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BioJulia

Bioinformatics and Computational Biology in Julia
Collective - Host: opensource - https://opencollective.com/biojulia - Website: https://biojulia.net - Code: https://github.com/BioJulia

Merge pull request #38 from pdimens/compathelper/new_version/2020-10-21-00-39-01-821-1863737854

CompatHelper: add new compat entry for "ProgressMeter" at version "1.4"

github.com/BioJulia/PopGen.jl_archive - 19bc662c4f2754eefd5c6b1003d85c2ca79032d4 authored about 4 years ago by Pavel V. Dimens <[email protected]>
Merge branch 'dev' into compathelper/new_version/2020-10-21-00-39-01-821-1863737854

github.com/BioJulia/PopGen.jl_archive - c3baa8ae6db20252b8ede9c86d7b865e70a88ea3 authored about 4 years ago by Pavel V. Dimens <[email protected]>
Merge branch 'dev' into compathelper/new_version/2020-10-21-00-39-01-821-1863737854

github.com/BioJulia/PopGen.jl - c3baa8ae6db20252b8ede9c86d7b865e70a88ea3 authored about 4 years ago by Pavel V. Dimens <[email protected]>
Merge pull request #37 from pdimens/compathelper/new_version/2020-10-21-00-38-48-549-3636675641

CompatHelper: add new compat entry for "PooledArrays" at version "0.5"

github.com/BioJulia/PopGen.jl - 80aa73407e795749ebfa2bf26a424fbdf45d5c9d authored about 4 years ago by Pavel V. Dimens <[email protected]>
Merge pull request #37 from pdimens/compathelper/new_version/2020-10-21-00-38-48-549-3636675641

CompatHelper: add new compat entry for "PooledArrays" at version "0.5"

github.com/BioJulia/PopGen.jl_archive - 80aa73407e795749ebfa2bf26a424fbdf45d5c9d authored about 4 years ago by Pavel V. Dimens <[email protected]>
Merge branch 'dev' into compathelper/new_version/2020-10-21-00-38-48-549-3636675641

github.com/BioJulia/PopGen.jl_archive - a8af53e33652a8c8a735f5d41087eb511b913519 authored about 4 years ago by Pavel V. Dimens <[email protected]>
Merge branch 'dev' into compathelper/new_version/2020-10-21-00-38-48-549-3636675641

github.com/BioJulia/PopGen.jl - a8af53e33652a8c8a735f5d41087eb511b913519 authored about 4 years ago by Pavel V. Dimens <[email protected]>
Merge pull request #36 from pdimens/compathelper/new_version/2020-10-21-00-38-35-372-195295088

CompatHelper: add new compat entry for "StaticArrays" at version "0.12"

github.com/BioJulia/PopGen.jl - 38ed8fb56cced6c40da9996fa489f34423c08d57 authored about 4 years ago by Pavel V. Dimens <[email protected]>
Merge pull request #36 from pdimens/compathelper/new_version/2020-10-21-00-38-35-372-195295088

CompatHelper: add new compat entry for "StaticArrays" at version "0.12"

github.com/BioJulia/PopGen.jl_archive - 38ed8fb56cced6c40da9996fa489f34423c08d57 authored about 4 years ago by Pavel V. Dimens <[email protected]>
Merge branch 'dev' into compathelper/new_version/2020-10-21-00-38-35-372-195295088

github.com/BioJulia/PopGen.jl_archive - 044e644314f183cc2d43193cb84a927ab61e806d authored about 4 years ago by Pavel V. Dimens <[email protected]>
Merge branch 'dev' into compathelper/new_version/2020-10-21-00-38-35-372-195295088

github.com/BioJulia/PopGen.jl - 044e644314f183cc2d43193cb84a927ab61e806d authored about 4 years ago by Pavel V. Dimens <[email protected]>
Merge pull request #35 from pdimens/compathelper/new_version/2020-10-21-00-38-22-290-3951012692

