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github.com/BioJulia/BioAlignments.jl

Sequence alignment tools
https://github.com/BioJulia/BioAlignments.jl

Release v3.1.0 (#89)

ceb3fe6ce85c794adde877b0bd048905557dc1e2 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Grantham's substitution matrix (#88)

Added support for R. Grantham's substitution matrix based on chemical properties from his 1974 p...

26be95a2e9a7776031bd910fbd7b61892403ff6e authored about 2 years ago by Kapara newbie <[email protected]>
Update project version number to 3.0.0

91a6d1e0301655aa5970fb46c6c3153012de7064 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Update changelog for v3.0.0

9a6a37defeef5176ae82332b67007a4f1ab8784d authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Merge pull request #64 from MillironX/operations-fix

c7bb5a849a270d4b84d306282c862e4a5f8d0718 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add clarification comments to soft clip anchor checking

Signed-off-by: Thomas A. Christensen II <[email protected]>

96f8ee7f99bbfe3fd2ff0d47e40326845b4faeed authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Make conditional non-empty

Co-authored-by: Kevin Bonham <[email protected]>

b99bada025798d49731e04f63a7aa4fda2b294e9 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add tests for padded alignments

Signed-off-by: Thomas A. Christensen II <[email protected]>

118ad0ec78fb78cb272e16599992bf3031ec4ff3 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add meta-operation support to PairwiseAlignment iterator

Signed-off-by: Thomas A. Christensen II <[email protected]>

bc19366d48c2e4a366f2d3766015736e9a09b773 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Revert count_aligned function to 0156de451254 ("alignment position support")

The `count_aligned` function was updated by @alyst to use the new `alnpos`
field in cc8237c48ad1...

f63ee256f68bb568224db27301d71b8d9e14688f authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Update CHANGELOG

Signed-off-by: Thomas A. Christensen II <[email protected]>

b60800927ad7fef8586446af57a8e7acaa019686 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add test for soft clip as second-to-last operation

Signed-off-by: Thomas A. Christensen II <[email protected]>

6bb6df5b8744a75c089a0088de1368a1ce89bda8 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add test for clips at end of alignment

Signed-off-by: Thomas A. Christensen II <[email protected]>

1d7ac42c180ed87f6bc16a4bc7d968cb2c5d706d authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add soft clips back into the alignment simulator

Signed-off-by: Thomas A. Christensen II <[email protected]>

b067303968dd1929ad11a63d3ba96ced9555d753 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add hard clips back into the alignment simulator

Signed-off-by: Thomas A. Christensen II <[email protected]>

0832146eee33ed4db6e7bb79dabe7c9828405e8c authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Remove never-reached code from random alignment generator

The test suite included logic for treating ends of alignment differently,
but due to the loop co...

f89415d951490d46b13fb31edcbe39996ae3be39 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add support to meta operations to test suite

Signed-off-by: Thomas A. Christensen II <[email protected]>

cf400cc9a4f5a39188f6ae9955b7874e0e6b437a authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Correct variable name typo in random alignment generation

Signed-off-by: Thomas A. Christensen II <[email protected]>

43541f81145db2c53eadf2dc75a54c34f25cb00f authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Remove SOFT_CLIP from insertion operations in random alignment generation

Signed-off-by: Thomas A. Christensen II <[email protected]>

28bd1d44b529b14c9e6147926f2426c5ae3768b2 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add check for valid OP_SOFT_CLIP location

Signed-off-by: Thomas A. Christensen II <[email protected]>

c6a531b93efe1402ea47076b45026b0825f35d71 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add check for invalid location of OP_HARD_CLIP

Signed-off-by: Thomas A. Christensen II <[email protected]>

0d6b90af886558bfb39e4de5acdb7554e3ca6563 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Switch to using alnpos to determine CIGAR numbers

Signed-off-by: Thomas A. Christensen II <[email protected]>

be9f93aa0141ae0974a5fdfa099aabfe2e922eeb authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Remove HARD_CLIP from insert operation list in test suite

According to the SAM spec, "H can only be present as the first and/or last
operation." In additi...

