@gmod/cram 1.5.9 → 1.6.2

package/dist/cramFile/sectionParsers.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"sectionParsers.js","sourceRoot":"","sources":["../../src/cramFile/sectionParsers.js"],"names":[],"mappings":";;;AAAA,qDAA4C;AAE5C,IAAM,UAAU,GAAG,IAAI,sBAAM,EAAE,CAAC,IAAI,EAAE,CAAA;AAEtC,IAAM,kBAAkB,GAAG;IACzB,MAAM,EAAE,IAAI,sBAAM,EAAE;SACjB,MAAM,CAAC,OAAO,EAAE,EAAE,MAAM,EAAE,CAAC,EAAE,CAAC;SAC9B,KAAK,CAAC,cAAc,CAAC;SACrB,KAAK,CAAC,cAAc,CAAC;SACrB,MAAM,CAAC,QAAQ,EAAE,EAAE,MAAM,EAAE,EAAE,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC;IACpD,SAAS,EAAE,EAAE;CACd,CAAA;AA+WQ,gDAAkB;AA7W3B,IAAM,eAAe,GAAG;IACtB,MAAM,EAAE,IAAI,sBAAM,EAAE;SACjB,KAAK,CAAC,mBAAmB,EAAE;QAC1B,SAAS,EAAE,0BAA0B,CAAC,UAA3B,0BAA0B,CAAC,CAAC;YACrC,IAAM,MAAM,GAAG;gBACb,KAAK;gBACL,MAAM;gBACN,OAAO;gBACP,MAAM;gBACN,MAAM;gBACN,UAAU;gBACV,OAAO;gBACP,SAAS;gBACT,MAAM;aACP,CAAC,CAAC,CAAC,CAAA;YACJ,IAAI,CAAC,MAAM,EAAE;gBACX,MAAM,IAAI,KAAK,CAAC,oCAA6B,CAAC,qBAAkB,CAAC,CAAA;aAClE;YACD,OAAO,MAAM,CAAA;QACf,CAAC;KACF,CAAC;SACD,KAAK,CAAC,aAAa,EAAE;QACpB,SAAS,EAAE,0BAA0B,CAAC,UAA3B,0BAA0B,CAAC,CAAC;YACrC,IAAM,IAAI,GAAG;gBACX,aAAa;gBACb,oBAAoB;gBACpB,qBAAqB;gBACrB,uBAAuB;gBACvB,eAAe;gBACf,WAAW;aACZ,CAAC,CAAC,CAAC,CAAA;YACJ,IAAI,CAAC,IAAI,EAAE;gBACT,MAAM,IAAI,KAAK,CAAC,wCAAiC,CAAC,CAAE,CAAC,CAAA;aACtD;YACD,OAAO,IAAI,CAAA;QACb,CAAC;KACF,CAAC;SACD,IAAI,CAAC,WAAW,CAAC;SACjB,IAAI,CAAC,gBAAgB,CAAC;SACtB,IAAI,CAAC,kBAAkB,CAAC;IAC3B,SAAS,EAAE,EAAE;CACd,CAAA;AAED,IAAM,cAAc,GAAG;IACrB,MAAM,EAAE,IAAI,sBAAM,EAAE,CAAC,MAAM,CAAC,OAAO,CAAC;IACpC,SAAS,EAAE,CAAC;CACb,CAAA;AAED,2BAA2B;AAC3B,iBAAiB;AACjB,qBAAqB;AACrB,mBAAmB;AACnB,wBAAwB;AACxB,2BAA2B;AAC3B,4BAA4B;AAC5B,iBAAiB;AACjB,mBAAmB;AACnB,wBAAwB;AACxB,kBAAkB;AAClB,IAAI;AAEJ,IAAM,iBAAiB,GAAG,IAAI,sBAAM,EAAE,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,MAAM,CAAC,MAAM,EAAE;IACjE,MAAM,EAAE,MAAM;IACd,SAAS,EAAE,0BAA0B,CAAC,UAA3B,0BAA0B,CAAC,MAAM;QAC1C,SAAS,UAAU,CAAC,WAAW,EAAE,SAAS;YACxC,IAAM,GAAG,GAAG,MAAM,CAAC,QAAQ,CAAC,MAAM,EAAE,WAAW,EAAE,SAAS,CAAC,CAAA;YAC3D,IAAM,IAAI,GAAG,EAAE,CAAA;YACf,KAAK,IAAI,GAAC,GAAG,CAAC,EAAE,GAAC,GAAG,GAAG,CAAC,MAAM,EAAE,GAAC,IAAI,CAAC,EAAE;gBACtC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,MAAM,CAAC,GAAC,EAAE,CAAC,CAAC,CAAC,CAAA;aAC5B;YACD,OAAO,IAAI,CAAA;QACb,CAAC;QACD,oBAAoB;QACpB,IAAI,OAAO,GAAG,EAAE,CAAA;QAChB,IAAI,WAAW,GAAG,CAAC,CAAA;QACnB,IAAI,CAAC,CAAA;QACL,mBAAmB;QACnB,KAAK,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;YACrC,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE;gBACd,OAAO,CAAC,IAAI,CAAC,UAAU,CAAC,WAAW,EAAE,CAAC,CAAC,CAAC,CAAA;gBACxC,WAAW,GAAG,CAAC,GAAG,CAAC,CAAA;aACpB;SACF;QACD,IAAI,CAAC,GAAG,WAAW,EAAE;YACnB,OAAO,CAAC,IAAI,CAAC,UAAU,CAAC,WAAW,EAAE,CAAC,CAAC,CAAC,CAAA;SACzC;QACD,OAAO,OAAO,CAAA;IAChB,CAAC;CACF,CAAC,CAAA;AAEF,iEAAiE;AACjE,IAAM,eAAe,GAAG,IAAI,sBAAM,EAAE,CAAC,KAAK,CAAC,IAAI,EAAE;IAC/C,SAAS,EAAE,0BAA0B,CAAC,UAA3B,0BAA0B,CAAC,GAAG,IAAI,OAAA,CAAC,CAAC,GAAG,EAAL,CAAK;CACnD,CAAC,CAAA;AAEF,IAAM,mBAAmB,GAAG,IAAI,sBAAM,EAAE;KACrC,IAAI,CAAC,SAAS,CAAC;KACf,IAAI,CAAC,UAAU,CAAC;KAChB,KAAK,CAAC,MAAM,EAAE;IACb,MAAM,EAAE,UAAU;IAClB,IAAI,EAAE,IAAI,sBAAM,EAAE;SACf,MAAM,CAAC,KAAK,EAAE;QACb,MAAM,EAAE,CAAC;QACT,SAAS,EAAE,KAAK;QAChB,uDAAuD;KACxD,CAAC;SACD,MAAM,CAAC,OAAO,EAAE;QACf,GAAG,EAAE,KAAK;QACV,OAAO,EAAE;YACP,EAAE,EAAE,eAAe;YACnB,EAAE,EAAE,eAAe;YACnB,EAAE,EAAE,eAAe;YACnB,EAAE,EAAE,eAAe;YACnB,EAAE,EAAE,eAAe;YACnB,EAAE,EAAE,eAAe;YACnB,EAAE,EAAE,IAAI,sBAAM,EAAE,CAAC,KAAK,CAAC,IAAI,EAAE,EAAE,IAAI,EAAE,OAAO,EAAE,MAAM,EAAE,CAAC,EAAE,CAAC;YAC1D,EAAE,EAAE,IAAI,sBAAM,EAAE,CAAC,IAAI,CAAC,IAAI,EAAE;gBAC1B,IAAI,EAAE,iBAAiB;gBACvB,SAAS,EAAE,0BAA0B,CAAC,UAA3B,0BAA0B,CAAC,IAAI,IAAI,OAAA,IAAI,CAAC,IAAI,EAAT,CAAS;aACxD,CAAC;SACH;KACF,CAAC;CACL,CAAC,CAAA;AAEJ,0BAA0B;AAC1B,SAAS,SAAS,CAAC,IAAI;IACrB,IAAM,GAAG,GAAG,EAAE,CAAA;IACd,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;QACtC,IAAA,KAAiB,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,EAA3B,GAAG,SAAA,EAAE,KAAK,WAAiB,CAAA;QACnC,IAAI,GAAG,CAAC,GAAG,CAAC,EAAE;YACZ,OAAO,CAAC,IAAI,CAAC,wBAAiB,GAAG,YAAS,CAAC,CAAA;SAC5C;QACD,GAAG,CAAC,GAAG,CAAC,GAAG,KAAK,CAAA;KACjB;IACD,OAAO,GAAG,CAAA;AACZ,CAAC;AAED,IAAM,kBAAkB,GAAG;IACzB,kBAAkB,oBAAA;IAClB,eAAe,iBAAA;IACf,cAAc,gBAAA;CACf,CAAA;AAED,6DAA6D;AAC7D,IAAM,gBAAgB,GAAG;IACvB,uEAAuE;IACvE,6DAA6D;IAC7D,uBAAuB,YAAC,YAAY;QAClC,IAAI,SAAS,GAAG,CAAC,CAAA;QACjB,IAAI,MAAM,GAAG,IAAI,sBAAM,EAAE,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;QAC5C,SAAS,IAAI,CAAC,CAAA;QAEd,6DAA6D;QAC7D,IAAI,YAAY,IAAI,CAAC,EAAE;YACrB,MAAM,GAAG,MAAM,CAAC,IAAI,CAAC,eAAe,CAAC,CAAA;YACrC,SAAS,IAAI,CAAC,CAAA;SACf;aAAM,IAAI,YAAY,KAAK,CAAC,EAAE;YAC7B,MAAM,GAAG,MAAM,CAAC,IAAI,CAAC,eAAe,CAAC,CAAA;YACrC,SAAS,IAAI,CAAC,CAAA;SACf;QAED,MAAM,GAAG,MAAM;aACZ,IAAI,CAAC,WAAW,CAAC;aACjB,IAAI,CAAC,eAAe,CAAC;aACrB,KAAK,CAAC,YAAY,EAAE;YACnB,IAAI,EAAE,UAAU;YAChB,MAAM,EAAE,eAAe;SACxB,CAAC,CAAA;QACJ,SAAS,IAAI,CAAC,GAAG,CAAC,CAAA,CAAC,oBAAoB;QAEvC,oCAAoC;QACpC,IAAI,YAAY,IAAI,CAAC,EAAE;YACrB,MAAM,GAAG,MAAM,CAAC,KAAK,CAAC,KAAK,EAAE,EAAE,IAAI,EAAE,OAAO,EAAE,MAAM,EAAE,EAAE,EAAE,CAAC,CAAA;YAC3D,SAAS,IAAI,EAAE,CAAA;SAChB;QAED,IAAM,aAAa,GAAG,UAAA,aAAa,IAAI,OAAA,SAAS,GAAG,aAAa,GAAG,CAAC,EAA7B,CAA6B,CAAA;QAEpE,OAAO,EAAE,MAAM,QAAA,EAAE,SAAS,EAAE,aAAa,EAAE,CAAA,CAAC,4EAA4E;IAC1H,CAAC;IAED,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package/dist/cramFile/slice/decodeRecord.d.ts

@@ -0,0 +1,2 @@
+export default function decodeRecord(slice: any, decodeDataSeries: any, compressionScheme: any, sliceHeader: any, coreDataBlock: any, blocksByContentId: any, cursors: any, majorVersion: any, recordNumber: any): CramRecord;
+import CramRecord from "../record";

package/dist/cramFile/slice/decodeRecord.js

@@ -1,327 +1,307 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime-corejs3/helpers/interopRequireDefault");
-
-var _concat = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/concat"));
-
-var _isNan = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/number/is-nan"));
-
-var _forEach = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/for-each"));
-
-var _flags = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/flags"));
-
-var _slice = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/slice"));
-
-var _toConsumableArray2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/toConsumableArray"));
-
-var _parseInt = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/number/parse-int"));
-
-var _minSafeInteger = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/number/min-safe-integer"));
-
-var _maxSafeInteger = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/number/max-safe-integer"));
