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Project description

Convert vcf in parquet 🧬 💻

License CI Documentation CodeCov

Install

mamba install vcf2parquet

Usage

vcf2parquet-bin

USAGE:
    vcf2parquet [OPTIONS] --input <INPUT> <SUBCOMMAND>

OPTIONS:
    -b, --batch-size <BATCH_SIZE>      Batch size (default 100,000)
    -c, --compression <COMPRESSION>    Compression method (default snappy) [possible values:
                                       uncompressed, snappy, gzip, lzo, brotli, lz4]
    -h, --help                         Print help information
    -i, --input <INPUT>                Input path

SUBCOMMANDS:
    convert    Convert a vcf in a parquet
    help       Print this message or the help of the given subcommand(s)
    split      Convert a vcf in multiple parquet file each file contains `batch_size` record

Subcommand convert and split change how output is write.

vcf2parquet -i {input}.vcf.[gz|bz2|xz] convert -o {output}.parquet
vcf2parquet -i {input}.vcf.[gz|bz2|xz] -c lz4 -b 10000 convert -o {output}.parquet
vcf2parquet -i {input}.vcf.[gz|bz2|xz] split -f format_partition_{}.parquet

Minimum supported Rust version

Currently the minimum supported Rust version is 1.74.1.

Project details


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SHA256 dd5d1f9d9601983ebd669b327e32dff09b922f278b054bcc5b42a59b651fad7c
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SHA256 a5839d767acc3f4578b62701906eb8a5c3c60690b40aa456e7454ca82cfe79a0
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SHA256 5da6e2bcb558d18b7282f48f6cd90998fe5c9eeab8a101079bb19b1b89b15b75
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SHA256 4354e9c93b84d1444d3fbe29bb8d4653bf65ad0a3e97b2764e441da978f03534
MD5 c53fc3414df3faeb3e5feac322d437c1
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SHA256 33d92965ee3084cfc6e0f4d1779ab71698a86e17f6e6af8b729efdc11168591c
MD5 3764abbba272b479d989dfca80a0e690
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SHA256 30e63c00c67cd03f9381e5d0d031214191884ee69725a4c28ab051afc9300a8d
MD5 b24c5a2ddf4bee847fb6a0b3569f917b
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SHA256 b785a442d4887d09271d9cd1f692b81ce62b53d7fcde15ba0596e4e16d2122b7
MD5 7e19164e9eff68ae8aaed46c068c1bfb
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SHA256 03323123aa3c5f8571ed1a92f6247ccd11dbb77c21f44f0f635700f950866513
MD5 036972d54994b83ce191bc9463d7d0d0
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SHA256 beae2aa01bac6547b1cd8470e81111f12ddfe22cbb28b5be0a6cf9a643b0545b
MD5 2e3feacd35988422e353869cb68f1a94
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SHA256 050ebcf73da86f63207843535a78aa7ce003a851e431ca0e83acbf0c6bea5325
MD5 a09eb458bb6170f2cfdc85197934ec67
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SHA256 29fffa80ed388bd729069311a820fe6cb0d33f5d25c59246a47a19249ac76e8b
MD5 a3f2a0b32d676652050c82c239fb61bb
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SHA256 e52884382bf22f84cd49ea42fe2b5e52b17787789d837de2212d154eb0c7202f
MD5 dd65d316621f16b4a042725bc4568a7c
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SHA256 011622faefd2beda05069fab6d51bf1647f9b9e2a2c4b107686001cb3fcc4428
MD5 e03f309d9b05694532cb8906699371ac
BLAKE2b-256 149d2d512a6243bebab683687af1c52921765afafe9635dc5bc601242d67bf4b

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SHA256 e906ee95eb41646cd331e9bf2ffe8950e2deda442b5b6c1a519bb27cebd396c2
MD5 5c9832f2cfc4f523c81d2f3e1dff3c2e
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SHA256 21e65d2dda626bf38ad32f326ddf9c8b70b070e69796809055d7bc976c3f3520
MD5 fbf8e14d5fe6af2d62bc25f0a8325474
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SHA256 6252c9c29b3d4e6a6f56356bd44ede17cb4e13a8f1df85262bea43faca11574a
MD5 482668a6030d2538710c70aafb42ef82
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SHA256 63c2820fb62c0bb72723101597cfdc52b156ce71354ca59a47d9278d5a3e4eac
MD5 fdbdf73f42cc455026fbff5aea374850
BLAKE2b-256 46df952c8f3f441331721067da1fbcba0196c13587f0380193e3b59717fd1812

