github.com/BioJulia/BioAlignments.jl commits | Ecosyste.ms: OpenCollective

Merge pull request #48 from alyst/fix_registry

Remove BioJuliaRegistry

118c5ad3b614228ac2b67b418b7fb46ca07bbcd8 authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>

alignment position support (seq2aln, ref2aln etc)

- add alnpos to each anchor
- add mapping to/from alnpos
- add alnpos support to traceback

0156de451254f9547af2b8b3f3d6a321bd3d4132 authored almost 4 years ago by Alexey Stukalov <[email protected]>

count_aligned(): optimize with alnpos

cc8237c48ad109036ed0f0da121f780447b7a6fa authored almost 4 years ago by Alexey Stukalov <[email protected]>

refactor seq2ref/ref2seq()

- add position getters for AlignmentAnchor
- convert findanchor() from generated function to nor...

eceb92d9b0346c53cd1d9015b0aed10bd24e43d9 authored almost 4 years ago by Alexey Stukalov <[email protected]>

Alignment: expand docstring

90513fbf4d229b4cf32f94297e703c5cb707b407 authored almost 4 years ago by Alexey Stukalov <[email protected]>

count(pairwisealn): add @inbounds

d920daa9d4b210d5eead01a15d7821b8d847dc4c authored almost 4 years ago by Alexey Stukalov <[email protected]>

AlnAnchor: drop Tuple-based ctor (use splatting)

8b0d70e055daf7bccc57b2df7dd14eaba1e7da0e authored almost 4 years ago by Alexey Stukalov <[email protected]>

check_aln_anchors(): optimize anchors access

ecc954332ae2e9ffe3d5cb4f46aa236bfbaa6cb2 authored almost 4 years ago by Alexey Stukalov <[email protected]>

print(op): don't throw Exception, print ? instead

otherwise Anchors with invalid operation (and these anchors are
created temporarily during trace...

be5b72b64e80a1d8759dd4101d61a23c5c6e6e7d authored almost 4 years ago by Alexey Stukalov <[email protected]>

CompatHelper: use Julia "1" and x64 arch

d830a532c9c1060384930ff097558d01510ca710 authored almost 4 years ago by Alexey Stukalov <[email protected]>

TagBot.yml: don't use BioJuliaRegistry

also it seems TagBot key is not required

de41d911ddda6a64d6bc8fdcbecb8ed84458216b authored almost 4 years ago by Alexey Stukalov <[email protected]>

TagBot.yml: correct when the action is being run

09075ef5db5f0398a25c173f9d6d6b64b04e74b9 authored almost 4 years ago by Alexey Stukalov <[email protected]>

README/index.md: remove BioJuliaRegistry mentions

502858c46394a155f4c3ea865ec3a7bff5337027 authored almost 4 years ago by Alexey Stukalov <[email protected]>

README/index.md: minor formatting corrections

5b60898aa74f2d98bf2657e575e34ad3754f0682 authored almost 4 years ago by Alexey Stukalov <[email protected]>

Merge pull request #47 from alyst/new_ci

New CI based on GH-actions

3e3910c6a750da27f9cdcc74a9fa28b34bae4e8d authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>

runtests.jl: fix sequence type for julia nightly

cc6dc4952d56c4ee194d0fc6fce0bfd00f37a1c8 authored almost 4 years ago by Alexey Stukalov <[email protected]>

ci: add windows-x64

f3dd0390f4fa8f1e6ab0e0f5f77d1f45c7f81e57 authored almost 4 years ago by Alexey Stukalov <[email protected]>

new CI based on GH-actions

* coverage script was removed since it should be handled by
julia-actions/julia-processcoverage@...