-
-var _slicedToArray2 = _interopRequireDefault(require("@babel/runtime-corejs3/helpers/slicedToArray"));
-
-var _indexOf = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/index-of"));
-
-var Long = require('long');
-
-var _require = require('../../errors'),
-    CramMalformedError = _require.CramMalformedError,
-    CramUnimplementedError = _require.CramUnimplementedError;
-
-var CramRecord = require('../record');
-
-var Constants = require('../constants');
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var long_1 = __importDefault(require("long"));
+var errors_1 = require("../../errors");
+var record_1 = __importDefault(require("../record"));
+var constants_1 = __importDefault(require("../constants"));
 /**
  * given a Buffer, read a string up to the first null character
  * @private
  */
-
-
 function readNullTerminatedStringFromBuffer(buffer) {
-  var zeroOffset = (0, _indexOf.default)(buffer).call(buffer, 0);
-  if (zeroOffset === -1) return buffer.toString('utf8');
-  return buffer.toString('utf8', 0, zeroOffset);
+    var zeroOffset = buffer.indexOf(0);
+    if (zeroOffset === -1) {
+        return buffer.toString('utf8');
+    }
+    return buffer.toString('utf8', 0, zeroOffset);
 }
 /**
  * parse a BAM tag's array value from a binary buffer
  * @private
  */
-
-
 function parseTagValueArray(buffer) {
-  var arrayType = String.fromCharCode(buffer[0]);
-  var length = buffer.readInt32LE(1);
-  var schema = {
-    c: ['readInt8', 1],
-    C: ['readUInt8', 1],
-    s: ['readInt16LE', 2],
-    S: ['readUInt16LE', 2],
-    i: ['readInt32LE', 4],
-    I: ['readUInt32LE', 4],
-    f: ['readFloatLE', 4]
-  }[arrayType];
-  if (!schema) throw new CramMalformedError("invalid tag value array type '".concat(arrayType, "'"));
-
-  var _schema = (0, _slicedToArray2.default)(schema, 2),
-      getMethod = _schema[0],
-      itemSize = _schema[1];
-
-  var array = new Array(length);
-  var offset = 5;
-
-  for (var i = 0; i < length; i += 1) {
-    array[i] = buffer[getMethod](offset);
-    offset += itemSize;
-  }
-
-  return array;
+    var arrayType = String.fromCharCode(buffer[0]);
+    var length = buffer.readInt32LE(1);
+    var schema = {
+        c: ['readInt8', 1],
+        C: ['readUInt8', 1],
+        s: ['readInt16LE', 2],
+        S: ['readUInt16LE', 2],
+        i: ['readInt32LE', 4],
+        I: ['readUInt32LE', 4],
+        f: ['readFloatLE', 4],
+    }[arrayType];
+    if (!schema) {
+        throw new errors_1.CramMalformedError("invalid tag value array type '".concat(arrayType, "'"));
+    }
+    var getMethod = schema[0], itemSize = schema[1];
+    var array = new Array(length);
+    var offset = 5;
+    for (var i = 0; i < length; i += 1) {
+        array[i] = buffer[getMethod](offset);
+        offset += itemSize;
+    }
+    return array;
 }
-
 function parseTagData(tagType, buffer) {
-  if (!buffer.readInt32LE) buffer = Buffer.from(buffer);
-  if (tagType === 'Z') return readNullTerminatedStringFromBuffer(buffer);
-  if (tagType === 'A') return String.fromCharCode(buffer[0]);
-
-  if (tagType === 'I') {
-    var val = Long.fromBytesLE(buffer);
-    if (val.greaterThan(_maxSafeInteger.default) || val.lessThan(_minSafeInteger.default)) throw new CramUnimplementedError('integer overflow');
