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Bump pysam from 0.22.1 to 0.23.0 in /pipeline/seq_retrieval #525

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Mar 3, 2025
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Bump pysam from 0.22.1 to 0.23.0 in /pipeline/seq_retrieval #525

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2 changes: 1 addition & 1 deletion pipeline/seq_retrieval/pyproject.toml
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Expand Up @@ -11,7 +11,7 @@ requires-python = "==3.12.*"
dependencies = [
"biopython==1.85",
"click==8.1.*",
"pysam==0.22.*",
"pysam==0.23.*",
"requests==2.32.*",
]

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60 changes: 32 additions & 28 deletions pipeline/seq_retrieval/requirements.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -201,34 +201,38 @@ numpy==2.2.3 \
--hash=sha256:f4ca91d61a4bf61b0f2228f24bbfa6a9facd5f8af03759fe2a655c50ae2c6610 \
--hash=sha256:f6b3dfc7661f8842babd8ea07e9897fe3d9b69a1d7e5fbb743e4160f9387833b
# via biopython
pysam==0.22.1 \
--hash=sha256:098e0bf12d8b0399613065843310c91ba31a02d014b1f6b4e9d7f2d0d1254ff8 \
--hash=sha256:17fac22fc89c86241a71084ca097878c61c97f6ff5fd4535d718681a849852a7 \
--hash=sha256:18a0b97be95bd71e584de698441c46651cdff378db1c9a4fb3f541e560253b22 \
--hash=sha256:18d886d50d75d8f853057fbbb284f0f0e98afad1f76b1a6f55660ea167d31c17 \
--hash=sha256:1be663a73cf56ddd1d309b91d314a0c94c9bf352eaa3c6eda30cef12699843f0 \
--hash=sha256:2b6cf1871c99cfc9c01261ec5f628519c2c889f0ff070e7a26aa5adbf9f69af1 \
--hash=sha256:44420290a619c02da48ca0956548eb82a1665ae97b6ee69c094f9da5a6206431 \
--hash=sha256:4447fdc2630519a00b6bf598995f1440e6f398eb0c084a7c141db026990ae07a \
--hash=sha256:4aff9b41856d5dba6585ffd60884b8f3778c5d2688f33989662aabe7f4cd0fe0 \
--hash=sha256:4dfae1de006d1c6491a59b00052a3f67c53a136165cf4edd7789b5dcb1e6806f \
--hash=sha256:503c833e6cf348d87aec9113b1386d5c85c031d64deb914c29f5ad1792d103e6 \
--hash=sha256:78ed746a39c9cebe489b8f0f86cf23c09c942e76c901260fb2794906e4cd0e26 \
--hash=sha256:79cd94eeb96541385fa99e759a8f83d21428e092c8b577d50b4eee5823e757cd \
--hash=sha256:860c7c78ddb1539b83d5476502ba14c8b4e8435810dc7a5b715196da3dfb86b6 \
--hash=sha256:ab3343f221994d163e1ba2691430ce0f6e7da13762473e0d7f9a2d5db3bec235 \
--hash=sha256:acff506c921af36f364c5a87f3a30b3c105ebeb270d0e821c2ca571eaf60ca20 \
--hash=sha256:aeb31472365014fd8b37da4a88af758094b5872a8a16a25635a52cf8ceff5a9f \
--hash=sha256:af9fb53157ba2431b7b20a550c0223f4a039304c9f180d8da98ea9d2d3ef3fbf \
--hash=sha256:b1addca11c5cfceefaebdfcf3d83bc42f4b89fb1e8ae645a4bdab971cbcd2bc0 \
--hash=sha256:c0e051fda433c1c7ff94532f60477bb83b97f4bb183567a0ae23f340e1c200b4 \
--hash=sha256:c71ea45461ee596949061f321a799a97c418164485fdd7e8db89aea2ff979092 \
--hash=sha256:cd9d457063272df16136640515183ea501bf3371f140a134b2f0a42f425a37d9 \