56438d6223a0df60342ce1df0e97a57cd0dad1b9 authored almost 4 years ago by Alexey Stukalov <[email protected]>

remove older CI scripts

c2678bb6718365c0c9131eebd6a80f5061096358 authored almost 4 years ago by Alexey Stukalov <[email protected]>

Update CompatHelper.yml

e4fd587642de713170fb03e65087b47541bdaf84 authored over 4 years ago by Ben J. Ward <[email protected]>

Fixup doctest

6e7cdd0f2cf21e8dacbd1cf1fa9a2d80be2fcc3f authored almost 5 years ago by Ben J. Ward <[email protected]>

Fixup docs again

20e9e28443a35b4654a6522a4449efa9e5518a2f authored almost 5 years ago by Ben J. Ward <[email protected]>

Fixup doctests

cffbb05812713799ca06fdb8be1213768500a4a8 authored almost 5 years ago by Ben J. Ward <[email protected]>

Fixup docs Project.toml

d223cae84073b43a3e670fba5bd38af0e46457f8 authored almost 5 years ago by Ben J. Ward <[email protected]>

Fixup docs makefile

12843b164c1a97c96ccf47306a5a8b8cc7801676 authored almost 5 years ago by Ben J. Ward <[email protected]>

Update logo and add Funding file

e2aa3cf1e258265adcbb03b8b972e26a75f08b5b authored almost 5 years ago by Ben J. Ward <[email protected]>

Add TagBot

a3bc19f608d2abbd056852f62aa2ea8d2bc7da8c authored almost 5 years ago by Ben J. Ward <[email protected]>

Increment version (#41)

1f96df7554f570f4472c1c188b7fded8672f4911 authored almost 5 years ago by Ciarán O'Mara <[email protected]>

Add Change log entries

e918d5d8cae805ecc048b799e38f299446a6f0f2 authored almost 5 years ago by Ciarán O'Mara <[email protected]>

Update index/README

784741e83d7bf19b201b80024a4ff3854ba7d048 authored almost 5 years ago by Ciarán O'Mara <[email protected]>

Compatibility updates for BioSequences v2.0.0

1b25c93ccf2367794f4b7d48ae1a7560fc4f9025 authored almost 5 years ago by Ciarán O'Mara <[email protected]>

Migrate from BioCore to BioGenerics

4af228abea47a20a5b0fb9e1bbe2aad9ec2a4901 authored almost 5 years ago by Ciarán O'Mara <[email protected]>

Add BioJulia registry and drop support for older versions of Julia

Pkg's registry handling requires at least Julia 1.1.

26e081b96a81e387ee531ddda7157c6ef4453fc6 authored almost 5 years ago by Ciarán O'Mara <[email protected]>

Remove SAM and BAM IO from documentation

d32d39626c84fbdc54f4293f58198faadaf60f99 authored almost 5 years ago by Ciarán O'Mara <[email protected]>

Remove SAM and BAM

SAM and BAM code has been moved to https://github.com/BioJulia/XAM.jl.

a7f9f1620803a5cfd2de1546277f1175f626de5e authored almost 5 years ago by Ciarán O'Mara <[email protected]>

CompatHelper: bump compat for "Automa" to "0.8" (#40)

Co-authored-by: Ben J. Ward <[email protected]>

09b7fd950750127024e8860e01f07e6639a91cb1 authored almost 5 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

Update an email address

7a3801289a9564acb24c1e364fe68c01cbd332e3 authored almost 5 years ago by Ben J. Ward <[email protected]>

Fix julia compat line

3d5439983b02ec67b204e5062fd93b16e907cea2 authored almost 5 years ago by Ben J. Ward <[email protected]>

Release/v1.0.1 (#39)

* Update .gitignore

* Remove obsolete house keeping files

Code of conduct and contributing...