-    return val.toNumber();
-  }
-
-  if (tagType === 'i') return buffer.readInt32LE(0);
-  if (tagType === 's') return buffer.readInt16LE(0);
-  if (tagType === 'S') return buffer.readUInt16LE(0);
-  if (tagType === 'c') return buffer.readInt8(0);
-  if (tagType === 'C') return buffer.readUInt8(0);
-  if (tagType === 'f') return buffer.readFloatLE(0);
-
-  if (tagType === 'H') {
-    var hex = readNullTerminatedStringFromBuffer(buffer);
-    return (0, _parseInt.default)(hex.replace(/^0x/, ''), 16);
-  }
-
-  if (tagType === 'B') return parseTagValueArray(buffer);
-  throw new CramMalformedError("Unrecognized tag type ".concat(tagType));
+    if (!buffer.readInt32LE) {
+        buffer = Buffer.from(buffer);
+    }
+    if (tagType === 'Z') {
+        return readNullTerminatedStringFromBuffer(buffer);
+    }
+    if (tagType === 'A') {
+        return String.fromCharCode(buffer[0]);
+    }
+    if (tagType === 'I') {
+        var val = long_1.default.fromBytesLE(buffer);
+        if (val.greaterThan(Number.MAX_SAFE_INTEGER) ||
+            val.lessThan(Number.MIN_SAFE_INTEGER)) {
+            throw new errors_1.CramUnimplementedError('integer overflow');
+        }
+        return val.toNumber();
+    }
+    if (tagType === 'i') {
+        return buffer.readInt32LE(0);
+    }
+    if (tagType === 's') {
+        return buffer.readInt16LE(0);
+    }
+    if (tagType === 'S') {
+        return buffer.readUInt16LE(0);
+    }
+    if (tagType === 'c') {
+        return buffer.readInt8(0);
+    }
+    if (tagType === 'C') {
+        return buffer.readUInt8(0);
+    }
+    if (tagType === 'f') {
+        return buffer.readFloatLE(0);
+    }
+    if (tagType === 'H') {
+        var hex = readNullTerminatedStringFromBuffer(buffer);
+        return Number.parseInt(hex.replace(/^0x/, ''), 16);
+    }
+    if (tagType === 'B') {
+        return parseTagValueArray(buffer);
+    }
+    throw new errors_1.CramMalformedError("Unrecognized tag type ".concat(tagType));
 }
-
 function decodeReadFeatures(cramRecord, readFeatureCount, decodeDataSeries, compressionScheme, majorVersion) {
-  var currentReadPos = 0;
-  var currentRefPos = cramRecord.alignmentStart - 1;
-  var readFeatures = new Array(readFeatureCount);
-
-  function decodeRFData(_ref) {
-    var _ref2 = (0, _slicedToArray2.default)(_ref, 2),
-        type = _ref2[0],
-        dataSeriesName = _ref2[1];
-
-    var data = decodeDataSeries(dataSeriesName);
-
-    if (type === 'character') {
-      return String.fromCharCode(data);
+    var currentReadPos = 0;
+    var currentRefPos = cramRecord.alignmentStart - 1;
+    var readFeatures = new Array(readFeatureCount);
+    function decodeRFData(_a) {
+        var type = _a[0], dataSeriesName = _a[1];
+        var data = decodeDataSeries(dataSeriesName);
+        if (type === 'character') {
+            return String.fromCharCode(data);
+        }
+        if (type === 'string') {
+            return data.toString('utf8');
+        }
+        if (type === 'numArray') {
+            return data.toArray();
+        }
+        // else if (type === 'number') {
+        //   return data[0]
+        // }
+        return data;
     }
-
-    if (type === 'string') {