CompatHelper: add new compat entry for "GZip" at version "0.5"

github.com/BioJulia/PopGen.jl - 103279a84f9504f52b9c2ee3522686ab68e3d0a0 authored about 4 years ago by Pavel V. Dimens <[email protected]>
Merge pull request #35 from pdimens/compathelper/new_version/2020-10-21-00-38-22-290-3951012692

CompatHelper: add new compat entry for "GZip" at version "0.5"

github.com/BioJulia/PopGen.jl_archive - 103279a84f9504f52b9c2ee3522686ab68e3d0a0 authored about 4 years ago by Pavel V. Dimens <[email protected]>
Merge pull request #34 from pdimens/compathelper/new_version/2020-10-21-00-38-08-626-3144937314

CompatHelper: add new compat entry for "Requires" at version "1.1"

github.com/BioJulia/PopGen.jl_archive - 8d5beae4a2157e84d4fe7c60fb46b9fba2fc1a8a authored about 4 years ago by Pavel V. Dimens <[email protected]>
Merge pull request #34 from pdimens/compathelper/new_version/2020-10-21-00-38-08-626-3144937314

CompatHelper: add new compat entry for "Requires" at version "1.1"

github.com/BioJulia/PopGen.jl - 8d5beae4a2157e84d4fe7c60fb46b9fba2fc1a8a authored about 4 years ago by Pavel V. Dimens <[email protected]>
CompatHelper: add new compat entry for "ProgressMeter" at version "1.4"

github.com/BioJulia/PopGen.jl - 62f3d4d669b9d911623a416f1c8c4bcc7dd3ee58 authored about 4 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
CompatHelper: add new compat entry for "ProgressMeter" at version "1.4"

github.com/BioJulia/PopGen.jl_archive - 62f3d4d669b9d911623a416f1c8c4bcc7dd3ee58 authored about 4 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
CompatHelper: add new compat entry for "PooledArrays" at version "0.5"

github.com/BioJulia/PopGen.jl_archive - 278f67f14bd3b25262ea3c69eac90641ab71910f authored about 4 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
CompatHelper: add new compat entry for "PooledArrays" at version "0.5"

github.com/BioJulia/PopGen.jl - 278f67f14bd3b25262ea3c69eac90641ab71910f authored about 4 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
CompatHelper: add new compat entry for "StaticArrays" at version "0.12"

github.com/BioJulia/PopGen.jl - 096c0e09c842bde1be47b75562e431bc0b38ba58 authored about 4 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
CompatHelper: add new compat entry for "StaticArrays" at version "0.12"

github.com/BioJulia/PopGen.jl_archive - 096c0e09c842bde1be47b75562e431bc0b38ba58 authored about 4 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
CompatHelper: add new compat entry for "GZip" at version "0.5"

github.com/BioJulia/PopGen.jl_archive - a048017f5b53d972fb8b614e42e8978776a96bbf authored about 4 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
CompatHelper: add new compat entry for "GZip" at version "0.5"

github.com/BioJulia/PopGen.jl - a048017f5b53d972fb8b614e42e8978776a96bbf authored about 4 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
CompatHelper: add new compat entry for "Requires" at version "1.1"

github.com/BioJulia/PopGen.jl - 363af4c970dec21a5bc97786811f2216ea66651c authored about 4 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
CompatHelper: add new compat entry for "Requires" at version "1.1"

github.com/BioJulia/PopGen.jl_archive - 363af4c970dec21a5bc97786811f2216ea66651c authored about 4 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Subset fastq record using string syntax (#35)

* Subset fastq record using string syntax

* fix code coverage

* start adding fastqRead

...

github.com/BioJulia/FASTX.jl - b0c50a4ede503a7e7df590953886835b537a3a6b authored about 4 years ago by Thomas Poulsen <[email protected]>
Make writers parametric and buffered (#26)

github.com/BioJulia/FASTX.jl - b3076c2ab10d328360d17fe91ff761fc26815634 authored about 4 years ago by Jakob Nybo Nissen <[email protected]>
Add constant time fasta index seeking [NEED REVIEW] (#31)

