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

Merge pull request #29 from CiaranOMara/hotfix/ensure_buffered_data

Correct `ensure_buffered_data`

bf71956a81a7d4affdcb422bd2686f119a900e1b authored over 1 year ago

Correct `ensure_buffered_data`

The `read_blocks!` function does not necessarily fill/overwrite blocks till `lastindex(stream.bl...

6bc27f91468e55a400fb69901800fa6ed12fe82c authored almost 2 years ago

Add threads to test environment

It appears that the number of threads allowed in CI is capped at 2.

0d628fdc17dc0edbeeada3819d344419874e863d authored almost 2 years ago

Add informational message

Displays the number of threads in used when testing.

5e7a38a4c4a7fa41911d35ba971fcf00422cb284 authored almost 2 years ago

Increment version

84661e854a4465825f2374dce363f7ce566819ec authored almost 2 years ago

Increment version

51af9df5ad5bf929c50cff3f45d4a18481fb276f authored almost 3 years ago

Add downstream tests

ecf347e1ecffc38d47b17c8c24da24a76f7f3ab7 authored almost 3 years ago

Update email addresses

12659aa5621238415037f2578c3762abdaa8b36f authored almost 3 years ago

Add an eof block check (#27)

* Add tests for virtual offset

The virtual offsets produced when writing data should be the s...

5597502592b088ea519e52b66d31011d69a3e23e authored about 3 years ago

Maintenance (#26)

* Update .gitignore

* Add Project.toml

* Update license

* Remove CHANGELOG.md

* Remo...

5535913baf4fbe38c8d83eae88e1f9830f02aa22 authored about 3 years ago

use CodecZlib in place of Libz

37f33e0416ce7c76768854602a2e7e7fecbd4781 authored over 6 years ago

Fix a deprecation (Void -> Cvoid)

cf334309d4c991f2a3d00e62cca93fcd23048adc authored over 6 years ago

update CI scripts

d35108caed5f3be2411260749e393ef2722e7718 authored over 6 years ago

drop Compat.jl

ef4d393454069d7721532cc1abbab084777c4062 authored over 6 years ago

Drop julia 0.6 support.

91e823300f68a270bee38f08ae45a4d9f6eaab45 authored over 6 years ago

Fix a few more deprecations.

7c513f206b045201873327d868b0fccef683e508 authored over 6 years ago

Fix deprecations (#14)

aa82d32c16031d9d85672003b7a347fc8442a7e8 authored over 6 years ago

Support do block syntax with BGZFStreams (#8)

53f6c052be83f01ce79d0fc0f3c1f53caf1fe67c authored over 6 years ago

Add CHANGELOG.md and HUMANS.md files

a41932a06cfe21091dbc7bce707f7f4bc909a7d2 authored over 6 years ago

Increace julia required version to 0.6

f156b6e6912044c9c2bb826088799dcd66c59cf0 authored over 6 years ago

Check if position is supported by a stream before calling. (#12)

c0e0f80286fd2d429b1a92a279685663dd037636 authored over 6 years ago

Contributing files rollout (#13)

* Rollout file CONTRIBUTING.md

* Rollout file CODE_OF_CONDUCT.md

* Rollout file .github/PU...

3de0114ddfa33e122dae6c6374f21a850406d2b4 authored almost 7 years ago

Update CI URLs to point to new caching infrastructure (#10)

e50cc55a73aa32833cc66e4d4e19d1e07efd3d49 authored over 7 years ago

add read and write methods for VirtualOffset (#11)

* add read and write methods for VirtualOffset

* replace nightly with 0.6

92f21180d0be80d382b13c6069e9841795a19284 authored over 7 years ago

drop 0.5 prerelease support

a2167ba32d33f119dee25288e84dc38825ccc2a1 authored almost 8 years ago

fix primitive type definition (#9)

1f1c02cad97baa12b2fa07a5dbc2e61ca423c0b2 authored almost 8 years ago

do not use the using keyword (#7)