-      return data.toString('utf8');
+    for (var i = 0; i < readFeatureCount; i += 1) {
+        var code = String.fromCharCode(decodeDataSeries('FC'));
+        var readPosDelta = decodeDataSeries('FP');
+        var readFeature = { code: code };
+        // map of operator name -> data series name
+        var data1Schema = {
+            B: ['character', 'BA'],
+            S: ['string', majorVersion > 1 ? 'SC' : 'IN'],
+            X: ['number', 'BS'],
+            D: ['number', 'DL'],
+            I: ['string', 'IN'],
+            i: ['character', 'BA'],
+            b: ['string', 'BB'],
+            q: ['numArray', 'QQ'],
+            Q: ['number', 'QS'],
+            H: ['number', 'HC'],
+            P: ['number', 'PD'],
+            N: ['number', 'RS'],
+        }[code];
+        if (!data1Schema) {
+            throw new errors_1.CramMalformedError("invalid read feature code \"".concat(code, "\""));
+        }
+        readFeature.data = decodeRFData(data1Schema);
+        // if this is a tag with two data items, make the data an array and add the second item
+        var data2Schema = { B: ['number', 'QS'] }[code];
+        if (data2Schema) {
+            readFeature.data = [readFeature.data, decodeRFData(data2Schema)];
+        }
+        currentReadPos += readPosDelta;
+        readFeature.pos = currentReadPos;
+        currentRefPos += readPosDelta;
+        readFeature.refPos = currentRefPos;
+        // for gapping features, adjust the reference position for read features that follow
+        if (code === 'D' || code === 'N') {
+            currentRefPos += readFeature.data;
+        }
+        else if (code === 'I' || code === 'S') {
+            currentRefPos -= readFeature.data.length;
+        }
+        else if (code === 'i') {
+            currentRefPos -= 1;
+        }
+        readFeatures[i] = readFeature;
     }
-
-    if (type === 'numArray') {
-      return data.toArray();
-    } // else if (type === 'number') {
-    //   return data[0]
-    // }
-
-
-    return data;
-  }
-
-  for (var i = 0; i < readFeatureCount; i += 1) {
-    var code = String.fromCharCode(decodeDataSeries('FC'));
-    var readPosDelta = decodeDataSeries('FP');
-    var readFeature = {
-      code: code
-    }; // map of operator name -> data series name
-
-    var data1Schema = {
-      B: ['character', 'BA'],
-      S: ['string', majorVersion > 1 ? 'SC' : 'IN'],
-      // IN if cram v1, SC otherwise
-      X: ['number', 'BS'],
-      D: ['number', 'DL'],
-      I: ['string', 'IN'],
-      i: ['character', 'BA'],
-      b: ['string', 'BB'],
-      q: ['numArray', 'QQ'],
-      Q: ['number', 'QS'],
-      H: ['number', 'HC'],
-      P: ['number', 'PD'],
-      N: ['number', 'RS']
-    }[code];
-    if (!data1Schema) throw new CramMalformedError("invalid read feature code \"".concat(code, "\""));
-    readFeature.data = decodeRFData(data1Schema); // if this is a tag with two data items, make the data an array and add the second item
-
-    var data2Schema = {
-      B: ['number', 'QS']
-    }[code];
-    if (data2Schema) readFeature.data = [readFeature.data, decodeRFData(data2Schema)];
-    currentReadPos += readPosDelta;
-    readFeature.pos = currentReadPos;
-    currentRefPos += readPosDelta;