0f3090c7058208b1685fefd1cb7cc7bcf52c1587 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add export for ismetaop function

Signed-off-by: Thomas A. Christensen II <[email protected]>

4a4e722ba13239f9f1446320aeef09ef2c733844 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add update on OP_PAD to docs

Signed-off-by: Thomas A. Christensen II <[email protected]>

268c69617a26e409d8464420700481afceda68f4 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Indicate that OP_PAD is now supported

Signed-off-by: Thomas A. Christensen II <[email protected]>

7fb5a46492d18a328847824796009b038b57b560 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Remove unused assignments from cigar function

Signed-off-by: Thomas A. Christensen II <[email protected]>

d7c3179ccbe9106925ba955eac41e499716fac53 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add skip for printing meta operations in cigar strings

Signed-off-by: Thomas A. Christensen II <[email protected]>

30478c486fe347422b7c76cee4715f50f0fe4763 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add meta operations into alignment building from CIGAR strings

Signed-off-by: Thomas A. Christensen II <[email protected]>

f48c9c63f88e9d9076aeb4edd970d21ec98bcb6c authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Remove OP_HARD_CLIP from isinsertop trait

Signed-off-by: Thomas A. Christensen II <[email protected]>

11ec678f5260142d8ff4f302c87c6a24312c97f0 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add new trait for operations, `ismetaop`

Signed-off-by: Thomas A. Christensen II <[email protected]>

3850382fe7f2cee449656f1c6804c7ba0fd24aea authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Merge pull request #62 from alyst/agn_figs

f0b768945a3ae38eabbd0f6951ce005abde4098d authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Merge pull request #85 from BioJulia/release/v2.3.0

Downstream tests are failing because the breaking change from
#44 was merged here.

b92ccf3e9ed8976496880c3a521f4622ffeffeda authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Merge branch 'master' into release/v2.3.0

eceafe684719a8490196440b5396999cf17c2fdf authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Update CHANGELOG for v2.3.0

53f975cd1f8581242ac9c349444b53c0a4448b62 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Bump version number in Project.toml

898beae1fb8888b8171a7cf2897d87373fe4f566 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Merge branch 'MillironX/feature/getter-methods'

This merge is basically merging a PR on top of the v2.2.0 tag, because
GitHub doesn't appreciate...

33477483e0474ce586cb7a5f84b1d0b69e9cb560 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Merge branch 'hotfix/2.2.0'

# Conflicts:
# CHANGELOG.md
# Project.toml
# src/submat.jl

782063c0fa02531dfdb62762455eeee93e7f79e2 authored over 2 years ago by Ciarán O’Mara <[email protected]>
Add getter function entry to CHANGELOG

797c5663749cb5ef3534b35820e68d606ab73848 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Clarify the docstring for alignment(::PairwiseAlignmentResult)

alignment(::AlignedSequence) and alignment(::PairwiseAlignmentResult)
both return an Alignment, ...

54aaab02c98f71cd99c2320d3ca1e6ca221e9b75 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add doctest for sequence(::PairwiseAlignmentResult)

2e3e16d5b93ace0c6e2eb66156f301713b4ced6f authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add sequence getter function for PairwiseAlignment

aaa5ecf3b21826bbaf2b657330e394aa5af409ef authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add getter function docs for `AlignedSequence`

d7a35a25a730ce4d1ee13625bbb969823613f0e1 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add sequence getter function for PairwiseAlignmentResult

99d6c0dd3c2c02a982c59578f4d1d0a6a3590d28 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add alignment getter function for PairwiseAlignment

cb02c85147002f6f9d00896a35510404c2f294d6 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add sequence getter function for AlignedSequence

514541ec7068fa7b45188ddda0a71c59039ce5b6 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add alignment getter function for AlignedSequence

09042be1d737c3fa48d6abbfb3d99c1bd1677111 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Apply suggestions from code review

Change type from `Int8` to `UInt8` for efficiency.

Co-authored-by: Jakob Nybo Nissen <jakobnyb...

6d96e79d7a518f28a83f42de7c59b90f25f63eec authored over 2 years ago by Ciarán O'Mara <[email protected]>
Apply suggestions from code review

Update `CHANGELOG.md` to better reflect the state of the project.

Co-authored-by: Thomas A. Ch...

7414bb4c847619aee031f9cbb0ebe9a8b5e8250c authored over 2 years ago by Ciarán O'Mara <[email protected]>
CHANGELOG entries

d86d69ddba9d98eadee996805f092e58e9f07786 authored over 2 years ago by Ciarán O’Mara <[email protected]>
Increment version

2f38c3a4007c666100e7915bddbe11123f4fe920 authored over 2 years ago by Ciarán O’Mara <[email protected]>
Add more SubstitutionMatrix operations (#60)

SubstitutionMatrix is not a subtype of AbstractArray.
This may or may not be intentional, but c...

c023a3c71a133ec688eaf09f0e758e39f9b731e4 authored over 2 years ago by Tim Holy <[email protected]>
Add more SubstitutionMatrix operations (#60)

SubstitutionMatrix is not a subtype of AbstractArray.
This may or may not be intentional, but c...