7c65d67451485e48a076c1907eb996a169295ba1 authored over 8 years ago

activate precompile (#6)

bc6341de8c2928146d548feb236b20f00fe07976 authored over 8 years ago

add inbounds macros (#5)

ce7430e3bc2d57b2441f10cbb7f21fbe8bccba96 authored over 8 years ago

update README.md

8b02f2b06ccc9486a5262745eadfffa762382154 authored over 8 years ago

support reading data from a pipe (#4)

8b410f0a4dc23cb861a685222441830774e9499a authored over 8 years ago

export BGZFDataError (#3)

a31cecbe801e2b563217f5fb6422efb5d20dd4e8 authored over 8 years ago

rename an internal field (#2)

0ec91c4b486467893be0fac52ca7314aadf71745 authored over 8 years ago

Merge pull request #1 from tkelman/patch-1

use dirname(@__FILE__) rather than Pkg.dir

904e81a5d1cef8002abc6b421171123e9294118b authored over 8 years ago

add testing against 0.5 to Travis

this is the RC now, will be releases once final is tagged

c0be7b64bd043e8b91ff17a2a1bc8325d9781613 authored over 8 years ago

use dirname(@__FILE__) rather than Pkg.dir

allows installing the package elsewhere

37642a4dbd7434a976e53dce758356a99c3cbd4e authored over 8 years ago

set lower bound of Libz requirement

fc5afdd080cc54d0e5f5cb3529a3c0de561e1357 authored over 8 years ago

add tests on BGZFStream

afb61d3c48207440204840f69ef4483368d899ac authored over 8 years ago

add tests on VirtualOffset

0058bd2c36026d15efcd97a12db1276ffdb37b74 authored over 8 years ago

activate code coverage

d74548c627fcc67538cd7f2138e4158a409bdcc4 authored over 8 years ago

fix .travis.yml

1edd90e9a4a1ca08566a130c04441f6126dc695f authored over 8 years ago

fix link of Travis CI

bca951fe6381c8e99935a7e2efd54b80ac938332 authored over 8 years ago

add getindex for VirtualOffset

77b2ac4492f43d0c6755e2e968eaeea4973018d9 authored over 8 years ago

fix some typo

07beac905367840f2661b526887fc0d21f3a116e authored over 8 years ago

update README.md

7ec71f4e2e04026827f0103875f076f9672523cc authored over 8 years ago

check zlib's return code

bd79e831abd2d602a93005102644ee5d6a1cc463 authored over 8 years ago

replacee some ccalls with wrapper functions

7512cb023cab6bd58bbb127622b142a961ea87ec authored over 8 years ago

remove Tabix (moved to a HTS-specific package)

88d88c46cc7496640e2e7f3a007468d172c16bf6 authored over 8 years ago

add seekstart(::BGZFStream)