* Add constant time fasta index seeking

* Add index seeking tests and comments

* Add windo...

github.com/BioJulia/FASTX.jl - bb8c980e5cd312e0e7201d8b71b38d84980cd65d authored about 4 years ago by Jakob Nybo Nissen <[email protected]>
Merge pull request #31 from pdimens/compathelper/new_version/2020-09-19-00-31-59-552-1643953571

CompatHelper: bump compat for "JLD2" to "0.2"

github.com/BioJulia/PopGen.jl_archive - 621473ce196a85d9e33d48e5dd103b9871357be2 authored about 4 years ago by Pavel V. Dimens <[email protected]>
Merge pull request #31 from pdimens/compathelper/new_version/2020-09-19-00-31-59-552-1643953571

CompatHelper: bump compat for "JLD2" to "0.2"

github.com/BioJulia/PopGen.jl - 621473ce196a85d9e33d48e5dd103b9871357be2 authored about 4 years ago by Pavel V. Dimens <[email protected]>
Merge pull request #32 from pdimens/compathelper/new_version/2020-10-08-00-29-11-667-4016622870

CompatHelper: bump compat for "Distributions" to "0.24"

github.com/BioJulia/PopGen.jl - bfe3d11c8b4dcf8472416a532314fabe4cc48f5f authored about 4 years ago by Pavel V. Dimens <[email protected]>
Merge pull request #32 from pdimens/compathelper/new_version/2020-10-08-00-29-11-667-4016622870

CompatHelper: bump compat for "Distributions" to "0.24"

github.com/BioJulia/PopGen.jl_archive - bfe3d11c8b4dcf8472416a532314fabe4cc48f5f authored about 4 years ago by Pavel V. Dimens <[email protected]>
Merge pull request #33 from pdimens/kinship

merge Kinship into dev for release staging

github.com/BioJulia/PopGen.jl_archive - d3b8f5bda9f09a9113c011b28333774547c36c36 authored about 4 years ago by Pavel V. Dimens <[email protected]>
Merge pull request #33 from pdimens/kinship

merge Kinship into dev for release staging

github.com/BioJulia/PopGen.jl - d3b8f5bda9f09a9113c011b28333774547c36c36 authored about 4 years ago by Pavel V. Dimens <[email protected]>
Update ci_dev.yaml

github.com/BioJulia/PopGen.jl - 7aae937afb391d5656aad55b14cb19824e1fbe14 authored about 4 years ago by Pavel V. Dimens <[email protected]>
Update ci_dev.yaml

github.com/BioJulia/PopGen.jl_archive - 7aae937afb391d5656aad55b14cb19824e1fbe14 authored about 4 years ago by Pavel V. Dimens <[email protected]>
Make BAM record layout match BAM specs

github.com/BioJulia/XAM.jl - b086fefbd5db44b68ac5945af3c28fbccb3ee30e authored about 4 years ago by Jakob Nissen <[email protected]>
Merge pull request #29 from CiaranOMara/feature/crosscheck

Begin crosschecks

github.com/BioJulia/XAM.jl - 8836b4dbb66e3d0e58c0243b02948542944aef26 authored about 4 years ago by Ciarán O'Mara <[email protected]>
Build website

github.com/BioJulia/biojulia.github.io - 0c7f0a94a3d8320be7ec1bbe0751cfa02c032ba4 authored about 4 years ago by Ben J. Ward <[email protected]>
CompatHelper: bump compat for "StableRNGs" to "1.0" (#122)

