@gmod/bam - npm Package Compare versions

Comparing version 1.0.18 to 1.0.19

CHANGELOG.md

@@ -0,1 +1,9 @@
+## [1.0.19](https://github.com/GMOD/bam-js/compare/v1.0.18...v1.0.19) (2019-05-30)
+
+
+
+- Added lineCount and hasRefSeq functions to BamFile, each accepting a string seqName
+- Fixed aborting on index retrieval code
+
+
 ## [1.0.18](https://github.com/GMOD/bam-js/compare/v1.0.17...v1.0.18) (2019-05-01)
@@ -2,0 +10,0 @@

dist/bamFile.js

@@ -368,14 +368,20 @@ "use strict";var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");Object.defineProperty(exports, "__esModule", { value: true });exports.default = void 0;var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime/helpers/slicedToArray"));var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime/helpers/toConsumableArray"));var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));var _abortablePromiseCache = _interopRequireDefault(require("abortable-promise-cache"));
       return sink;
-    } }, { key: "hasRefSeq", value: function hasRefSeq(
+    } }, { key: "hasRefSeq", value: function () {var _hasRefSeq = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee6(
 
-    seqId) {
-      return this.index.hasRefSeq(seqId);
-    } }, { key: "indexCov", value: function () {var _indexCov = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee6(
+      seqName) {var refId;return _regenerator.default.wrap(function _callee6$(_context6) {while (1) {switch (_context6.prev = _context6.next) {case 0:
+                refId = this.chrToIndex && this.chrToIndex[seqName];return _context6.abrupt("return",
+                this.index.hasRefSeq(refId));case 2:case "end":return _context6.stop();}}}, _callee6, this);}));function hasRefSeq(_x14) {return _hasRefSeq.apply(this, arguments);}return hasRefSeq;}() }, { key: "lineCount", value: function () {var _lineCount = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee7(
 
-      seqName, start, end) {var range, seqId;return _regenerator.default.wrap(function _callee6$(_context6) {while (1) {switch (_context6.prev = _context6.next) {case 0:_context6.next = 2;return (
+
+      seqName) {var refId;return _regenerator.default.wrap(function _callee7$(_context7) {while (1) {switch (_context7.prev = _context7.next) {case 0:
+                refId = this.chrToIndex && this.chrToIndex[seqName];return _context7.abrupt("return",
+                this.index.lineCount(refId));case 2:case "end":return _context7.stop();}}}, _callee7, this);}));function lineCount(_x15) {return _lineCount.apply(this, arguments);}return lineCount;}() }, { key: "indexCov", value: function () {var _indexCov = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee8(
+
+
+      seqName, start, end) {var range, seqId;return _regenerator.default.wrap(function _callee8$(_context8) {while (1) {switch (_context8.prev = _context8.next) {case 0:_context8.next = 2;return (
                   this.index.parse());case 2:
                 range = start !== undefined;
-                seqId = this.chrToIndex && this.chrToIndex[seqName];return _context6.abrupt("return",
+                seqId = this.chrToIndex && this.chrToIndex[seqName];return _context8.abrupt("return",
                 range ?
                 this.index.indexCov(seqId, start, end) :
-                this.index.indexCovTotal(seqId));case 5:case "end":return _context6.stop();}}}, _callee6, this);}));function indexCov(_x14, _x15, _x16) {return _indexCov.apply(this, arguments);}return indexCov;}() }]);return BamFile;}();exports.default = BamFile;
+                this.index.indexCovTotal(seqId));case 5:case "end":return _context8.stop();}}}, _callee8, this);}));function indexCov(_x16, _x17, _x18) {return _indexCov.apply(this, arguments);}return indexCov;}() }]);return BamFile;}();exports.default = BamFile;

dist/indexFile.js

@@ -24,7 +24,7 @@ "use strict";var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime/helpers/classCallCheck"));var _createClass2 = _interopRequireDefault(require("@babel/runtime/helpers/createClass"));var _abortablePromiseCache = _interopRequireDefault(require("abortable-promise-cache"));
 
-      abortSignal) {return _regenerator.default.wrap(function _callee$(_context) {while (1) {switch (_context.prev = _context.next) {case 0:
+      abortSignal) {var _this = this;return _regenerator.default.wrap(function _callee$(_context) {while (1) {switch (_context.prev = _context.next) {case 0:
                 if (!this._parseCache)
                 this._parseCache = new _abortablePromiseCache.default({
                   cache: new _quickLru.default({ maxSize: 1 }),
-                  fill: this._parse.bind(this) });return _context.abrupt("return",
+                  fill: function fill(data, signal) {return _this._parse(signal);} });return _context.abrupt("return",
 
@@ -31,0 +31,0 @@ this._parseCache.get('index', null, abortSignal));case 2:case "end":return _context.stop();}}}, _callee, this);}));function parse(_x) {return _parse.apply(this, arguments);}return parse;}()

package.json

 {
   "name": "@gmod/bam",
-  "version": "1.0.18",
+  "version": "1.0.19",
   "description": "Parser for BAM and BAM index (bai) files",
@@ -5,0 +5,0 @@ "license": "MIT",

README.md

@@ -47,3 +47,3 @@ [![Generated with nod](https://img.shields.io/badge/generator-nod-2196F3.svg?style=flat-square)](https://github.com/diegohaz/nod)
 
-#### getRecordsForRange(refName, start, end, opts)
+#### async getRecordsForRange(refName, start, end, opts)
 
@@ -58,3 +58,3 @@ * refName - a string for the chrom to fetch from
 
-### indexCov(refName, start, end)
+### async indexCov(refName, start, end)
 
@@ -67,2 +67,15 @@ * refName - a string for the chrom to fetch from
 
+
+### async lineCount(refName)
+
+* refName - a string for the chrom to fetch from
+
+Returns number of features on refName, uses special pseudo-bin from the BAI/CSI index (e.g. bin 37450 from bai, returning n_mapped from SAM spec pdf) or -1 if refName not exist in sample
+
+### async hasRefSeq(refName)
+
+* refName - a string for the chrom to check
+
+Returns whether we have this refName in the sample
+
 ### Returned features
@@ -69,0 +82,0 @@

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Improved metrics

Total package byte prevSize

101717

increased by1.78%

Lines of code

1406

increased by0.36%

Number of lines in readme file

115

increased by12.75%

No dependency changes