-    readFeature.refPos = currentRefPos; // for gapping features, adjust the reference position for read features that follow
-
-    if (code === 'D' || code === 'N') currentRefPos += readFeature.data;else if (code === 'I' || code === 'S') currentRefPos -= readFeature.data.length;else if (code === 'i') currentRefPos -= 1;
-    readFeatures[i] = readFeature;
-  }
-
-  return readFeatures;
+    return readFeatures;
 }
-
 function thingToString(thing) {
-  if (thing instanceof Buffer) {
-    return readNullTerminatedStringFromBuffer(thing);
-  }
-
-  if (thing.length && (0, _indexOf.default)(thing)) {
-    // array-like
-    if (!thing[thing.length - 1]) {
-      // trim zeroes off the end if necessary
-      var termIndex = (0, _indexOf.default)(thing).call(thing, 0);
-      return String.fromCharCode.apply(String, (0, _toConsumableArray2.default)((0, _slice.default)(thing).call(thing, 0, termIndex)));
+    if (thing instanceof Buffer) {
+        return readNullTerminatedStringFromBuffer(thing);
+    }
+    if (thing.length && thing.indexOf) {
+        // array-like
+        if (!thing[thing.length - 1]) {
+            // trim zeroes off the end if necessary
+            var termIndex = thing.indexOf(0);
+            return String.fromCharCode.apply(String, thing.slice(0, termIndex));
+        }
+        return String.fromCharCode.apply(String, thing);
     }
-
-    return String.fromCharCode.apply(String, (0, _toConsumableArray2.default)(thing));
-  }
-
-  return String(thing);
+    return String(thing);
 }
-
 function decodeRecord(slice, decodeDataSeries, compressionScheme, sliceHeader, coreDataBlock, blocksByContentId, cursors, majorVersion, recordNumber) {
-  var cramRecord = new CramRecord();
-  cramRecord.flags = decodeDataSeries('BF'); // note: the C data type of compressionFlags is byte in cram v1
-  // and int32 in cram v2+, but that does not matter for us here
-  // in javascript land.
-
-  cramRecord.cramFlags = decodeDataSeries('CF');
-  if (majorVersion > 1 && sliceHeader.content.refSeqId === -2) cramRecord.sequenceId = decodeDataSeries('RI');else cramRecord.sequenceId = sliceHeader.content.refSeqId;
-  cramRecord.readLength = decodeDataSeries('RL'); // if APDelta, will calculate the true start in a second pass
-
-  cramRecord.alignmentStart = decodeDataSeries('AP');
-  if (compressionScheme.APdelta) cramRecord.alignmentStart += cursors.lastAlignmentStart;
-  cursors.lastAlignmentStart = cramRecord.alignmentStart;
-  cramRecord.readGroupId = decodeDataSeries('RG');
-  if (compressionScheme.readNamesIncluded) cramRecord.readName = thingToString(decodeDataSeries('RN')); // mate record
-
-  if (cramRecord.isDetached()) {
-    // note: the MF is a byte in 1.0, int32 in 2+, but once again this doesn't matter for javascript
-    var mate = {};
-    mate.flags = decodeDataSeries('MF');
-
-    if (!compressionScheme.readNamesIncluded) {
-      mate.readName = thingToString(decodeDataSeries('RN'));
-      cramRecord.readName = mate.readName;
+    var cramRecord = new record_1.default();
+    cramRecord.flags = decodeDataSeries('BF');
+    // note: the C data type of compressionFlags is byte in cram v1
+    // and int32 in cram v2+, but that does not matter for us here
+    // in javascript land.