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

github.com/BioJulia/BioSequences.jl - 6f0e437e8a2382a68be845486539f8596eb874ab authored about 4 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Make same-type conversion noop (#123)

github.com/BioJulia/BioSequences.jl - 6d99f5e9cacd67d6c2284fa9e04ffc941c7d6c31 authored about 4 years ago by Jakob Nybo Nissen <[email protected]>
Simplify seekrecord (#30)

github.com/BioJulia/FASTX.jl - d5b23c103ec3c8c48bd3527458ee9bf1c8bdf902 authored about 4 years ago by Jakob Nybo Nissen <[email protected]>
Fix windows newline bug (issue 25) (#28)

github.com/BioJulia/FASTX.jl - 8f8218b2e100bf49f67267b59c136efe17a7b3e8 authored about 4 years ago by Jakob Nybo Nissen <[email protected]>
Add header function (#33)

github.com/BioJulia/FASTX.jl - 492275622cbae654de861b8a241ff16c9548b078 authored about 4 years ago by Jakob Nybo Nissen <[email protected]>
fix benchmark import clash

github.com/BioJulia/BioStructures.jl - 7625c94683259314346e5d8f0388a95191987b33 authored about 4 years ago by Joe Greener <[email protected]>
bump version

github.com/BioJulia/BioStructures.jl - 60cf74d60d3ad1fba7de48941efad47b4b1b81ea authored about 4 years ago by Joe Greener <[email protected]>
minor formatting

github.com/BioJulia/BioStructures.jl - a02fad64f6b95f714dce5bf1353b784f7904e35a authored about 4 years ago by Joe Greener <[email protected]>
Add readmultimmcif, writemultimmcif functions (#28)

An mmCIF file can have multiple data_ blocks, thereby
containing multiple `MMCIFDict`s. An exam...

github.com/BioJulia/BioStructures.jl - bfe2c91652d5a0bdef696e024e3ecf55c3603c82 authored about 4 years ago by Marco Matthies <[email protected]>
CompatHelper: bump compat for "Distributions" to "0.24"

github.com/BioJulia/PopGen.jl_archive - 3ec4dfc3fee12e0bb992bc6755afa6abe2dae653 authored about 4 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
CompatHelper: bump compat for "Distributions" to "0.24"

github.com/BioJulia/PopGen.jl - 3ec4dfc3fee12e0bb992bc6755afa6abe2dae653 authored about 4 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
minor formatting

github.com/BioJulia/BioStructures.jl - 467eb8110f14189f3df686333bf83bdd815ecbd7 authored about 4 years ago by Joe Greener <[email protected]>
Tab completion in the REPL for MMCIFDict and MMTFDict (#27)

* Add support for tab-completion of MMCIFDict keys

This is achieved by subtyping from `Abstra...

github.com/BioJulia/BioStructures.jl - e44e4873e2900b9cfa63cbb9aff0d081aaec2c3c authored about 4 years ago by Marco Matthies <[email protected]>
Initial commit

github.com/BioJulia/SequenceVariation.jl - ad3fe4303f29b59a0fe765c0644cbf243c368bb6 authored about 4 years ago by Jakob Nybo Nissen <[email protected]>
bump version

github.com/BioJulia/BioStructures.jl - cbdb7df2fd33eb6d24a1aba75b5d71defe3ef1e3 authored about 4 years ago by Joe Greener <[email protected]>
get method for MMTFDict

github.com/BioJulia/BioStructures.jl - f16e6891d11ea05345951b8cfe67008d19202955 authored about 4 years ago by Joe Greener <[email protected]>
Add ProteinStructure constructors from MMCIFDict and MMTFDict (#26)

* Add ProteinStructure constructors from MMCIFDict and MMTFDict

* Add docs for constructing P...

github.com/BioJulia/BioStructures.jl - 643f1e4139391f64ff19d8372cb76fb4507a5864 authored about 4 years ago by Marco <[email protected]>
bump version

github.com/BioJulia/BioStructures.jl - 996de9a4348115e5770dfc65ce61dc5226caa2b4 authored about 4 years ago by Joe Greener <[email protected]>
Add MMCIF reading and writing with gzip compression (#25)

* Add gzip keyword argument to function signature in docstring for mmtf functions.