e8e6413ce71a0a085444042a04747d20da38ade6 authored over 8 years ago

add details on overlapchunks

bf213d7e37d4adb62f40e7846b5d7c2e682f4b22 authored over 8 years ago

add test files

66d10027bf45cab0aaf7946845691d0c11dd7b0c authored over 8 years ago

group tests

6c0c91eaabf3e124f6bb9038bef08cab19302ea6 authored over 8 years ago

add tests on Tabix

e320456ecea9ee439cd297b48cb1f23b46c901ee authored over 8 years ago

add PseudoBin

087bcc689d07f8192ceec1ea07d58667e474311e authored over 8 years ago

fix Tabix fields

c6cb97e5be6ae72f53f06c0289992f175072429f authored over 8 years ago

add reducer of chunks to minimize seek operations

69a1e1faf9b9c591d3800e72734ee7fd7ad94045 authored over 8 years ago

add a docstring for overlapchunks

4b6082f7fd0079ffff23ce82f34c727eeacc51f6 authored over 8 years ago

add (limited) implementation of Tabix

8bc76bab4001c0a4513e0e5970e6a511fb556400 authored over 8 years ago

small renaming and refactoring

27a32727fac2613f8046926a3a15bfbc47c69704 authored over 8 years ago

fix maximum block size

e6152472aaa52d394a1184e1ed6a1f48b2ebd441 authored over 8 years ago

remove a type annotation

d4220e00086b4ba634926dc8e9c9cc538e2dc266 authored over 8 years ago

improve read(x, UInt8) performance

0ddf04bf62b3cdd8b42d6fe6b042a2080e0f1e07 authored over 8 years ago

refactor virtual offset functions

84f03e640f3f9a198becf3da68f8159a8aea8aee authored over 8 years ago

fix threading

1c0bbf141951c71b66c3d74f837423b59267bf04 authored over 8 years ago

fix virtualoffset

1a54e350fefca90eaf4c49a8e142ede7be219d5a authored over 8 years ago

clean up

1fe10f27802563181cda90dcfe7a0f3611252555 authored over 8 years ago

support multi-threading (disable seek tests for a while)

2f6d9f9b1ec69419ab925e69d393eda00115f0d8 authored over 8 years ago

add pretty show method

293f5174822dbbbbf643035d291d3b6fe0151bf5 authored over 8 years ago

test byte-by-byte read/write

e14a98a1bba61802bfae17ac7c17fed659f98f8f authored over 8 years ago

improve performance of reading

5e4ddfae7ac827916b65ef340216dde8ce4c64d5 authored over 8 years ago

check stream is open

28199ad053d049128c6dcdbbf5ca8978865c8bbc authored over 8 years ago

check open mode

9e5047c76deab075367ec2556fd47651d6a46a0f authored over 8 years ago

add tests for empty blocks

254a908da3039c09c60ba6191bba69e4f015bab2 authored over 8 years ago

fix read

39d162bb6f37017bdb4331ddba85f2e56aabfbcb authored over 8 years ago

fix write and unsafe_write

318b74d6e3250854ba6c76741bc0eb8c13d6f509 authored over 8 years ago

do not use temporary files in round-trip tests

2da15672452be97489edabbaf3bbeefc869bd98f authored over 8 years ago

add onclose

e157739eaa7143d0bcf842bd79abb8b8bdd4f04b authored over 8 years ago

clean up things

c5fa98fc344e9d4287e753e8114d22c3eba0e5b5 authored over 8 years ago

add an ASCII figure on internals

44e9cb23a24a43df1687272e752885da3f82cc49 authored over 8 years ago

add unsafe_write

8c4c2add35b8b8546f34340bf02d7ca3dc5ea647 authored over 8 years ago

implement unsafe_read

161764614ca4cd33cefd82c9818e9b6c2b8827af authored over 8 years ago

test zero-length BGZF block

dfe824c8fc5d4eaac46b5f781b033aeea5e6a1b0 authored over 8 years ago

fix deprecated warnings

bc68541806c476e4045f6862b914deda7ab48614 authored over 8 years ago

remove the == definition for virtual offset

274f90c5b824029e32b949e8fb2381c84cc1eba0 authored over 8 years ago

fix zstream initialization

a5f893fd9ae41b496f33de1c23d3b47321e6cc79 authored over 8 years ago

refactor

66fd1d0b4b9eba52be200c1f3f7984109aa24c6c authored over 8 years ago

fix a serious data corruption bug

bc8adf94b088127e93287595b90e2221e593b29d authored over 8 years ago

add virtualoffset(stream)

869174499bb706c53d6e3cb2c556992aa7bc2751 authored over 8 years ago

add a docstring for BGZFStream

db5f46076fb5782f69818de1ad5d4b72ef5b3d36 authored over 8 years ago

add a docstring for virtual offset

99b45b9e57365bdd02d600e0bb12faeda2714912 authored over 8 years ago

fix README

c1742d429cbeea53765e99d154a91703f3c14945 authored over 8 years ago

add README

57c9b03e6f9d301deac63be8fb672f0dc71b9399 authored over 8 years ago

add contents

929e0554318535447d82f5da9c89cac7b493c972 authored over 8 years ago

BGZFStreams.jl generated files.

license: MIT
authors: Kenta Sato
years: 2016
user: bicycle1885

Julia V...

9bace1a6ddc9a7bbaa5134a4b080770b6111e953 authored over 8 years ago

initial empty commit

d61d3abc7b939122cdcaaf1bbfcc13ed20be5eb6 authored over 8 years ago