@gmod/cram 1.5.9 → 1.6.2

package/dist/cramFile/file.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"file.js","sourceRoot":"","sources":["../../src/cramFile/file.js"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,kCAAgC;AAChC,8DAAgC;AAChC,wDAA2B;AAE3B,oCAAsE;AACtE,iDAAoC;AACpC,mDAGyB;AACzB,oEAA6C;AAC7C,0DAAuC;AAEvC,4BAA4B;AAC5B,+BAA+C;AAC/C,8BAAwC;AAExC;IACE;;;;;;;;;;;OAWG;IACH,kBAAY,IAAI;QACd,IAAI,CAAC,IAAI,GAAG,IAAA,SAAI,EAAC,IAAI,CAAC,GAAG,EAAE,IAAI,CAAC,IAAI,EAAE,IAAI,CAAC,UAAU,CAAC,CAAA;QACtD,IAAI,CAAC,iBAAiB,GAAG,IAAI,CAAA;QAC7B,IAAI,CAAC,8BAA8B,GAAG,IAAI,CAAC,QAAQ,CAAA;QACnD,IAAI,CAAC,OAAO,GAAG;YACb,gBAAgB,EAAE,IAAI,CAAC,gBAAgB,KAAK,KAAK;YACjD,SAAS,EAAE,IAAI,CAAC,SAAS,KAAK,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,KAAK;SACjE,CAAA;QAED,6CAA6C;QAC7C,gEAAgE;QAChE,4DAA4D;QAC5D,qCAAqC;QACrC,IAAI,CAAC,YAAY,GAAG,IAAI,mBAAG,CAAC;YAC1B,OAAO,EAAE,IAAI,CAAC,OAAO,CAAC,SAAS;SAChC,CAAC,CAAA;IACJ,CAAC;IAED,2BAAQ,GAAR;QACE,IAAI,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE;YACtB,OAAO,IAAI,CAAC,IAAI,CAAC,QAAQ,CAAA;SAC1B;QACD,IAAI,IAAI,CAAC,IAAI,CAAC,GAAG,EAAE;YACjB,OAAO,IAAI,CAAC,IAAI,CAAC,GAAG,CAAA;SACrB;QAED,OAAO,aAAa,CAAA;IACtB,CAAC;IAED,8CAA8C;IAC9C,uBAAI,GAAJ,UAAK,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,QAAQ;QACnC,OAAO,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,QAAQ,CAAC,CAAA;IACzD,CAAC;IAED,8CAA8C;IAC9C,uBAAI,GAAJ;QACE,OAAO,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;IACzB,CAAC;IAED,WAAW;IACL,gCAAa,GAAnB;;;;;;wBACQ,SAAS,GAAG,MAAM,CAAC,WAAW,CAAC,mCAAwB,CAAC,SAAS,CAAC,CAAA;wBACxE,qBAAM,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,SAAS,EAAE,CAAC,EAAE,mCAAwB,CAAC,SAAS,EAAE,CAAC,CAAC,EAAA;;wBAAzE,SAAyE,CAAA;wBACnE,UAAU,GAAG,mCAAwB,CAAC,MAAM,CAAC,KAAK,CAAC,SAAS,CAAC,CAAC,MAAM,CAAA;wBAC1E,IAAI,UAAU,CAAC,YAAY,KAAK,CAAC,IAAI,UAAU,CAAC,YAAY,KAAK,CAAC,EAAE;4BAClE,MAAM,IAAI,+BAAsB,CAC9B,uBAAgB,UAAU,CAAC,YAAY,mBAAgB,CACxD,CAAA;yBACF;wBACD,sBAAO,UAAU,EAAA;;;;KAClB;IAED,UAAU;IACJ,+BAAY,GAAlB;;;;;4BACyB,qBAAM,IAAI,CAAC,gBAAgB,CAAC,CAAC,CAAC,EAAA;;wBAA/C,cAAc,GAAG,SAA8B;wBACrD,IAAI,CAAC,cAAc,EAAE;4BACnB,MAAM,IAAI,2BAAkB,CAAC,6BAA6B,CAAC,CAAA;yBAC5D;wBAEmB,qBAAM,cAAc,CAAC,aAAa,EAAE;4BACxD,wDAAwD;0BADA;;wBAAhD,OAAO,GAAK,CAAA,SAAoC,CAAA,QAAzC;wBAET,YAAY,GAAG,OAAO,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;wBACrC,SAAS,GAAG,CAAC,CAAA;wBAIb,IAAI,GAAG,OAAO,CAAC,QAAQ,CAAC,MAAM,EAAE,SAAS,EAAE,SAAS,GAAG,YAAY,CAAC,CAAA;wBAC1E,IAAI,CAAC,MAAM,GAAG,IAAI,CAAA;wBAClB,sBAAO,IAAA,qBAAe,EAAC,IAAI,CAAC,EAAA;;;;KAC7B;IAEK,gCAAa,GAAnB;;;;4BACE,qBAAM,IAAI,CAAC,YAAY,EAAE,EAAA;;wBAAzB,SAAyB,CAAA;wBACzB,sBAAO,IAAI,CAAC,MAAM,EAAA;;;;KACnB;IAED,UAAU;IACJ,oCAAiB,GAAvB;;;;;4BAC2B,qBAAM,IAAI,CAAC,aAAa,EAAE,EAAA;;wBAA3C,YAAY,GAAK,CAAA,SAA0B,CAAA,aAA/B;wBACpB,sBAAO,IAAA,kCAAiB,EAAC,YAAY,CAAC,EAAA;;;;KACvC;IAEK,mCAAgB,GAAtB,UAAuB,eAAe;;;;;4BACb,qBAAM,IAAI,CAAC,iBAAiB,EAAE,EAAA;;wBAA/C,cAAc,GAAG,SAA8B;wBACjD,QAAQ,GAAG,cAAc,CAAC,kBAAkB,CAAC,SAAS,CAAA;wBAC/B,qBAAM,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,EAAA;;wBAAnC,QAAQ,GAAK,CAAA,SAAsB,CAAA,KAA3B;wBACd,oBAAoB,GAAK,cAAc,qBAAnB,CAAmB;wBAItC,CAAC,GAAG,CAAC;;;6BAAE,CAAA,CAAC,IAAI,eAAe,CAAA;wBAClC,gDAAgD;wBAChD,uDAAuD;wBACvD,IAAI,QAAQ,GAAG,oBAAoB,CAAC,SAAS,GAAG,CAAC,IAAI,QAAQ,EAAE;4BAC7D,sBAAO,SAAS,EAAA;yBACjB;wBAED,gBAAgB,GAAG,IAAI,CAAC,sBAAsB,CAAC,QAAQ,CAAC,CAAA;wBAClC,qBAAM,gBAAgB,CAAC,SAAS,EAAE,EAAA;;wBAAlD,aAAa,GAAG,SAAkC;wBACxD,IAAI,CAAC,aAAa,EAAE;4BAClB,MAAM,IAAI,2BAAkB,CAC1B,oBAAa,eAAe,uBAAoB,CACjD,CAAA;yBACF;6BAKG,CAAA,CAAC,KAAK,CAAC,CAAA,EAAP,wBAAO;wBACT,QAAQ,GAAG,aAAa,CAAC,YAAY,CAAA;wBAC5B,CAAC,GAAG,CAAC;;;6BAAE,CAAA,CAAC,GAAG,aAAa,CAAC,SAAS,CAAA;wBAC3B,qBAAM,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,EAAA;;wBAAtC,KAAK,GAAG,SAA8B;wBAC5C,QAAQ,GAAG,KAAK,CAAC,YAAY,CAAA;;;wBAFc,CAAC,IAAI,CAAC,CAAA;;;;wBAKnD,8EAA8E;wBAC9E,QAAQ,IAAI,aAAa,CAAC,KAAK,GAAG,aAAa,CAAC,MAAM,CAAA;;;wBA1BpB,CAAC,IAAI,CAAC,CAAA;;6BA8B5C,sBAAO,gBAAgB,EAAA;;;;KACxB;IAEK,6BAAU,GAAhB,UAAiB,QAAQ,EAAE,MAAM,EAAE,aAAa,EAAE,WAAW;;;;;;wBACrD,CAAC,GAAG,MAAM,CAAC,WAAW,CAAC,MAAM,CAAC,CAAA;wBACpC,qBAAM,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC,EAAE,MAAM,EAAE,QAAQ,CAAC,EAAA;;wBAA5C,SAA4C,CAAA;wBACtC,eAAe,GAAG,sBAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;wBACzC,IAAI,eAAe,KAAK,aAAa,EAAE;4BACrC,MAAM,IAAI,2BAAkB,CAC1B,0BAAmB,WAAW,gCAAsB,aAAa,sCAA4B,eAAe,CAAE,CAC/G,CAAA;yBACF;;;;;KACF;IAED;;OAEG;IACG,iCAAc,GAApB;;;;;4BACyB,qBAAM,IAAI,CAAC,iBAAiB,EAAE,EAAA;;wBAA/C,cAAc,GAAG,SAA8B;wBAC1B,qBAAM,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,EAAA;;wBAAnC,QAAQ,GAAK,CAAA,SAAsB,CAAA,KAA3B;wBACd,oBAAoB,GAAK,cAAc,qBAAnB,CAAmB;wBAE3C,cAAc,GAAG,CAAC,CAAA;wBAClB,QAAQ,GAAG,cAAc,CAAC,kBAAkB,CAAC,SAAS,CAAA;;;6BACnD,CAAA,QAAQ,GAAG,oBAAoB,CAAC,SAAS,GAAG,CAAC,GAAG,QAAQ,CAAA;wBACvC,qBAAM,IAAI,CAAC,sBAAsB,CACrD,QAAQ,CACT,CAAC,SAAS,EAAE,EAAA;;wBAFP,aAAa,GAAG,SAET;wBACb,IAAI,CAAC,aAAa,EAAE;4BAClB,yBAAK;yBACN;6BAIG,CAAA,cAAc,KAAK,CAAC,CAAA,EAApB,wBAAoB;wBACtB,QAAQ,GAAG,aAAa,CAAC,YAAY,CAAA;wBAC5B,CAAC,GAAG,CAAC;;;6BAAE,CAAA,CAAC,GAAG,aAAa,CAAC,SAAS,CAAA;wBAC3B,qBAAM,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,EAAA;;wBAAtC,KAAK,GAAG,SAA8B;wBAC5C,QAAQ,GAAG,KAAK,CAAC,YAAY,CAAA;;;wBAFc,CAAC,IAAI,CAAC,CAAA;;;;wBAKnD,8EAA8E;wBAC9E,QAAQ,IAAI,aAAa,CAAC,KAAK,GAAG,aAAa,CAAC,MAAM,CAAA;;;wBAExD,cAAc,IAAI,CAAC,CAAA;;6BAGrB,sBAAO,cAAc,EAAA;;;;KACt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package/dist/cramFile/index.d.ts

