diff --git a/package.json b/package.json index 6c13106..7c7cd51 100644 --- a/package.json +++ b/package.json @@ -39,32 +39,32 @@ "genomics" ], "dependencies": { - "@gmod/bgzf-filehandle": "^1.4.4", + "@gmod/bgzf-filehandle": "^1.4.7", "abortable-promise-cache": "^1.5.0", "buffer-crc32": "^0.2.13", - "generic-filehandle": "^3.0.0", + "generic-filehandle": "^3.1.1", "long": "^4.0.0", "quick-lru": "^4.0.0" }, "devDependencies": { - "@types/buffer-crc32": "^0.2.2", - "@types/jest": "^29.5.1", + "@types/buffer-crc32": "^0.2.4", + "@types/jest": "^29.5.11", "@types/long": "^4.0.0", - "@types/node": "^18.16.0", - "@typescript-eslint/eslint-plugin": "^5.59.6", - "@typescript-eslint/parser": "^5.59.6", - "eslint": "^8.40.0", - "eslint-config-prettier": "^8.7.0", - "eslint-plugin-import": "^2.27.5", - "eslint-plugin-prettier": "^4.2.1", - "eslint-plugin-unicorn": "^47.0.0", - "jest": "^29.5.0", + "@types/node": "^20.10.4", + "@typescript-eslint/eslint-plugin": "^6.13.2", + 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BamFile { buffer = (await this.bam.readFile(opts)) as Buffer } - const uncba = await unzip(buffer) + const uncba = isGzip(buffer) ? await unzip(buffer) : buffer if (uncba.readInt32LE(0) !== BAM_MAGIC) { throw new Error('Not a BAM file') @@ -215,9 +219,8 @@ export default class BamFile { if (!bytesRead) { throw new Error('Error reading refseqs from header') } - const uncba = await unzip( - buffer.subarray(0, Math.min(bytesRead, refSeqBytes)), - ) + const ret = buffer.subarray(0, Math.min(bytesRead, refSeqBytes)) + const uncba = isGzip(ret) ? await unzip(ret) : ret const nRef = uncba.readInt32LE(start) let p = start + 4 const chrToIndex: { [key: string]: number } = {} diff --git a/src/record.ts b/src/record.ts index 4a4072a..4d1e53a 100644 --- a/src/record.ts +++ b/src/record.ts @@ -1,4 +1,3 @@ -/* eslint-disable @typescript-eslint/no-empty-function */ import Constants from './constants' const SEQRET_DECODER = '=ACMGRSVTWYHKDBN'.split('') diff --git a/yarn.lock b/yarn.lock index d57795a..18dc275 100644 --- a/yarn.lock +++ b/yarn.lock @@ -2,6 +2,11 @@ # yarn lockfile v1 +"@aashutoshrathi/word-wrap@^1.2.3": + version "1.2.6" + resolved "https://registry.yarnpkg.com/@aashutoshrathi/word-wrap/-/word-wrap-1.2.6.tgz#bd9154aec9983f77b3a034ecaa015c2e4201f6cf" + integrity sha512-1Yjs2SvM8TflER/OD3cOjhWWOZb58A2t7wpE2S9XfBYTiIl+XFhQG2bjy4Pu1I+EAlCNUzRDYDdFwFYUKvXcIA== + "@ampproject/remapping@^2.2.0": version "2.2.1" resolved "https://registry.yarnpkg.com/@ampproject/remapping/-/remapping-2.2.1.tgz#99e8e11851128b8702cd57c33684f1d0f260b630" @@ -10,157 +15,155 @@ "@jridgewell/gen-mapping" "^0.3.0" "@jridgewell/trace-mapping" "^0.3.9" -"@babel/code-frame@^7.0.0", "@babel/code-frame@^7.12.13", "@babel/code-frame@^7.18.6", "@babel/code-frame@^7.21.4": - version "7.21.4" - resolved "https://registry.yarnpkg.com/@babel/code-frame/-/code-frame-7.21.4.tgz#d0fa9e4413aca81f2b23b9442797bda1826edb39" - integrity 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callsites@^3.0.0: version "3.1.0" resolved "https://registry.yarnpkg.com/callsites/-/callsites-3.1.0.tgz#b3630abd8943432f54b3f0519238e33cd7df2f73" integrity sha512-P8BjAsXvZS+VIDUI11hHCQEv74YT67YUi5JJFNWIqL235sBmjX4+qx9Muvls5ivyNENctx46xQLQ3aTuE7ssaQ== -camelcase-keys@^6.2.2: - version "6.2.2" - resolved "https://registry.yarnpkg.com/camelcase-keys/-/camelcase-keys-6.2.2.tgz#5e755d6ba51aa223ec7d3d52f25778210f9dc3c0" - integrity sha512-YrwaA0vEKazPBkn0ipTiMpSajYDSe+KjQfrjhcBMxJt/znbvlHd8Pw/Vamaz5EB4Wfhs3SUR3Z9mwRu/P3s3Yg== - dependencies: - camelcase "^5.3.1" - map-obj "^4.0.0" - quick-lru "^4.0.1" - camelcase@^5.3.1: version "5.3.1" resolved "https://registry.yarnpkg.com/camelcase/-/camelcase-5.3.1.tgz#e3c9b31569e106811df242f715725a1f4c494320" @@ -1183,12 +1243,12 @@ camelcase@^6.2.0: resolved "https://registry.yarnpkg.com/camelcase/-/camelcase-6.3.0.tgz#5685b95eb209ac9c0c177467778c9c84df58ba9a" integrity 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-2392,11 +2433,6 @@ is-path-inside@^3.0.3: resolved "https://registry.yarnpkg.com/is-path-inside/-/is-path-inside-3.0.3.tgz#d231362e53a07ff2b0e0ea7fed049161ffd16283" integrity sha512-Fd4gABb+ycGAmKou8eMftCupSir5lRxqf4aD/vd0cD2qc4HL07OjCeuHMr8Ro4CoMaeCKDB0/ECBOVWjTwUvPQ== -is-plain-obj@^1.1.0: - version "1.1.0" - resolved "https://registry.yarnpkg.com/is-plain-obj/-/is-plain-obj-1.1.0.tgz#71a50c8429dfca773c92a390a4a03b39fcd51d3e" - integrity sha512-yvkRyxmFKEOQ4pNXCmJG5AEQNlXJS5LaONXo5/cLdTZdWvsZ1ioJEonLGAosKlMWE8lwUy/bJzMjcw8az73+Fg== - is-regex@^1.1.4: version "1.1.4" resolved "https://registry.yarnpkg.com/is-regex/-/is-regex-1.1.4.tgz#eef5663cd59fa4c0ae339505323df6854bb15958" @@ -2417,6 +2453,11 @@ is-stream@^2.0.0: resolved "https://registry.yarnpkg.com/is-stream/-/is-stream-2.0.1.tgz#fac1e3d53b97ad5a9d0ae9cef2389f5810a5c077" integrity sha512-hFoiJiTl63nn+kstHGBtewWSKnQLpyb155KHheA1l39uvtO9nWIop1p3udqPcUd/xbF1VLMO4n7OI6p7RbngDg== +is-stream@^3.0.0: + version "3.0.0" + resolved 