  jackwadden

  committed
  7f9b051

• misc updates to high confidence mode

  jackwadden

  committed
  73194c1

Commits on Jun 10, 2021

• Swapped swalign for scikit-bio sw aligner. Huge speed improvements, but small change to results.

  jackwadden

  committed
  47044eb

Commits on May 12, 2021

• Shrunk example dataset and updated quick start usage.

  jackwadden

  committed
  32fe89f

• Merge branch 'master' of https://github.com/jackwadden/lamprey

  jackwadden

  committed
  c074c6d

• Removing .gitignore

  jackwadden

  committed
  0d3bf1b

• Fixed missing script issue and also a relative path in process_candidates.sh

  jackwadden

  committed
  60332fc

• Updating README.md

  jackwadden

  committed
  6697a7f

• Adding progressbar to requrements.

  jackwadden

  committed
  c0cf5e5

• Fixed wrong link to run script.

  jackwadden

  committed
  83d737f

• Removed .gitignore

  jackwadden

  committed
  59f1a85

• Updated README to be more specific and added cython to requirements.txt

  jackwadden

  committed
  c151943

• Adding proper paths to example run scripts.

  jackwadden

  committed
  8d7925f

• Adding lib directory path.

  jackwadden

  committed
  e22ecb6

• Merge pull request #1 from jackwadden/add-license-1

  Show description for 0a6bafa
  jackwadden

  authored
  0a6bafa

• Create LICENSE

  jackwadden

  authored
  3f814d3

• Updating README.

  jackwadden

  committed
  ba09c66

• Updating README.

  jackwadden

  committed
  6a62540

• Updated instructions for downloading and installing lamprey and accelerated swalign.

  jackwadden

  committed
  6e22e4c

• Updating README.

  jackwadden

  committed
  0a90deb

• Adding scripts and data for example use.

  jackwadden

  committed
  e309af2

Commits on May 7, 2021

• Updates to classification algorithm to fix issues with off target classifications.

  jackwadden

  committed
  174164e

Pagination

PreviousNext