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SHA256 905fe25f7127c3965602687e0b6316e60b40f85d6581f8dec45056a731f6926d
MD5 85e14d8586659f68e693b3ba855c8efe
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SHA256 f8b185388fec3fd5705a510e519be8949666774fca4082aef8af3c29c17dbca5
MD5 ba6f2de913be904893d2d4892e4e1d9e
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SHA256 bba0305f7a7d6f46254257b0bc20a274375bce8ff9fd50563764fc90dd917621
MD5 66c9e983282e2038d68eaaa79758ddd1
BLAKE2b-256 521c2875d1815ff5658a918a6c33da8c0bc891b31ed58170c725c55f649f384d

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SHA256 08c6acfeebe501caa02805978c632b2fe49a729a26c0ca23fdd527aca221ebe4
MD5 6010eabb0b8be0373f6eb86285a818d0
BLAKE2b-256 a6b93446a51bdf404a5ce5df4d8d983639474caf93d655156eac0e7e7b19c1b4

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SHA256 2a405f43a2c4ef0f172a7bd69f5fbb93e6b73010e8ef24e5ce690c6e2318bab2
MD5 3972826ffb6a667c3f2e1d132fc38f13
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SHA256 557b6cefa30be4ee99f21a510e49865f7ecf1b07ecdbafdaed9e818d80ec57cf
MD5 b38d97cfeb7e4b84ba0799b2f2901d40
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SHA256 86b065ec823d6b08e970228a652a205dc082aab3d74656bee835dd78a83eda70
MD5 ff452ac0cb5969190b8ee56e0f7c402c
BLAKE2b-256 15544ebdc8377f71ce1867afe5fa7dc2e49bb878227aed98fa01a413aabe22c4

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SHA256 ae715026b2e1dd5e29cc0d07a3b57793367d58e11d0ff7bf687bdd879edd5bae
MD5 fa35e04702547869d0be9b6b0ce72ba9
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SHA256 dcfc9e24518954c4a9301dbd2d2c4db2d6dfed626a55ef940eb69b080dea83c9
MD5 f577611ca0e0e34a5ab765132139453f
BLAKE2b-256 591a4f5774f78f541129ce0b7e91e8ac1828c01810088ca1e00e14d69204eb99

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Algorithm Hash digest
SHA256 ca13acac0c5d05838627c0f56ecfb51dafe044494512c095b5e39a8b28262a11
MD5 a589b40d18f422485a36295b609061fe
BLAKE2b-256 eb754bb5a6b4ed7050104ea880626748e82088ec0642b3844e2d20b9a3aa1cff

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Algorithm Hash digest
SHA256 4e1671321107a818fef13744af5fb61bfbbd45b1c862a2dad751d8b353e18618
MD5 5b98e29dcd00957c21baf808a5264db5
BLAKE2b-256 887c5402398e853d6007a7afbcee0b6008ac092c72dd749ead248bbbc49fe01b

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Algorithm Hash digest
SHA256 39cc9435dd700b1cce0105f7106bb8b817977c3b29b36dd8e531997ac5584272
MD5 32020d402c679b34ad7eb884fc470c2d
BLAKE2b-256 213969c5578671d814d2cfa12954a4d0624e6276f4173b5fabaa7a5167362066

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SHA256 1585ababb701ed1e7674f9cf834ce79f9ec8dbcdccc0519ddd5596e510e0cec8
MD5 9a9e30263fa0396f7c2e2fb2cd5bf11c
BLAKE2b-256 397624307fc189251cc34a5b0cb8609d9224f20dd44a532a458c81311e084ba1

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Algorithm Hash digest
SHA256 34d5df4e636d6f904bc5909dc56c82b8e97cdf0fb1c8b490df4361b7ded6fa13
MD5 ceb8771d8aa0f253f37706050cbfae99
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Algorithm Hash digest
SHA256 0cd26ab668804c8d73655c57d4ae8a3b07b15ed3214df183cf7a35d7d7a94072
MD5 26b01df0e8661b43047cfceae85f9212
BLAKE2b-256 e1e3b7adb2f7568852e0aff8b147a877947483f5716adc47e87e990d9d258382