1ea30c7b51170d95478921ea6e4a16e61d7c8b87 authored over 2 years ago by Tim Holy <[email protected]>
alignment.svg: use embedded fonts

2d3be18fef3b68925ce18f6d4d536ab0bb2db756 authored over 2 years ago by Alexey Stukalov <[email protected]>
alignment.svg: try workaround unsafe-inline secpol

4bb08d9e9e0e08a73f0be8de0d1604e12b7dc2cf authored over 2 years ago by Alexey Stukalov <[email protected]>
docs: update the alignment figure

d5f7385cb6cb47f2a5e463bf2dce3060e755f382 authored over 2 years ago by Alexey Stukalov <[email protected]>
Merge pull request #72 from CiaranOMara/develop

- Increments BioSequences compatibility to v3.
- Increments BioSymbols compatibility to v5.
- ...

25602e1f5834b2749dd17df291200c572b1e3a10 authored over 2 years ago by Ciarán O'Mara <[email protected]>
Merge pull request #72 from CiaranOMara/develop

- Increments BioSequences compatibility to v3.
- Increments BioSymbols compatibility to v5.
- ...

ed087374d3dc199f35fc02a45a974d1e67f01898 authored over 2 years ago by Ciarán O'Mara <[email protected]>
CHANGELOG entries

8125f960dc85b34a001d46d3c6b948d4bad315ca authored over 2 years ago by Ciarán O’Mara <[email protected]>
Merge pull request #78 from CiaranOMara/doctests

- Include doctests as part of the unit tests.
- Doctest corrections.

a5bba8e5833ea4ac8b10d12c78e43bdae727108a authored over 2 years ago by Ciarán O'Mara <[email protected]>
Merge pull request #77 from CiaranOMara/housekeeping

- Backfill CHANGELOG entries.
- Updates CI.

af441d326499924d026ba257d548e3fa491656a1 authored over 2 years ago by Ciarán O'Mara <[email protected]>
Doctest corrections

7e6d24b20de7438ec4997022afead486ef1bd9fd authored over 2 years ago by Ciarán O’Mara <[email protected]>
Adjust test matrix for minimum compatibility

BioSequences v3 requires julia v1.6.

9a61761d841c3131e43b74b42818dab0f7248dc3 authored over 2 years ago by Ciarán O’Mara <[email protected]>
Remove doctest version adjustments

6e1a5484ea5b01c180f40435a8f080d299217edd authored over 2 years ago by Ciarán O’Mara <[email protected]>
Increment compatibilities for BioSequences v3

ff57108c89b779908ed9b1e2a400a45affbf68ce authored over 2 years ago by Ciarán O’Mara <[email protected]>
Merge pull request #78 from CiaranOMara/doctests

- Include doctests as part of the unit tests.
- Doctest corrections.

4045711665388a66d5ba5b2efead361569a7d371 authored over 2 years ago by Ciarán O'Mara <[email protected]>
CHANGELOG entries

30e34fc41b93d85e1aca0fea440bf4f271e31928 authored over 2 years ago by Ciarán O’Mara <[email protected]>
Include doctests as part of the unit tests

fceeeaf5939621daf03307f8d1664fd0632cb08b authored over 2 years ago by Ciarán O’Mara <[email protected]>
Doctest corrections

fd633913ee242545a6a4bec4bda414742348e6ee authored over 2 years ago by Ciarán O’Mara <[email protected]>
Merge pull request #77 from CiaranOMara/housekeeping

- Backfill CHANGELOG entries.
- Updates CI.

84b0d903e80c288a81c9f671c7e8216633ebe49d authored over 2 years ago by Ciarán O'Mara <[email protected]>
CHANGELOG entries

8f97073c82934d9fd39d4981f0f9fa002d889faa authored over 2 years ago by Ciarán O’Mara <[email protected]>
Add julia v1.6 to test matrix

9c7f286cca53cc9d9e8b875f36c9c00193c89c59 authored over 2 years ago by Ciarán O’Mara <[email protected]>
Update workflows

- Update CompatHelper workflow.
- Update TagBot workflow.
- Update docs job in CI workflow.
- Lo...