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dependencies: ansi-regex "^5.0.1" +strip-ansi@^7.0.1: + version "7.1.0" + resolved "https://registry.yarnpkg.com/strip-ansi/-/strip-ansi-7.1.0.tgz#d5b6568ca689d8561370b0707685d22434faff45" + integrity sha512-iq6eVVI64nQQTRYq2KtEg2d2uU7LElhTJwsH4YzIHZshxlgZms/wIc4VoDQTlG/IvVIrBKG06CrZnp0qv7hkcQ== + dependencies: + ansi-regex "^6.0.1" + strip-bom@^3.0.0: version "3.0.0" resolved "https://registry.yarnpkg.com/strip-bom/-/strip-bom-3.0.0.tgz#2334c18e9c759f7bdd56fdef7e9ae3d588e68ed3" @@ -3961,6 +3944,11 @@ strip-final-newline@^2.0.0: resolved "https://registry.yarnpkg.com/strip-final-newline/-/strip-final-newline-2.0.0.tgz#89b852fb2fcbe936f6f4b3187afb0a12c1ab58ad" integrity sha512-BrpvfNAE3dcvq7ll3xVumzjKjZQ5tI1sEUIKr3Uoks0XUl45St3FlatVqef9prk4jRDzhW6WZg+3bk93y6pLjA== +strip-final-newline@^3.0.0: + version "3.0.0" + resolved "https://registry.yarnpkg.com/strip-final-newline/-/strip-final-newline-3.0.0.tgz#52894c313fbff318835280aed60ff71ebf12b8fd" + integrity 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-text-extensions@^1.0.0: - version "1.9.0" - resolved "https://registry.yarnpkg.com/text-extensions/-/text-extensions-1.9.0.tgz#1853e45fee39c945ce6f6c36b2d659b5aabc2a26" - integrity sha512-wiBrwC1EhBelW12Zy26JeOUkQ5mRu+5o8rpsJk5+2t+Y5vE7e842qtZDQ2g1NpX/29HdyFeJ4nSIhI47ENSxlQ== +text-extensions@^2.0.0: + version "2.4.0" + resolved "https://registry.yarnpkg.com/text-extensions/-/text-extensions-2.4.0.tgz#a1cfcc50cf34da41bfd047cc744f804d1680ea34" + integrity sha512-te/NtwBwfiNRLf9Ijqx3T0nlqZiQ2XrrtBvu+cLL8ZRrGkO0NHTug8MYFKyoSrv/sHTaSKfilUkizV6XhxMJ3g== text-table@^0.2.0: version "0.2.0" resolved "https://registry.yarnpkg.com/text-table/-/text-table-0.2.0.tgz#7f5ee823ae805207c00af2df4a84ec3fcfa570b4" integrity sha512-N+8UisAXDGk8PFXP4HAzVR9nbfmVJ3zYLAWiTIoqC5v5isinhr+r5uaO8+7r3BMfuNIufIsA7RdpVgacC2cSpw== -through2@^2.0.0: - version "2.0.5" - resolved "https://registry.yarnpkg.com/through2/-/through2-2.0.5.tgz#01c1e39eb31d07cb7d03a96a70823260b23132cd" - integrity 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+ tmpl@1.0.5: version "1.0.5" resolved "https://registry.yarnpkg.com/tmpl/-/tmpl-1.0.5.tgz#8683e0b902bb9c20c4f726e3c0b69f36518c07cc" @@ -4073,15 +4046,15 @@ tr46@~0.0.3: resolved "https://registry.yarnpkg.com/tr46/-/tr46-0.0.3.tgz#8184fd347dac9cdc185992f3a6622e14b9d9ab6a" integrity sha512-N3WMsuqV66lT30CrXNbEjx4GEwlow3v6rr4mCcv6prnfwhS01rkgyFdjPNBYd9br7LpXV1+Emh01fHnq2Gdgrw== -trim-newlines@^3.0.0: - version "3.0.1" - resolved "https://registry.yarnpkg.com/trim-newlines/-/trim-newlines-3.0.1.tgz#260a5d962d8b752425b32f3a7db0dcacd176c144" - integrity sha512-c1PTsA3tYrIsLGkJkzHF+w9F2EyxfXGo4UyJc4pFL++FMjnq0HJS69T3M7d//gKrFKwy429bouPescbjecU+Zw== +ts-api-utils@^1.0.1: + version "1.0.3" + resolved "https://registry.yarnpkg.com/ts-api-utils/-/ts-api-utils-1.0.3.tgz#f12c1c781d04427313dbac808f453f050e54a331" + integrity sha512-wNMeqtMz5NtwpT/UZGY5alT+VoKdSsOOP/kqHFcUW1P/VRhH2wJ48+DN2WwUliNbQ976ETwDL0Ifd2VVvgonvg== -ts-jest@^29.1.0: - version "29.1.0" - resolved 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+4206,16 @@ uri-js@^4.2.2: dependencies: punycode "^2.1.0" -util-deprecate@^1.0.1, util-deprecate@~1.0.1: - version "1.0.2" - resolved "https://registry.yarnpkg.com/util-deprecate/-/util-deprecate-1.0.2.tgz#450d4dc9fa70de732762fbd2d4a28981419a0ccf" - integrity sha512-EPD5q1uXyFxJpCrLnCc1nHnq3gOa6DZBocAIiI2TaSCA7VCJ1UJDMagCzIkXNsUYfD1daK//LTEQ8xiIbrHtcw== - -uuid@^3.3.2: - version "3.4.0" - resolved "https://registry.yarnpkg.com/uuid/-/uuid-3.4.0.tgz#b23e4358afa8a202fe7a100af1f5f883f02007ee" - integrity sha512-HjSDRw6gZE5JMggctHBcjVak08+KEVhSIiDzFnT9S9aegmp85S/bReBVTb4QTFaRNptJ9kuYaNhnbNEOkbKb/A== - v8-to-istanbul@^9.0.1: - version "9.1.0" - resolved "https://registry.yarnpkg.com/v8-to-istanbul/-/v8-to-istanbul-9.1.0.tgz#1b83ed4e397f58c85c266a570fc2558b5feb9265" - integrity sha512-6z3GW9x8G1gd+JIIgQQQxXuiJtCXeAjp6RaPEPLv62mH3iPHPxV6W3robxtCzNErRo6ZwTmzWhsbNvjyEBKzKA== + version "9.2.0" + resolved "https://registry.yarnpkg.com/v8-to-istanbul/-/v8-to-istanbul-9.2.0.tgz#2ed7644a245cddd83d4e087b9b33b3e62dfd10ad" + integrity sha512-/EH/sDgxU2eGxajKdwLCDmQ4FWq+kpi3uCmBGpw1xJtnAxEjlD8j8PEiGWpCIMIs3ciNAgH0d3TTJiUkYzyZjA== dependencies: "@jridgewell/trace-mapping" "^0.3.12" "@types/istanbul-lib-coverage" "^2.0.1" - convert-source-map "^1.6.0" + convert-source-map "^2.0.0" -validate-npm-package-license@^3.0.1: +validate-npm-package-license@^3.0.1, validate-npm-package-license@^3.0.4: version "3.0.4" resolved "https://registry.yarnpkg.com/validate-npm-package-license/-/validate-npm-package-license-3.0.4.tgz#fc91f6b9c7ba15c857f4cb2c5defeec39d4f410a" integrity sha512-DpKm2Ui/xN7/HQKCtpZxoRWBhZ9Z0kqtygG8XCgNQ8ZlDnxuQmWhj566j8fN4Cu3/JmbhsDo7fcAJq4s9h27Ew== @@ -4253,17 +4254,16 @@ which-boxed-primitive@^1.0.2: is-string "^1.0.5" is-symbol "^1.0.3" -which-typed-array@^1.1.9: - version "1.1.9" - resolved "https://registry.yarnpkg.com/which-typed-array/-/which-typed-array-1.1.9.tgz#307cf898025848cf995e795e8423c7f337efbde6" - integrity sha512-w9c4xkx6mPidwp7180ckYWfMmvxpjlZuIudNtDf4N/tTAUB8VJbX25qZoAsrtGuYNnGw3pa0AXgbGKRB8/EceA== +which-typed-array@^1.1.11, which-typed-array@^1.1.13: + version "1.1.13" + resolved "https://registry.yarnpkg.com/which-typed-array/-/which-typed-array-1.1.13.tgz#870cd5be06ddb616f504e7b039c4c24898184d36" + integrity sha512-P5Nra0qjSncduVPEAr7xhoF5guty49ArDTwzJ/yNuPIbZppyRxFQsRCWrocxIY+CnMVG+qfbU2FmDKyvSGClow== dependencies: available-typed-arrays "^1.0.5" - call-bind "^1.0.2" + call-bind "^1.0.4" for-each "^0.3.3" gopd "^1.0.1" has-tostringtag "^1.0.0" - is-typed-array "^1.1.10" which@^2.0.1: version "2.0.2" @@ -4272,17 +4272,12 @@ which@^2.0.1: dependencies: isexe "^2.0.0" -word-wrap@^1.2.3: - version "1.2.3" - resolved "https://registry.yarnpkg.com/word-wrap/-/word-wrap-1.2.3.tgz#610636f6b1f703891bd34771ccb17fb93b47079c" - integrity sha512-Hz/mrNwitNRh/HUAtM/VT/5VH+ygD6DV7mYKZAtHOrbs8U7lvPS6xf7EJKMF0uW1KJCl0H701g3ZGus+muE5vQ== - wordwrap@^1.0.0: version "1.0.0" resolved "https://registry.yarnpkg.com/wordwrap/-/wordwrap-1.0.0.tgz#27584810891456a4171c8d0226441ade90cbcaeb" integrity sha512-gvVzJFlPycKc5dZN4yPkP8w7Dc37BtP1yczEneOb4uq34pXZcvrtRTmWV8W+Ume+XCxKgbjM+nevkyFPMybd4Q== -wrap-ansi@^7.0.0: +"wrap-ansi-cjs@npm:wrap-ansi@^7.0.0", wrap-ansi@^7.0.0: version "7.0.0" resolved "https://registry.yarnpkg.com/wrap-ansi/-/wrap-ansi-7.0.0.tgz#67e145cff510a6a6984bdf1152911d69d2eb9e43" integrity sha512-YVGIj2kamLSTxw6NsZjoBxfSwsn0ycdesmc4p+Q21c5zPuZ1pl+NfxVdxPtdHvmNVOQ6XSYG4AUtyt/Fi7D16Q== @@ -4291,6 +4286,15 @@ wrap-ansi@^7.0.0: string-width "^4.1.0" strip-ansi "^6.0.0" +wrap-ansi@^8.1.0: + version "8.1.0" + resolved "https://registry.yarnpkg.com/wrap-ansi/-/wrap-ansi-8.1.0.tgz#56dc22368ee570face1b49819975d9b9a5ead214" + integrity sha512-si7QWI6zUMq56bESFvagtmzMdGOtoxfR+Sez11Mobfc7tm+VkUckk9bW2UeffTGVUbOksxmSw0AA2gs8g71NCQ== + dependencies: + ansi-styles "^6.1.0" + string-width "^5.0.1" + strip-ansi "^7.0.1" + wrappy@1: version "1.0.2" resolved "https://registry.yarnpkg.com/wrappy/-/wrappy-1.0.2.tgz#b5243d8f3ec1aa35f1364605bc0d1036e30ab69f" @@ -4304,11 +4308,6 @@ write-file-atomic@^4.0.2: imurmurhash "^0.1.4" signal-exit "^3.0.7" -xtend@~4.0.1: - version "4.0.2" - resolved "https://registry.yarnpkg.com/xtend/-/xtend-4.0.2.tgz#bb72779f5fa465186b1f438f674fa347fdb5db54" - integrity sha512-LKYU1iAXJXUgAXn9URjiu+MWhyUXHsvfp7mcuYm9dSUKK0/CjtrUwFAxD82/mCWbtLsGjFIad0wIsod4zrTAEQ== - y18n@^5.0.5: version "5.0.8" resolved "https://registry.yarnpkg.com/y18n/-/y18n-5.0.8.tgz#7f4934d0f7ca8c56f95314939ddcd2dd91ce1d55" @@ -4324,33 +4323,15 @@ yallist@^4.0.0: resolved "https://registry.yarnpkg.com/yallist/-/yallist-4.0.0.tgz#9bb92790d9c0effec63be73519e11a35019a3a72" integrity sha512-3wdGidZyq5PB084XLES5TpOSRA3wjXAlIWMhum2kRcv/41Sn2emQ0dycQW4uZXLejwKvg6EsvbdlVL+FYEct7A== -yargs-parser@^20.2.2, yargs-parser@^20.2.3: - version "20.2.9" - resolved "https://registry.yarnpkg.com/yargs-parser/-/yargs-parser-20.2.9.tgz#2eb7dc3b0289718fc295f362753845c41a0c94ee" - integrity sha512-y11nGElTIV+CT3Zv9t7VKl+Q3hTQoT9a1Qzezhhl6Rp21gJ/IVTW7Z3y9EWXhuUBC2Shnf+DX0antecpAwSP8w== - yargs-parser@^21.0.1, yargs-parser@^21.1.1: version "21.1.1" resolved "https://registry.yarnpkg.com/yargs-parser/-/yargs-parser-21.1.1.tgz#9096bceebf990d21bb31fa9516e0ede294a77d35" integrity sha512-tVpsJW7DdjecAiFpbIB1e3qxIQsE6NoPc5/eTdrbbIC4h0LVsWhnoa3g+m2HclBIujHzsxZ4VJVA+GUuc2/LBw== -yargs@^16.2.0: - version "16.2.0" - resolved "https://registry.yarnpkg.com/yargs/-/yargs-16.2.0.tgz#1c82bf0f6b6a66eafce7ef30e376f49a12477f66" - integrity sha512-D1mvvtDG0L5ft/jGWkLpG1+m0eQxOfaBvTNELraWj22wSVUMWxZUvYgJYcKh6jGGIkJFhH4IZPQhR4TKpc8mBw== - dependencies: - cliui "^7.0.2" - escalade "^3.1.1" - get-caller-file "^2.0.5" - require-directory "^2.1.1" - string-width "^4.2.0" - y18n "^5.0.5" - yargs-parser "^20.2.2" - yargs@^17.3.1: - version "17.7.1" - resolved "https://registry.yarnpkg.com/yargs/-/yargs-17.7.1.tgz#34a77645201d1a8fc5213ace787c220eabbd0967" - integrity sha512-cwiTb08Xuv5fqF4AovYacTFNxk62th7LKJ6BL9IGUpTJrWoU7/7WdQGTP2SjKf1dUNBGzDd28p/Yfs/GI6JrLw== + version "17.7.2" + resolved "https://registry.yarnpkg.com/yargs/-/yargs-17.7.2.tgz#991df39aca675a192b816e1e0363f9d75d2aa269" + integrity sha512-7dSzzRQ++CKnNI/krKnYRV7JKKPUXMEh61soaHKg9mrWEhzFWhFnxPxGl+69cD1Ou63C13NUPCnmIcrvqCuM6w== dependencies: cliui "^8.0.1" escalade "^3.1.1" @@ -4364,3 +4345,8 @@ yocto-queue@^0.1.0: version "0.1.0" resolved "https://registry.yarnpkg.com/yocto-queue/-/yocto-queue-0.1.0.tgz#0294eb3dee05028d31ee1a5fa2c556a6aaf10a1b" integrity sha512-rVksvsnNCdJ/ohGc6xgPwyN8eheCxsiLM8mxuE/t/mOVqJewPuO1miLpTHQiRgTKCLexL4MeAFVagts7HmNZ2Q== + +yocto-queue@^1.0.0: + version "1.0.0" + resolved "https://registry.yarnpkg.com/yocto-queue/-/yocto-queue-1.0.0.tgz#7f816433fb2cbc511ec8bf7d263c3b58a1a3c251" + integrity sha512-9bnSc/HEW2uRy67wc+T8UwauLuPJVn28jb+GtJY16iiKWyvmYJRXVT4UamsAEGQfPohgr2q4Tq0sQbQlxTfi1g==