4219d6522a976d6b92406cd30e23c4cc3d588602 authored almost 5 years ago by Ciarán O'Mara <[email protected]>

USe @info instead of info (#36)

645f76a4b00d34098db2f6b55b63035633a45ff9 authored about 5 years ago by tanhevg <[email protected]>

Fix reading BAM files from processes. (#29)

cb5427ac704f5845a05c5bfeef583a5b2866caf0 authored almost 6 years ago by Daniel C. Jones <[email protected]>

:bug: Fix haskey(x::BAM.Record, y::String) (#24)

Fixes issue #20 by adding a `stop` argument to `getauxvalue` and `findauxtag`

1057799e93ea535d54802b3844e1169c66801260 authored about 6 years ago by Jakob Nybo Nissen <[email protected]>

:bug: Update covert(BAM.Record, x::Vector{UInt8}) (#23)

Implement proposed solution in issue #22
Added test for the fixed function
Changed the format ...

d6650300cd24848313b227a644740876ac92b112 authored about 6 years ago by Jakob Nybo Nissen <[email protected]>

Cap Documenter.jl to 0.19 on Travis (#21)

Documenter 0.20 will introduce breaking changes that will invalidate
existing make.jl setups. T...

8d3e6734f858000b09b1d78c6277983ca50c4baf authored about 6 years ago by Morten Piibeleht <[email protected]>

Ignore .DS_Store files and update docs

54319fd63f964a9d26a8d7a836203b9ab772e9c2 authored over 6 years ago by Ben J. Ward <[email protected]>

Add package sticker

a936274c0ef532ebd081492ddd2ffa3354944188 authored over 6 years ago by Ben J. Ward <[email protected]>

Julia 1.0 support (#18)

8f1bdca96013b855665458c1d2ddbd9614d46ba6 authored over 6 years ago by Daniel C. Jones <[email protected]>

Fix deprecations (#15)

35f1fb702e6348ecb036662adc1f4359e5c6c1c4 authored over 6 years ago by femtocleaner[bot] <femtocleaner[bot]@users.noreply.github.com>

Update CHANGELOG before release

4afde86399e0ae9eea6b0d788ef44a2fedcd20ef authored over 6 years ago by Ben J. Ward <[email protected]>

Remove alias of BioCore

52419aadf69f009b4070b7b9c6f85495b29d35ed authored over 6 years ago by Ben J. Ward <[email protected]>

Update license

3def85be9a9c498e1155d8971be38c48a38fce05 authored over 6 years ago by Ben J. Ward <[email protected]>

Merge github.com:BioJulia/BioAlignments.jl

24556e886b09ace764d2fabf6a72ecf092646a6d authored over 6 years ago by Ben J. Ward <[email protected]>

Make README and HUMANS consistent with that of Bio

63b0b883cb55915eaa730825489c93774dfa37e1 authored over 6 years ago by Ben J. Ward <[email protected]>

Support >65535 CIGAR op-codes in BAM files (#13)

These changes add support for >65535 CIGAR op-codes in
CIGAR strings in BAM records. SAM records...

37abec46a1e4effc3c92d4aaf2ce46e48fcb49ec authored over 6 years ago by Ben J. Ward <[email protected]>

Support >65535 CIGAR op-codes in BAM files (#13)

These changes add support for >65535 CIGAR op-codes in
CIGAR strings in BAM records. SAM records...

2dd8ae1b377a792f1a570546aa2cd8c0a269d072 authored over 6 years ago by Ben J. Ward <[email protected]>

Add flag test for alignment to the positive strand (#14)

* add ispositivestrand flag test for a BAM record

* test for ispositivestrand

* revert a f...

1489ebe01dd507c565e316c0d8585099c89477e2 authored over 6 years ago by Peter Haverty <[email protected]>

Contributing files rollout (#11)

* Rollout file CONTRIBUTING.md

* Rollout file CODE_OF_CONDUCT.md

* Rollout file .github/PU...