--hash=sha256:d3fd6fe5aca79933632f38e5b568ce8d4e67e5c4f3bd39bff55fd9646af814d2 \
--hash=sha256:e72e129d245574801125029a5892c9e18d2956b13c4203ea585cbd64ccde9351 \
--hash=sha256:f18e72013ef2db9a9bb7e8ac421934d054427f6c03e66ce8abc39b09c846ba72 \
--hash=sha256:f8f00bb1fb977fc33c87cf5fe9023eefc2ba3d43d30ab4875a1765827018c949 \
--hash=sha256:faa5298291b54f185c7b8f84510224918bddc64bbdcb2e8426ff43e83452310f
pysam==0.23.0 \
--hash=sha256:03f50e567ccbac028aec7ce5edc1d4962489cfd5eeeee423ca276abe01dc0a24 \
--hash=sha256:0bb793bd7fcabb416991607877fe4dfdc7109f73256ed5d2e1e7ed4a68c39167 \
--hash=sha256:1631c173363475c409352d9bf3ad96e7ff851ba903e5b979f55330f0b41d9b5d \
--hash=sha256:2572519dc4b668e8e45d38335233e119cc93fa671fa03099e6f651be032370a6 \
--hash=sha256:2ed8717c12580e76b9656af231c03254bb745bf1afc6d6556d0a27626443c48d \
--hash=sha256:338d7e292f76d157ba2c7bb3ccdd9a071f164b44250ea89672b4946e3518146f \
--hash=sha256:3e1e12d078f3780173ee34990ba737427768fb332d3a1910aae5fb32bb2499fa \
--hash=sha256:3e3616d3e0a86a87cfde1e89896315961a7a409170dca038c24a756309c8e0d5 \
--hash=sha256:41272520d47a428c4d17441eab88d7c5b1ad609ba729cc0cd96960b8a8589e93 \
--hash=sha256:45abd654f6f53e938238bb9472a7c0b992c384c0bef7e51f248b0502c99964b1 \
--hash=sha256:4923c614adf642ffc7620a76faf38f57f2d834b1ba4ab567596db2ac6266038f \
--hash=sha256:4e00a02e9d5e34902c90817d742c58862493b57ccb70144927869d28a91accfc \
--hash=sha256:4f1b976bff84b99acb90276f396e7853359a8ea3a2a5fbcb69f3ceed4027761d \
--hash=sha256:4fd54bae72a832317aab23ad45970f9091ac2c7c233c5a6826941095fbd7f103 \
--hash=sha256:5a0ef49772d4546b2a75f0448b91cf9b9e6d4124bda8747e891383570d51b50e \
--hash=sha256:5a795db60b648902d1886faf9d3575dbd3f199736fda27504b8237b684b74710 \
--hash=sha256:79201b1ed82308540e7be69de9f73719e381f45d9e0e6310a46c6e56092967b2 \
--hash=sha256:81488b3c7e0efc614395e21acde8bdb21c7adafea31736e733173ac7afac0c3e \
--hash=sha256:81dc7b4418d6006ff3e16e5419f5d26a25d959efc1e9807cf56190ca0f68012a \
--hash=sha256:86c5ce45690348dcd11dfe7163624ba18dd945ba57d7a064593b78ddcb8e3e72 \
--hash=sha256:9ee2ef5f3452bc84834163a881269efed56d1be5045865b5af74d010aee4b44c \
--hash=sha256:a061857f8bd723f0f223ec986b0b955f28ddea3b330a767f3c39daaca5908e39 \
--hash=sha256:ab8d993dbbe5af916f1b5f0dac00705a1fa20185b64ed9f3dd66d15850338c65 \
--hash=sha256:ada6096aca1f188289832d7963137d5e9ffe9454d688c57a2cca563de4601545 \
--hash=sha256:b13eb322ad3726b214df3fe54249af5d91bfca6e4a64abe9f293348edae397e8 \
--hash=sha256:caf8f1cef87663d38228b01885f8ffb13d6a9bc2ba3ff958f79d6c1af3fb84c2 \
--hash=sha256:e0426928e676e5d9f8320cd09741be905f90be5c7133f3ad386c7d1be84930ff \
--hash=sha256:e32afcd92a6686696147bbad7e7a8d779791e495a9f1ab814daba5e211659716 \
--hash=sha256:e454f282f6ace01c5c293e3f1bc4bb2ee844f6d5b8686bffe7e02d7e0089a73e \