+    cramRecord.cramFlags = decodeDataSeries('CF');
+    if (majorVersion > 1 && sliceHeader.content.refSeqId === -2) {
+        cramRecord.sequenceId = decodeDataSeries('RI');
+    }
+    else {
+        cramRecord.sequenceId = sliceHeader.content.refSeqId;
+    }
+    cramRecord.readLength = decodeDataSeries('RL');
+    // if APDelta, will calculate the true start in a second pass
+    cramRecord.alignmentStart = decodeDataSeries('AP');
+    if (compressionScheme.APdelta) {
+        cramRecord.alignmentStart += cursors.lastAlignmentStart;
+    }
+    cursors.lastAlignmentStart = cramRecord.alignmentStart;
+    cramRecord.readGroupId = decodeDataSeries('RG');
+    if (compressionScheme.readNamesIncluded) {
+        cramRecord.readName = thingToString(decodeDataSeries('RN'));
+    }
+    // mate record
+    if (cramRecord.isDetached()) {
+        // note: the MF is a byte in 1.0, int32 in 2+, but once again this doesn't matter for javascript
+        var mate = {};
+        mate.flags = decodeDataSeries('MF');
+        if (!compressionScheme.readNamesIncluded) {
+            mate.readName = thingToString(decodeDataSeries('RN'));
+            cramRecord.readName = mate.readName;
+        }
+        mate.sequenceId = decodeDataSeries('NS');
+        mate.alignmentStart = decodeDataSeries('NP');
+        if (mate.flags || mate.sequenceId > -1) {
+            cramRecord.mate = mate;
+        }
+        cramRecord.templateSize = decodeDataSeries('TS');
+        // set mate unmapped if needed
+        if (mate.flags & constants_1.default.CRAM_M_UNMAP) {
+            cramRecord.flags |= constants_1.default.BAM_FMUNMAP;
+        }
+        // set mate reversed if needed
+        if (mate.flags & constants_1.default.CRAM_M_REVERSE) {
+            cramRecord.flags |= constants_1.default.BAM_FMREVERSE;
+        }
+        // detachedCount++
+    }
+    else if (cramRecord.hasMateDownStream()) {
+        cramRecord.mateRecordNumber = decodeDataSeries('NF') + recordNumber + 1;
+    }
+    // TODO: the aux tag parsing will have to be refactored if we want to support
+    // cram v1
+    var TLindex = decodeDataSeries('TL');
+    if (TLindex < 0) {
+        /* TODO: check nTL: TLindex >= compressionHeader.tagEncoding.size */
+        throw new errors_1.CramMalformedError('invalid TL index');
     }
-
-    mate.sequenceId = decodeDataSeries('NS');
-    mate.alignmentStart = decodeDataSeries('NP');
-    if ((0, _flags.default)(mate) || mate.sequenceId > -1) cramRecord.mate = mate;
-    cramRecord.templateSize = decodeDataSeries('TS'); // set mate unmapped if needed
-
-    if ((0, _flags.default)(mate) & Constants.CRAM_M_UNMAP) {
-      cramRecord.flags |= Constants.BAM_FMUNMAP;
-    } // set mate reversed if needed
-
-
-    if ((0, _flags.default)(mate) & Constants.CRAM_M_REVERSE) {
-      cramRecord.flags |= Constants.BAM_FMREVERSE;
-    } // detachedCount++
-
-  } else if (cramRecord.hasMateDownStream()) {
-    cramRecord.mateRecordNumber = decodeDataSeries('NF') + recordNumber + 1;
-  } // TODO: the aux tag parsing will have to be refactored if we want to support
-  // cram v1
-
-
-  var TLindex = decodeDataSeries('TL');
-  if (TLindex < 0)
-    /* TODO: check nTL: TLindex >= compressionHeader.tagEncoding.size */
-    throw new CramMalformedError('invalid TL index'); // TN = tag names
-
-  var TN = compressionScheme.getTagNames(TLindex);
-  var ntags = TN.length;
-
-  for (var i = 0; i < ntags; i += 1) {
-    var tagId = TN[i];
-    var tagName = tagId.substr(0, 2);
-    var tagType = tagId.substr(2, 1);
-    var tagCodec = compressionScheme.getCodecForTag(tagId);
-    if (!tagCodec) throw new CramMalformedError("no codec defined for auxiliary tag ".concat(tagId));
-    var tagData = tagCodec.decode(slice, coreDataBlock, blocksByContentId, cursors);
-    cramRecord.tags[tagName] = parseTagData(tagType, tagData);
-  }
-
-  if (!cramRecord.isSegmentUnmapped()) {
-    var _context;
-
-    // reading read features
-    var
-    /* int */
-    readFeatureCount = decodeDataSeries('FN');
-
-    if (readFeatureCount) {
-      cramRecord.readFeatures = decodeReadFeatures(cramRecord, readFeatureCount, decodeDataSeries, compressionScheme, majorVersion);
-    } // compute the read's true span on the reference sequence, and the end coordinate of the alignment on the reference
-
-
-    var lengthOnRef = cramRecord.readLength;
-    if (cramRecord.readFeatures) (0, _forEach.default)(_context = cramRecord.readFeatures).call(_context, function (_ref3) {
-      var code = _ref3.code,
-          data = _ref3.data;