* Add MMCI...

github.com/BioJulia/BioStructures.jl - c93edfb51f7d05c67572935be1443e3d8bb7a257 authored about 4 years ago by Marco <[email protected]>
bump version

github.com/BioJulia/BioStructures.jl - 68c891a6237160f5ea49b705d2d9deaa2465c5ea authored about 4 years ago by Joe Greener <[email protected]>
Add get(mmcif, key, default) method for MMCIFDict. (#24)

github.com/BioJulia/BioStructures.jl - e25b96993000a5db816323bbf997a6d2c651505b authored about 4 years ago by Marco <[email protected]>
script to compare mmCIF dicts to Biopython

github.com/BioJulia/BioStructures.jl - e58f6c1fc86ab1e233dc0c0fef207c0161ee343e authored about 4 years ago by Joe Greener <[email protected]>
bump version

github.com/BioJulia/BioStructures.jl - cfa6bc45ad125b865cdde3b58c53a982dbe9e002 authored about 4 years ago by Joe Greener <[email protected]>
allow comment character in mmCIF data value

github.com/BioJulia/BioStructures.jl - 32809c225f79dba59e22741f8cc4c77cc01ef9df authored about 4 years ago by Joe Greener <[email protected]>
parse length(pairs) once

github.com/BioJulia/PopGen.jl - ec116dfa8e3dd06bd52b99d5de86b19d338045ca authored about 4 years ago by Pavel Dimens <[email protected]>
parse length(pairs) once

github.com/BioJulia/PopGen.jl_archive - ec116dfa8e3dd06bd52b99d5de86b19d338045ca authored about 4 years ago by Pavel Dimens <[email protected]>
CompatHelper: bump compat for "JLD2" to "0.2"

github.com/BioJulia/PopGen.jl_archive - 7c762595e2b837b9d5055ca50652c2199f0c3886 authored about 4 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
CompatHelper: bump compat for "JLD2" to "0.2"

github.com/BioJulia/PopGen.jl - 7c762595e2b837b9d5055ca50652c2199f0c3886 authored about 4 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
add Structure file support

github.com/BioJulia/PopGen.jl - 3be7b5fd9a1d8a23c646713a18b8bfca027b23e7 authored about 4 years ago by Pavel Dimens <[email protected]>
add Structure file support

github.com/BioJulia/PopGen.jl_archive - 3be7b5fd9a1d8a23c646713a18b8bfca027b23e7 authored about 4 years ago by Pavel Dimens <[email protected]>
move Simulations.jl to PopGenSims.jl

github.com/BioJulia/PopGen.jl_archive - 3212cc60a459a60650cc939e1b78bbc90274a168 authored about 4 years ago by Pavel Dimens <[email protected]>
move Simulations.jl to PopGenSims.jl

github.com/BioJulia/PopGen.jl - 3212cc60a459a60650cc939e1b78bbc90274a168 authored about 4 years ago by Pavel Dimens <[email protected]>
docstring

github.com/BioJulia/PopGen.jl - ede0c23970c926f24c3855b9bcba15684a4e199f authored about 4 years ago by Pavel Dimens <[email protected]>
add conditions for sim relatedness

github.com/BioJulia/PopGen.jl_archive - a014ca2b778632cb8ea42e6d281c8360b6b4c021 authored about 4 years ago by Pavel Dimens <[email protected]>
add conditions for sim relatedness

github.com/BioJulia/PopGen.jl - a014ca2b778632cb8ea42e6d281c8360b6b4c021 authored about 4 years ago by Pavel Dimens <[email protected]>
add StaticArrays and sort method

github.com/BioJulia/PopGen.jl - cfff2eec335d37b76beb35b030e3a74082d76ef7 authored about 4 years ago by Pavel Dimens <[email protected]>
add StaticArrays and sort method