--hash=sha256:e681d04efe21040b3888f7484f84a2636433503cfb903bbf9b91d671726ceaed \
--hash=sha256:fd936bdd2a2a7412e96a0797da052d7a50745f0254a934ee590d10485776be58
# via seq-retrieval (pyproject.toml)
requests==2.32.3 \
--hash=sha256:55365417734eb18255590a9ff9eb97e9e1da868d4ccd6402399eaf68af20a760 \
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60 changes: 32 additions & 28 deletions pipeline/seq_retrieval/tests/requirements.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -338,34 +338,38 @@ pyflakes==3.2.0 \
--hash=sha256:1c61603ff154621fb2a9172037d84dca3500def8c8b630657d1701f026f8af3f \
--hash=sha256:84b5be138a2dfbb40689ca07e2152deb896a65c3a3e24c251c5c62489568074a
# via flake8
pysam==0.22.1 \
--hash=sha256:098e0bf12d8b0399613065843310c91ba31a02d014b1f6b4e9d7f2d0d1254ff8 \
--hash=sha256:17fac22fc89c86241a71084ca097878c61c97f6ff5fd4535d718681a849852a7 \
--hash=sha256:18a0b97be95bd71e584de698441c46651cdff378db1c9a4fb3f541e560253b22 \
--hash=sha256:18d886d50d75d8f853057fbbb284f0f0e98afad1f76b1a6f55660ea167d31c17 \
--hash=sha256:1be663a73cf56ddd1d309b91d314a0c94c9bf352eaa3c6eda30cef12699843f0 \
--hash=sha256:2b6cf1871c99cfc9c01261ec5f628519c2c889f0ff070e7a26aa5adbf9f69af1 \
--hash=sha256:44420290a619c02da48ca0956548eb82a1665ae97b6ee69c094f9da5a6206431 \
--hash=sha256:4447fdc2630519a00b6bf598995f1440e6f398eb0c084a7c141db026990ae07a \
--hash=sha256:4aff9b41856d5dba6585ffd60884b8f3778c5d2688f33989662aabe7f4cd0fe0 \
--hash=sha256:4dfae1de006d1c6491a59b00052a3f67c53a136165cf4edd7789b5dcb1e6806f \
--hash=sha256:503c833e6cf348d87aec9113b1386d5c85c031d64deb914c29f5ad1792d103e6 \
--hash=sha256:78ed746a39c9cebe489b8f0f86cf23c09c942e76c901260fb2794906e4cd0e26 \
--hash=sha256:79cd94eeb96541385fa99e759a8f83d21428e092c8b577d50b4eee5823e757cd \
--hash=sha256:860c7c78ddb1539b83d5476502ba14c8b4e8435810dc7a5b715196da3dfb86b6 \
--hash=sha256:ab3343f221994d163e1ba2691430ce0f6e7da13762473e0d7f9a2d5db3bec235 \
--hash=sha256:acff506c921af36f364c5a87f3a30b3c105ebeb270d0e821c2ca571eaf60ca20 \
--hash=sha256:aeb31472365014fd8b37da4a88af758094b5872a8a16a25635a52cf8ceff5a9f \
--hash=sha256:af9fb53157ba2431b7b20a550c0223f4a039304c9f180d8da98ea9d2d3ef3fbf \
--hash=sha256:b1addca11c5cfceefaebdfcf3d83bc42f4b89fb1e8ae645a4bdab971cbcd2bc0 \
--hash=sha256:c0e051fda433c1c7ff94532f60477bb83b97f4bb183567a0ae23f340e1c200b4 \
--hash=sha256:c71ea45461ee596949061f321a799a97c418164485fdd7e8db89aea2ff979092 \
--hash=sha256:cd9d457063272df16136640515183ea501bf3371f140a134b2f0a42f425a37d9 \
--hash=sha256:d3fd6fe5aca79933632f38e5b568ce8d4e67e5c4f3bd39bff55fd9646af814d2 \
--hash=sha256:e72e129d245574801125029a5892c9e18d2956b13c4203ea585cbd64ccde9351 \
--hash=sha256:f18e72013ef2db9a9bb7e8ac421934d054427f6c03e66ce8abc39b09c846ba72 \
--hash=sha256:f8f00bb1fb977fc33c87cf5fe9023eefc2ba3d43d30ab4875a1765827018c949 \