-      if (code === 'D' || code === 'N') lengthOnRef += data;else if (code === 'I' || code === 'S') lengthOnRef -= data.length;else if (code === 'i') lengthOnRef -= 1;
-    });
-
-    if ((0, _isNan.default)(lengthOnRef)) {
-      var _context2;
-
-      console.warn("".concat(cramRecord.readName || (0, _concat.default)(_context2 = "".concat(cramRecord.sequenceId, ":")).call(_context2, cramRecord.alignmentStart), " record has invalid read features"));
-      lengthOnRef = cramRecord.readLength;
+    // TN = tag names
+    var TN = compressionScheme.getTagNames(TLindex);
+    var ntags = TN.length;
+    for (var i = 0; i < ntags; i += 1) {
+        var tagId = TN[i];
+        var tagName = tagId.substr(0, 2);
+        var tagType = tagId.substr(2, 1);
+        var tagCodec = compressionScheme.getCodecForTag(tagId);
+        if (!tagCodec) {
+            throw new errors_1.CramMalformedError("no codec defined for auxiliary tag ".concat(tagId));
+        }
+        var tagData = tagCodec.decode(slice, coreDataBlock, blocksByContentId, cursors);
+        cramRecord.tags[tagName] = parseTagData(tagType, tagData);
     }
-
-    cramRecord.lengthOnRef = lengthOnRef; // mapping quality
-
-    cramRecord.mappingQuality = decodeDataSeries('MQ');
-
-    if (cramRecord.isPreservingQualityScores()) {
-      var bases = new Array(cramRecord.readLength);
-
-      for (var _i = 0; _i < bases.length; _i += 1) {
-        bases[_i] = decodeDataSeries('QS');
-      }
-
-      cramRecord.qualityScores = bases;
+    if (!cramRecord.isSegmentUnmapped()) {
+        // reading read features
+        var /* int */ readFeatureCount = decodeDataSeries('FN');
+        if (readFeatureCount) {
+            cramRecord.readFeatures = decodeReadFeatures(cramRecord, readFeatureCount, decodeDataSeries, compressionScheme, majorVersion);
+        }
+        // compute the read's true span on the reference sequence, and the end coordinate of the alignment on the reference
+        var lengthOnRef_1 = cramRecord.readLength;
+        if (cramRecord.readFeatures) {
+            cramRecord.readFeatures.forEach(function (_a) {
+                var code = _a.code, data = _a.data;
+                if (code === 'D' || code === 'N') {
+                    lengthOnRef_1 += data;
+                }
+                else if (code === 'I' || code === 'S') {
+                    lengthOnRef_1 -= data.length;
+                }
+                else if (code === 'i') {
+                    lengthOnRef_1 -= 1;
+                }
+            });
+        }
+        if (Number.isNaN(lengthOnRef_1)) {
+            console.warn("".concat(cramRecord.readName ||
+                "".concat(cramRecord.sequenceId, ":").concat(cramRecord.alignmentStart), " record has invalid read features"));
+            lengthOnRef_1 = cramRecord.readLength;
+        }
+        cramRecord.lengthOnRef = lengthOnRef_1;
+        // mapping quality
+        cramRecord.mappingQuality = decodeDataSeries('MQ');
+        if (cramRecord.isPreservingQualityScores()) {
+            var bases = new Array(cramRecord.readLength);
+            for (var i = 0; i < bases.length; i += 1) {
+                bases[i] = decodeDataSeries('QS');
+            }
+            cramRecord.qualityScores = bases;
+        }
     }
-  } else if (cramRecord.isUnknownBases()) {
-    cramRecord.readBases = null;
-    cramRecord.qualityScores = null;
-  } else {
-    var _bases = new Array(cramRecord.readLength);
-
-    for (var _i2 = 0; _i2 < _bases.length; _i2 += 1) {
-      _bases[_i2] = decodeDataSeries('BA');
+    else if (cramRecord.isUnknownBases()) {
+        cramRecord.readBases = null;
+        cramRecord.qualityScores = null;
     }
-
-    cramRecord.readBases = String.fromCharCode.apply(String, _bases);
-
-    if (cramRecord.isPreservingQualityScores()) {
-      for (var _i3 = 0; _i3 < _bases.length; _i3 += 1) {
-        _bases[_i3] = decodeDataSeries('QS');
-      }
-
-      cramRecord.qualityScores = _bases;
+    else {
+        var bases = new Array(cramRecord.readLength);
+        for (var i = 0; i < bases.length; i += 1) {
+            bases[i] = decodeDataSeries('BA');
+        }
+        cramRecord.readBases = String.fromCharCode.apply(String, bases);
+        if (cramRecord.isPreservingQualityScores()) {
+            for (var i = 0; i < bases.length; i += 1) {
+                bases[i] = decodeDataSeries('QS');
+            }
+            cramRecord.qualityScores = bases;
+        }
     }
-  }
-
-  return cramRecord;
+    return cramRecord;
 }
-
-module.exports = decodeRecord;
+exports.default = decodeRecord;
+//# sourceMappingURL=decodeRecord.js.map