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Algorithm Hash digest
SHA256 ffcbebb250434aae5d63788bff1cdf7c42767fae209cca13c7e89405581099e0
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SHA256 b3d584b22c98d63336aa93ab0a04fb5dfca9a034c3502262d72e9eedd76745eb
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SHA256 b52cba829645b537e5883c8ff48b627115e2fd09fff81d7a8c491f32391f8d5c
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SHA256 e322db3a4cf4f863a0e66e6e23009fc6adc9f47da64ec6399ba2198d65101b27
MD5 e1db9a1cc3a710a2456d77ceff553be3
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SHA256 c9b22e0135ab2c20dad860f17365c7f211e7ec879078116c6ce80beb9bde842f
MD5 74eadea0bfeecf1c0720a4a129fd4da7
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SHA256 8b24db4b557d364b40c9d5eb0fd4d6e58a5f250607e2a070294ff71ae925db40
MD5 b58948842ac8757ebd4eb6af9738b378
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SHA256 d114068337c7639f189ba2d167c9428bd80bf80c7cc28666ddb15a10863cc39c
MD5 5eaa94899cdf801d85d2edd2cf61d313
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SHA256 2df5256f9e731703f10df1055f2674571af8f4699ec166583b0fd912c15e59cd
MD5 8de223a13fe86fc9ee2ac159299910a6
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SHA256 62c9ddb70a69cf70dd748d93ccebc6b11d984a84fffdb3094be58b64dd0e7d3f
MD5 769e5ec05c9727ddc64c6d2ff09926d9
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SHA256 58a089d5c30e31654be3582b26e7bfacbbbba6b34b1cf5ad0b58d9a27bf23c54
MD5 b13117008cb4eaef96e80f958bfe9fdf
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SHA256 c9220010f38b2e0a9b9a76094f9ae6f84121508394901b95d9df2a2d359c985c
MD5 0fcf510546160bc98f56c8c46b1d9201
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SHA256 5d61a6daad40cf0c91dabfc615f061d1fcf4f94b9064a30bbcd1ac4bdac97094
MD5 bcf7c7e597d43c0d9c7b59d3da77f20a
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SHA256 c0a2e3d3c427ef00143933540f62f4c84bb1879e4156fb38952291626e400bb3
MD5 314d7aabd770f650b3d9c30cace7ce9d
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Algorithm Hash digest
SHA256 e3897c67b7c111be66be1608745d1ca891d92fadaffec2a9b49c2a770c6d4d6f
MD5 e5625778439a8fe3f1afaee265d61c51
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Algorithm Hash digest
SHA256 48a734f45a143e288e0b421627fe9e621e4d19ca92fd83cfa825c10ea22b9f04
MD5 ace52c1a1dd8816617dbc9f004588a70
BLAKE2b-256 8bafdca21f0444df763dfac087d227f306c65470e795df9b8ab24a87933bbd51

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Algorithm Hash digest
SHA256 28dfdf5576ec4782937ac0c8eb8546ee2d8adbc1e5b9fd4b9776737d123897b5
MD5 bca31c6f975f89f1b0232348ef33ee3d
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Algorithm Hash digest
SHA256 c515d8f69517ac9b06b1e53889229d272c989136bc3942a5a49d4fccc31b54a6
MD5 827aa1a9d497930e2231f229369fdb6a
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Algorithm Hash digest
SHA256 21b3561bb041820f0cfd42505c7b9749d3807506d7915fead8d3f244560330aa
MD5 332e492a34b7fe2ce23fb418521a0020
BLAKE2b-256 27bfe9b9e301da49ee043355f37c36072714eef3dcdf4d17abc29df0f149c379

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Algorithm Hash digest
SHA256 99fabd90864a8bfae56ccfd63731a7449aaf7b68567318f622a896444243fa5e
MD5 412b0cdde4cf5ad8427f802b1a6e976c
BLAKE2b-256 db91a69cfdf14215f89ede8cd77567a8ea4ea81483f12f8ae9718a5f302c32c0

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Algorithm Hash digest
SHA256 b1e783a244269e473246c8d34e2e75af3a815d88eb59cae56e3efb7a916f7ee5
MD5 6128ac4e949b6426c9305926f0d6ae6d
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SHA256 951901c3264671307a265fd3441aa79bf2734383252d832f908db7d73f77783b
MD5 df5d4d48eef320018bb2d7e3d95fac62
BLAKE2b-256 312e0ea8629704b23f40baa45e8eb966f75a59add38b1fa9e51d94e3bd185f50

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SHA256 7884ed4be40d72c2d376c8db8e9f20556c527e635b671f85925a5a4d6378336b
MD5 1ba0acd2e36d62e16155379fededee62
BLAKE2b-256 662454dd8bf7bddd4dfe3d3da0e94d29a219e2eeecf6c3674775382ddb4f84a2