--hash=sha256:faa5298291b54f185c7b8f84510224918bddc64bbdcb2e8426ff43e83452310f
pysam==0.23.0 \
--hash=sha256:03f50e567ccbac028aec7ce5edc1d4962489cfd5eeeee423ca276abe01dc0a24 \
--hash=sha256:0bb793bd7fcabb416991607877fe4dfdc7109f73256ed5d2e1e7ed4a68c39167 \
--hash=sha256:1631c173363475c409352d9bf3ad96e7ff851ba903e5b979f55330f0b41d9b5d \
--hash=sha256:2572519dc4b668e8e45d38335233e119cc93fa671fa03099e6f651be032370a6 \
--hash=sha256:2ed8717c12580e76b9656af231c03254bb745bf1afc6d6556d0a27626443c48d \
--hash=sha256:338d7e292f76d157ba2c7bb3ccdd9a071f164b44250ea89672b4946e3518146f \
--hash=sha256:3e1e12d078f3780173ee34990ba737427768fb332d3a1910aae5fb32bb2499fa \
--hash=sha256:3e3616d3e0a86a87cfde1e89896315961a7a409170dca038c24a756309c8e0d5 \
--hash=sha256:41272520d47a428c4d17441eab88d7c5b1ad609ba729cc0cd96960b8a8589e93 \
--hash=sha256:45abd654f6f53e938238bb9472a7c0b992c384c0bef7e51f248b0502c99964b1 \
--hash=sha256:4923c614adf642ffc7620a76faf38f57f2d834b1ba4ab567596db2ac6266038f \
--hash=sha256:4e00a02e9d5e34902c90817d742c58862493b57ccb70144927869d28a91accfc \
--hash=sha256:4f1b976bff84b99acb90276f396e7853359a8ea3a2a5fbcb69f3ceed4027761d \
--hash=sha256:4fd54bae72a832317aab23ad45970f9091ac2c7c233c5a6826941095fbd7f103 \
--hash=sha256:5a0ef49772d4546b2a75f0448b91cf9b9e6d4124bda8747e891383570d51b50e \
--hash=sha256:5a795db60b648902d1886faf9d3575dbd3f199736fda27504b8237b684b74710 \
--hash=sha256:79201b1ed82308540e7be69de9f73719e381f45d9e0e6310a46c6e56092967b2 \
--hash=sha256:81488b3c7e0efc614395e21acde8bdb21c7adafea31736e733173ac7afac0c3e \
--hash=sha256:81dc7b4418d6006ff3e16e5419f5d26a25d959efc1e9807cf56190ca0f68012a \
--hash=sha256:86c5ce45690348dcd11dfe7163624ba18dd945ba57d7a064593b78ddcb8e3e72 \
--hash=sha256:9ee2ef5f3452bc84834163a881269efed56d1be5045865b5af74d010aee4b44c \
--hash=sha256:a061857f8bd723f0f223ec986b0b955f28ddea3b330a767f3c39daaca5908e39 \
--hash=sha256:ab8d993dbbe5af916f1b5f0dac00705a1fa20185b64ed9f3dd66d15850338c65 \
--hash=sha256:ada6096aca1f188289832d7963137d5e9ffe9454d688c57a2cca563de4601545 \
--hash=sha256:b13eb322ad3726b214df3fe54249af5d91bfca6e4a64abe9f293348edae397e8 \
--hash=sha256:caf8f1cef87663d38228b01885f8ffb13d6a9bc2ba3ff958f79d6c1af3fb84c2 \
--hash=sha256:e0426928e676e5d9f8320cd09741be905f90be5c7133f3ad386c7d1be84930ff \
--hash=sha256:e32afcd92a6686696147bbad7e7a8d779791e495a9f1ab814daba5e211659716 \
--hash=sha256:e454f282f6ace01c5c293e3f1bc4bb2ee844f6d5b8686bffe7e02d7e0089a73e \
--hash=sha256:e681d04efe21040b3888f7484f84a2636433503cfb903bbf9b91d671726ceaed \
--hash=sha256:fd936bdd2a2a7412e96a0797da052d7a50745f0254a934ee590d10485776be58
# via seq-retrieval (pyproject.toml)
pytest==8.3.5 \
--hash=sha256:c69214aa47deac29fad6c2a4f590b9c4a9fdb16a403176fe154b79c0b4d4d820 \
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