github.com/BioJulia/PopGen.jl_archive - cfff2eec335d37b76beb35b030e3a74082d76ef7 authored about 4 years ago by Pavel Dimens <[email protected]>
boot output from df to NamedTuple + merge function

github.com/BioJulia/PopGen.jl_archive - 2e3717fb20e702cf5f5c4902b3c0f6d2db3206f2 authored about 4 years ago by Pavel Dimens <[email protected]>
boot output from df to NamedTuple + merge function

github.com/BioJulia/PopGen.jl - 2e3717fb20e702cf5f5c4902b3c0f6d2db3206f2 authored about 4 years ago by Pavel Dimens <[email protected]>
parallelize permutations

github.com/BioJulia/PopGen.jl - b946a37f7ce598e92db2ae0f82af249f59f62622 authored about 4 years ago by Pavel Dimens <[email protected]>
parallelize permutations

github.com/BioJulia/PopGen.jl_archive - b946a37f7ce598e92db2ae0f82af249f59f62622 authored about 4 years ago by Pavel Dimens <[email protected]>
rm depr line

github.com/BioJulia/PopGen.jl_archive - 436172df4f9ab2203d4e8f8f81c66b4adde2b791 authored about 4 years ago by Pavel Dimens <[email protected]>
rm depr line

github.com/BioJulia/PopGen.jl - 436172df4f9ab2203d4e8f8f81c66b4adde2b791 authored about 4 years ago by Pavel Dimens <[email protected]>
fix typo introduced in last commit (oops!)

github.com/BioJulia/PopGen.jl - ccbb96a73558070375b0ea74cac21ee527d598d5 authored about 4 years ago by Pavel Dimens <[email protected]>
fix typo introduced in last commit (oops!)

github.com/BioJulia/PopGen.jl_archive - ccbb96a73558070375b0ea74cac21ee527d598d5 authored about 4 years ago by Pavel Dimens <[email protected]>
swap long<->lat cols in genepop importer

github.com/BioJulia/PopGen.jl_archive - 50cf2565bd73fd57f4ec997ee30b1133c324631a authored about 4 years ago by Pavel Dimens <[email protected]>
swap long<->lat cols in genepop importer

github.com/BioJulia/PopGen.jl - 50cf2565bd73fd57f4ec997ee30b1133c324631a authored about 4 years ago by Pavel Dimens <[email protected]>
Compat fixes

github.com/BioJulia/GeneticVariation.jl - 06cf1001642be35e8e05a7831de33893390e6803 authored about 4 years ago by Rasmus Henningsson <[email protected]>
add write-to-structure

github.com/BioJulia/PopGen.jl_archive - c92dc189d500f05acbcd63ee6b244ccbc5bd1405 authored about 4 years ago by Pavel Dimens <[email protected]>
add write-to-structure

github.com/BioJulia/PopGen.jl - c92dc189d500f05acbcd63ee6b244ccbc5bd1405 authored about 4 years ago by Pavel Dimens <[email protected]>
add fastStructure formatting support

github.com/BioJulia/PopGen.jl - 202c14fd99e4d52efed77e942506918fecee9a5b authored about 4 years ago by Pavel Dimens <[email protected]>
add fastStructure formatting support

github.com/BioJulia/PopGen.jl_archive - 202c14fd99e4d52efed77e942506918fecee9a5b authored about 4 years ago by Pavel Dimens <[email protected]>
add Structure file importer

github.com/BioJulia/PopGen.jl_archive - 70a8d124f30386987a00adafc68cefffc8c4d44d authored about 4 years ago by Pavel Dimens <[email protected]>
add Structure file importer

github.com/BioJulia/PopGen.jl - 70a8d124f30386987a00adafc68cefffc8c4d44d authored about 4 years ago by Pavel Dimens <[email protected]>
fix genepop writing error

github.com/BioJulia/PopGen.jl - bcef39e7363889312f02713e873e6905f3e4928f authored about 4 years ago by Pavel Dimens <[email protected]>