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SHA256 4d12e91c919583bff76cd7fc02c0a6d75ea5e8b51777d88dfdd1320158e32e4a
MD5 4024af8622b410dbf375ff36273bf81e
BLAKE2b-256 cf62c3b42da0b58478cb538d722a7134f5baf888347e1ff7b0ab4609516f10a4

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Algorithm Hash digest
SHA256 e0161d599fe76f0a98f664a71c7b8971e08b5d8e33de1d34c8c96c54e151ce42
MD5 0258a7337c3420893c4366b45698d056
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SHA256 ebf44fdca51179c5033e411d57670a4667013f4230988bbf8540ef2a1df634d7
MD5 5b9d10984c7a05660dd6f576aa458b8a
BLAKE2b-256 82b9eb40d849298d2450aada09113f4fc70975dd71a2f201892d694ed5251f71

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SHA256 cc6a88633c4658fea573590f7fb4e3a0b6b5f2b1fdbd908fb9f914a7296546a7
MD5 be3f49d4372a7543dd96ccb98bf6bb49
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Algorithm Hash digest
SHA256 695116c459614ac9b1d0212536251118a77903e73a2977c12f199b94076c5419
MD5 b7488e48d77797ae866b67953dded6e5
BLAKE2b-256 078d852e9c9d8c118e6ab54edd81f7a9f71672848ed71f1b9652fa532534e9d3

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SHA256 7602dfc8f4092519228455200dff67829200d3c0a68138c398987e1bb8409dbc
MD5 78432f220c0a7a0397d1ea5e5cd3d2cc
BLAKE2b-256 dd42eaa352e902ae98368709eb5ffc2426520dea7375e7e6f3172651df19091b

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SHA256 645f1f78f088888d51e42610dcce6e798be047f6c0267fc19d277cf091b30629
MD5 e69ca452ce4f6582c49855de5e47055c
BLAKE2b-256 6530130f03edea9eb6d68ea9cf5c7ebe77ceb985f7e75aeadb15909f4d51ac45

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SHA256 a51077c20ca6210f81bb90a91a5f7a376a50ab4ae48dbf708478ad50af754e0f
MD5 7cc36164df40474f828aa787c78af7d1
BLAKE2b-256 40e32473622f2472ef357eeaec241766b8a2f663c3d52a882bf8a4272b556a10

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SHA256 5ce1451cfaa8fe66f1243595218bad810050d521c2b94633a6089ad7f06075af
MD5 087dec8ebf8e9a3b5120821d23d333ab
BLAKE2b-256 8242e417789e17cb0da7d01f5e0a607d55572b17684ae7b06ec56498c790804d

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SHA256 0f5e18a50d7c604c4fd20ef24058c0893b31a310511bb9bad8c58a1a605bebb5
MD5 990d94aa6464e246c9c5b87b075d5dbd
BLAKE2b-256 8bb1b93068160b8ef7f4d542debc76a478e6003b4bd158229d74797ba8045236

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SHA256 4a442d55bc8b826e2834f9b9ff35d92dfcc75e608413dfa10fa78691528ad561
MD5 4915570eeba9a041484985ccbc5b58d7
BLAKE2b-256 e550d60ac4cc43f9727e11ac9af531a325cbc90dee14d4fa883b26cbc741755f

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SHA256 9c0cb4e494901b3c8b510c3fb6dbb06894389206f42bc37c48a6e73fa2d166f1
MD5 40ef4efcbb742f1d3327b144a5bda733
BLAKE2b-256 6f9f9879a141c874868d107b582d83e3b50eed80093477c4a0690eeb94fe5dd8

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Algorithm Hash digest
SHA256 a5c762af3ccf22c09f7ccbdf7f67969f2a33f18b87965e5d21ae86e84204f7df
MD5 b5a254b3f958f1093669e988be9bd196
BLAKE2b-256 744b8f60dfdfa1bf5e87b2c65cf52f7c64a35f8af9b034099ce66657f2a96331

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Algorithm Hash digest
SHA256 ed6f6e88fc90ba1c3b4f72d6bbd4e47f27f461b1f7fdd9c754adb5089ca8ffe5
MD5 45a2176c9ee6888480a094dd45be40fb
BLAKE2b-256 8bb1939678cdaac41cc40f5a0f73294a33ef247cd551c06c95ac507cedde6f41

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