11d47d7aad4d51270dc791d0f0a67f2cbdd00e1d authored over 6 years ago by Ben J. Ward <[email protected]>

use where clause for type parameters (#7)

5592f3e0296e099e857c381056af63ad76701e9d authored over 7 years ago by Kenta Sato (佐藤建太) <[email protected]>

Update docs (#6)

1b0a99e1cc37452cd3447ccf515f7992fc7e95ec authored over 7 years ago by Kenta Sato (佐藤建太) <[email protected]>

Drop support of Julia 0.5 (#3)

* require Julia ≥0.6

* drop Compat.jl

* update old-fashioned innter constructors

* upda...

afc14ad80c0b062f231ebc94c656a13f4f313029 authored over 7 years ago by Kenta Sato (佐藤建太) <[email protected]>

README update

d06c829b229388c494de7c5ce4dea7b99635928b authored over 7 years ago by Ben J. Ward <[email protected]>

Merge branch 'release-0.1'

4305fcbbd6e031406808239883d04887f4235401 authored over 7 years ago by Ben J. Ward <[email protected]>

Added Automa, BufferedSteams, and BGZFStreams, and Compat0.17 to require

b7f71910c25fbcdfcf18a78aebdadbc42586c4fb authored over 7 years ago by Ben J. Ward <[email protected]>

fix appveyor.yml (#2)

- Test on 64-bit.
- Add Julia 0.6.
- Allow failure on nightly.

61fc3b4d965496065cbc07cf1a4ca2f620d10256 authored over 7 years ago by Kenta Sato (佐藤建太) <[email protected]>

Update README and docs

9d0806336965f4793bcbc9e1b34df6640046bb4c authored over 7 years ago by Ben J. Ward <[email protected]>

remove max(x) method

286034f9f1bbce80bf225828174447840cf844ea authored over 7 years ago by Kenta Sato <[email protected]>

make eachoverlap accept an Interval-convertible object

c54bb87fd5f68020c10a6bf49c8ea8db211d660c authored over 7 years ago by Kenta Sato <[email protected]>

move HTS docs

896cbd1570e87fd582fe8fca5fe177e9a776dd6b authored over 7 years ago by Kenta Sato <[email protected]>

add __precompile__

a89656d6074fa684af30d7babbd51ea621c509b3 authored over 7 years ago by Kenta Sato <[email protected]>

separate docs on pairwise alignments

8c2600694f28ef00ad2edf1ae535df83385124e9 authored over 7 years ago by Kenta Sato <[email protected]>

add Usage section in the index page

9af6d397f7c26680fa647096d10f00a0491b6276 authored over 7 years ago by Kenta Sato <[email protected]>

print info only when interactive mode

4e505384f50ebeaf5fdc6d9b9aa6b96d760e7174 authored over 7 years ago by Kenta Sato <[email protected]>

make eachoverlap faster for BAM

2154672e6a03456d87579e8c39135156b2929a4e authored over 7 years ago by Kenta Sato <[email protected]>

add docs

23df00a855a6e4151526bc29371fbc5ac8875ef8 authored over 7 years ago by Kenta Sato <[email protected]>

support Julia v0.6 (#1)

* fix type keywords

* fix finish_traceback macro

* use take! instead of takebuf*

* fix ...

e4e2bdf6dd0925a9f3461cdda1f1960e9a37fc76 authored over 7 years ago by Kenta Sato (佐藤建太) <[email protected]>

fix docs link [ci skip]

fcfb4c90803ff02e6c705b2128ff3e9fd8ca6396 authored over 7 years ago by Kenta Sato <[email protected]>

move code from Bio.jl

93d784bc57c653ba4e3873eb29aaf8c18f72c0a6 authored over 7 years ago by Kenta Sato <[email protected]>

BioAlignments.jl generated files.

license: MIT
authors: Kenta Sato
years: 2017
user: bicycle1885

Julia V...

4b15c879871d0eaede2c1408e0d353b89135c1a9 authored over 7 years ago by Kenta Sato <[email protected]>

initial empty commit

6deb8bd9766a2d4e8eb359ee27ac9e846be16d31 authored over 7 years ago by Kenta Sato <[email protected]>