Commits

Branch selector

 master

User selector

All users

Datepicker

All time

Commit History

Commits on Aug 10, 2025

• Bump to Python 3.13

  philiptzou

  committed
  6bcc530

  Copy full SHA for 6bcc530

Commits on Aug 23, 2023

• Fix "expected list, got tuple" error

  philiptzou

  committed
  8e2ee11

  Copy full SHA for 8e2ee11

Commits on Jun 11, 2023

• Remove edit dep

  philiptzou

  committed
  8892951

  Copy full SHA for 8892951

• Upgrade dependency

  philiptzou

  committed
  cb28b83

  Copy full SHA for cb28b83

Commits on May 23, 2023

• Fix an issue that empty sequence is ignored in report; should report error

  philiptzou

  committed
  3f99cc8

  Copy full SHA for 3f99cc8

Commits on Apr 26, 2023

• Fix a bug that AA pos could exceed the gene maximum and properly warn the user if input sequence is mistakenly concatenated

  philiptzou

  committed
  5ea22aa

  Copy full SHA for 5ea22aa

Commits on Jan 5, 2023

• Add payload to NAPosition; upgrade dependencies

  philiptzou

  committed
  cd8cfb6

  Copy full SHA for cd8cfb6

Commits on Oct 16, 2022

• Allow multiple --gap-placement-score options

  philiptzou

  committed
  59e7285

  Copy full SHA for 59e7285

Commits on Oct 11, 2022

• CodonAlignment: avoid penaltizing gaps post/pre each end of inputseq

  philiptzou

  committed
  5ba0eb0

  Copy full SHA for 5ba0eb0

Commits on Oct 6, 2022

• Fix a bug that could cause infinite loop

  philiptzou

  committed
  608702a

  Copy full SHA for 608702a

• Fix an obivious bug when calculating ref unaligned size

  philiptzou

  committed
  7e0befb

  Copy full SHA for 7e0befb

• Fix a bug of removing unaligned pos when they were aligned somewhere else

  philiptzou

  committed
  f72047f

  Copy full SHA for f72047f

• If a fragment is aligned somewhere else, it shouldn't be used as unaligned

  philiptzou

  committed
  55ef852

  Copy full SHA for 55ef852

• The codon alignment ends can be dealt by IUPAC scores without anchoring

  philiptzou

  committed
  0d5a06b

  Copy full SHA for 0d5a06b

• When calc_match_score, also consider NAs placements; Bump dependencies

  philiptzou

  committed
  f857755

  Copy full SHA for f857755

• Improve gap handling when the gaps are at each end of the alignment

  philiptzou

  committed
  d99afc3

  Copy full SHA for d99afc3

• Remove print

  philiptzou

  committed
  2d2e26d

  Copy full SHA for 2d2e26d

• Place unaligned region closer to aligned sequence for processing by codon-alignment

  philiptzou

  committed
  2b47f43

  Copy full SHA for 2b47f43

• Fix get cigar_string when using Cython

  philiptzou

  committed
  83e9109

  Copy full SHA for 83e9109

• Better strategy of handling overlapped alignments by minimap2

  philiptzou

  committed
  037707a

  Copy full SHA for 037707a

Commits on Oct 5, 2022

• Add ability for codon-alignment to handle boundary gaps

  philiptzou

  committed
  b9e2d05

  Copy full SHA for b9e2d05

• Retain unaligned regions in aligned results as gaps - this allows

  Show description for ebd0be4
  philiptzou

  committed
  ebd0be4

  Copy full SHA for ebd0be4

Commits on Aug 26, 2022

• Fix an issue that prevent codon being aligned

  philiptzou

  committed
  4613ebe

  Copy full SHA for 4613ebe

Commits on Jul 4, 2022

• Fix a bug that postalign crashed when --minimap2-opts not specified

  philiptzou

  committed
  1c7ca78

  Copy full SHA for 1c7ca78

• Add support for specify minimap2 options

  philiptzou

  committed
  6c685bb

  Copy full SHA for 6c685bb

Commits on Apr 26, 2022

• Avoid extending codon-alignment process out of query sequence boundary

  philiptzou

  committed
  419cb67

  Copy full SHA for 419cb67

Commits on Mar 26, 2022

• Internally use seqid as unique id

  philiptzou

  committed
  a1ae475

  Copy full SHA for a1ae475

Commits on Jan 30, 2022

• skip codon alignment if no gap exists

  philiptzou

  committed
  c612c60

  Copy full SHA for c612c60

Commits on Jan 25, 2022

• Update requirements.txt

  philiptzou

  committed
  b5851f0

  Copy full SHA for b5851f0

• Update Pipfile.lock

  philiptzou

  committed
  fccfdc7

  Copy full SHA for fccfdc7

• Separate gap_placement_score parser out from Click callback

  philiptzou

  committed
  fafd5f9

  Copy full SHA for fafd5f9

• Add py.typed

  philiptzou

  committed
  e1dd887

  Copy full SHA for e1dd887

Commits on Jan 17, 2022

• Add cython to pyproject.toml

  philiptzou

  committed
  db567f3

  Copy full SHA for db567f3

Commits on Dec 28, 2021

• Add gap_placement_score for allowing manually designate gap position

  philiptzou

  committed
  cbec3c3

  Copy full SHA for cbec3c3

• Fix a few bug and try to get pyinstaller work (still not)

  philiptzou

  committed
  4b53004

  Copy full SHA for 4b53004

Pagination

Previous

Next