@@ -0,0 +1,2 @@
+export default CramFile;
+import CramFile from "./file";

package/dist/cramFile/index.js

@@ -1,5 +1,8 @@
 "use strict";
-
-var CramFile = require('./file');
-
-module.exports = CramFile;
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var file_1 = __importDefault(require("./file"));
+exports.default = file_1.default;
+//# sourceMappingURL=index.js.map

package/dist/cramFile/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/cramFile/index.js"],"names":[],"mappings":";;;;;AAAA,gDAA6B;AAE7B,kBAAe,cAAQ,CAAA"}

package/dist/cramFile/record.d.ts

@@ -0,0 +1,79 @@
+/**
+ * Class of each CRAM record returned by this API.
+ */
+export default class CramRecord {
+    tags: {};
+    /**
+     * @returns {boolean} true if the read is paired, regardless of whether both segments are mapped
+     */
+    isPaired(): boolean;
+    /** @returns {boolean} true if the read is paired, and both segments are mapped */
+    isProperlyPaired(): boolean;
+    /** @returns {boolean} true if the read itself is unmapped; conflictive with isProperlyPaired */
+    isSegmentUnmapped(): boolean;
+    /** @returns {boolean} true if the read itself is unmapped; conflictive with isProperlyPaired */
+    isMateUnmapped(): boolean;
+    /** @returns {boolean} true if the read is mapped to the reverse strand */
+    isReverseComplemented(): boolean;
+    /** @returns {boolean} true if the mate is mapped to the reverse strand */
+    isMateReverseComplemented(): boolean;
+    /** @returns {boolean} true if this is read number 1 in a pair */
+    isRead1(): boolean;
+    /** @returns {boolean} true if this is read number 2 in a pair */
+    isRead2(): boolean;
+    /** @returns {boolean} true if this is a secondary alignment */
+    isSecondary(): boolean;
+    /** @returns {boolean} true if this read has failed QC checks */
+    isFailedQc(): boolean;
+    /** @returns {boolean} true if the read is an optical or PCR duplicate */
+    isDuplicate(): boolean;
+    /** @returns {boolean} true if this is a supplementary alignment */
+    isSupplementary(): boolean;
+    /**
+     * @returns {boolean} true if the read is detached
+     */
+    isDetached(): boolean;
+    /** @returns {boolean} true if the read has a mate in this same CRAM segment */
+    hasMateDownStream(): boolean;
+    /** @returns {boolean} true if the read contains qual scores */
+    isPreservingQualityScores(): boolean;
+    /** @returns {boolean} true if the read has no sequence bases */
+    isUnknownBases(): boolean;
+    /**
+     * Get the original sequence of this read.
+     * @returns {String} sequence basepairs
+     */
+    getReadBases(): string;
+    readBases: any;
+    /**
+     * Get the pair orientation of a paired read. Adapted from igv.js
+     * @returns {String} of paired orientatin
+     */
+    getPairOrientation(): string;
+    /**
+     * Annotates this feature with the given reference sequence basepair
+     * information. This will add a `sub` and a `ref` item to base
+     * subsitution read features given the actual substituted and reference
+     * base pairs, and will make the `getReadSequence()` method work.
+     *
+     * @param {object} refRegion
+     * @param {number} refRegion.start
+     * @param {number} refRegion.end
+     * @param {string} refRegion.seq
+     * @param {CramContainerCompressionScheme} compressionScheme
+     * @returns {undefined} nothing
+     */
+    addReferenceSequence(refRegion: {
+        start: number;
+        end: number;
+        seq: string;
+    }, compressionScheme: CramContainerCompressionScheme): undefined;
+    _refRegion: {
+        start: number;
+        end: number;
+        seq: string;
+    } | undefined;
+    toJSON(): {
+        readBases: string;
+    };
+}