4a5af007cd189b4436c474960788e7862923c93c authored over 2 years ago by Ciarán O’Mara <[email protected]>
Merge pull request #70 from CiaranOMara/develop

Add downstream tests

f9a84fe6493c497fd75c85f32e375064f48a7dd0 authored over 2 years ago by Ciarán O'Mara <[email protected]>
Merge pull request #53 from jakobnissen/master

Allow compact printing of alignments

cdfa4529fd2d8a5a399c69efb56279a9bef67ac3 authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
Remove Gitter chat links

e9b5c578347c45540cabb9d02db59649881a2840 authored over 2 years ago by Ciarán O’Mara <[email protected]>
Add Zenodo badge

c3b9052f9174266ab8e9a33d6e3c66deadbfbd01 authored over 2 years ago by Kevin Bonham <[email protected]>
update authors

8c978d29b95ce3eb036cf7ed1c65b2967c354e04 authored over 2 years ago by Kevin Bonham <[email protected]>
Merge pull request #71 from CiaranOMara/tagbot

Add ssh key to TagBot workflow

e578e83fb5327491dacb788cc44087d810e93fe7 authored over 2 years ago by Ciarán O'Mara <[email protected]>
Merge pull request #50 from alyst/reinstate_master

Prepare for minor release

0c54bfe14ed9acd93e7a8a7757b4b747a03fe898 authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
Remove Gitter chat links

ebea200c803398ef918e7d7a897553457a4b999e authored almost 3 years ago by Ciarán O’Mara <[email protected]>
Merge pull request #71 from CiaranOMara/tagbot

Add ssh key to TagBot workflow

5f2c790ebf9afa2a7ff38e6e0c44970dff55984e authored almost 3 years ago by Ciarán O'Mara <[email protected]>
Add ssh key to TagBot workflow

The ssh secret is needed to deploy documentation builds triggered by the tag event as the defaul...

81aaf7ce3fd9d2c1624222d55f93f9639267136f authored almost 3 years ago by Ciarán O’Mara <[email protected]>
Merge pull request #70 from CiaranOMara/develop

Add downstream tests

807204eba4ac511f4d42727076fd426b56f8359e authored almost 3 years ago by Ciarán O'Mara <[email protected]>
Add downstream tests

541ea68248a2e0dccbbbaff4bb535907ebb49b0b authored almost 3 years ago by Ciarán O’Mara <[email protected]>
Because of julia version change

1195d3ec8b7059d49b0c9aeaf612eda2ffba0f5e authored almost 3 years ago by Kevin Bonham <[email protected]>
Add Zenodo badge

c49bb0a3cd377ce1652ad6de0718881d05a942d8 authored almost 3 years ago by Kevin Bonham <[email protected]>
Patch version

a97628422b30eac077957439c242a62dea20d8e4 authored almost 3 years ago by Kevin Bonham <[email protected]>
Merge pull request #66 from BioJulia/zenodo-prep

Zenodo Prep

a823d73b390e36965da6cde29082c0aeda9c13a6 authored almost 3 years ago by Ciarán O'Mara <[email protected]>
update authors

81ebf34886bf47ade3d51ba9eb786efcee7433ae authored almost 3 years ago by Kevin Bonham <[email protected]>
update docs with alignment pos introduced by #44 (#61)

36a5e75778ec80cb3b556ea9963184917839c1f9 authored about 3 years ago by Alexey Stukalov <[email protected]>
Merge pull request #53 from jakobnissen/master

Allow compact printing of alignments

5a3354eed4039d9e845adb82da6e144416451132 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Add info to printing and add tests

2c6f47f9a87091872e484d5394fd6ce86c241fdd authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Allow compact printing of alignments

d71c3999f2d2c47ebd02abfe4b2a6decbab724f0 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>
Merge pull request #50 from alyst/reinstate_master

Prepare for minor release

492cd5884b4a8094e003a4e28f0578cb468143f7 authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>
refer to "master" as "cutting edge" dev branch

also switch to "master" for CI documentation builds

fixes #49

ec443b4fd2b6768092c2d7cb49dbcb18f206f127 authored almost 4 years ago by Alexey Stukalov <[email protected]>
Project.toml: remove julia 0.7 from compat

65437b08e90a9f15c9cea3ce9125f3339b8f6a6a authored almost 4 years ago by Alexey Stukalov <[email protected]>
README: use GH actions for build status badge

f4b47176215c1eb56f422d92a65499e4531cf8a9 authored almost 4 years ago by Alexey Stukalov <[email protected]>
update CHANGELOG

401bf3ff6759f3544b4cd879e5250b6d57f10d0e authored almost 4 years ago by Alexey Stukalov <[email protected]>
Merge pull request #44 from alyst/agn_pos

Add alignment string position support

bc9ad529766034f227c71454bb13e7f1354f2e5f authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>