@gmod/bam 1.1.18 → 2.0.1

package/dist/htsget.js.map

@@ -1 +1 @@
-{"version":3,"file":"htsget.js","sourceRoot":"","sources":["../src/htsget.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AACA,qDAA8C;AAC9C,gCAA6B;AAE7B,2DAA6C;AAC7C,+BAAuC;AAWvC,SAAe,MAAM,CAAC,GAAsB,EAAE,IAAyB;;QACrE,MAAM,GAAG,GAAG,MAAM,OAAO,CAAC,GAAG,CAC3B,GAAG,CAAC,GAAG,CAAC,CAAO,KAAkB,EAAE,EAAE;YACnC,MAAM,EAAE,GAAG,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;YAC9B,IAAI,GAAG,CAAC,UAAU,CAAC,OAAO,CAAC,EAAE;gBAC3B,OAAO,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,QAAQ,CAAC,CAAA;aAChD;iBAAM;gBACL,+DAA+D;gBAC/D,YAAY;gBACZ,4DAA4D;gBAC5D,MAAM,EAAE,OAAO,KAAc,OAAO,EAAhB,IAAI,UAAK,OAAO,EAA9B,WAAoB,CAAU,CAAA;gBACpC,MAAM,GAAG,GAAG,MAAM,KAAK,CAAC,GAAG,kCACtB,IAAI,KACP,OAAO,kCAAO,IAAI,CAAC,OAAO,GAAK,IAAI,KACnC,CAAA;gBACF,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE;oBACX,MAAM,IAAI,KAAK,CAAC,mBAAmB,GAAG,CAAC,UAAU,EAAE,CAAC,CAAA;iBACrD;gBACD,OAAO,MAAM,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,WAAW,EAAE,CAAC,CAAA;aAC5C;QACH,CAAC,CAAA,CAAC,CACH,CAAA;QAED,OAAO,MAAM,CAAC,MAAM,CAAC,MAAM,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,IAAA,uBAAK,EAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAA;IACrE,CAAC;CAAA;AAED,MAAqB,UAAW,SAAQ,iBAAO;IAK7C,YAAY,IAA0C;QACpD,mCAAmC;QACnC,KAAK,CAAC,EAAE,aAAa,EAAE,GAAG,EAAE,aAAa,EAAE,GAAG,EAAE,CAAC,CAAA;QACjD,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;QAC3B,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;IAC7B,CAAC;IAEM,qBAAqB,CAC1B,GAAW,EACX,GAAW,EACX,GAAW,EACX,OAAgB;QACd,WAAW,EAAE,KAAK;QAClB,aAAa,EAAE,KAAK;QACpB,aAAa,EAAE,MAAM;KACtB;;YAED,MAAM,IAAI,GAAG,GAAG,IAAI,CAAC,OAAO,IAAI,IAAI,CAAC,OAAO,EAAE,CAAA;YAC9C,MAAM,GAAG,GAAG,GAAG,IAAI,kBAAkB,GAAG,UAAU,GAAG,QAAQ,GAAG,aAAa,CAAA;YAC7E,MAAM,KAAK,GAAG,IAAI,CAAC,UAAU,IAAI,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,CAAA;YACrD,MAAM,MAAM,GAAG,cAAM,KAAK,CAAC,GAAG,oBAAO,IAAI,EAAG,CAAA,CAAA;YAC5C,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE;gBACd,MAAM,IAAI,KAAK,CAAC,MAAM,CAAC,UAAU,CAAC,CAAA;aACnC;YACD,MAAM,IAAI,GAAG,cAAM,MAAM,CAAC,IAAI,EAAE,CAAA,CAAA;YAChC,MAAM,KAAK,GAAG,cAAM,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA,CAAA;YAC3D,MAAM,KAAK,GAAG;gBACZ,MAAM,EAAE,KAAK;gBACb,KAAK,EAAE,EAAE,IAAI,EAAE,EAAE,YAAY,EAAE,CAAC,EAAE,EAAE;gBACpC,QAAQ;oBACN,OAAO,GAAG,GAAG,IAAI,GAAG,IAAI,GAAG,EAAE,CAAA;gBAC/B,CAAC;aACF,CAAA;YAED,cAAA,KAAK,CAAC,CAAC,iBAAA,cAAA,IAAI,CAAC,mBAAmB;YAC7B,aAAa;YACb,CAAC,KAAK,CAAC,EACP,KAAK,EACL,GAAG,EACH,GAAG,EACH,IAAI,CACL,CAAA,CAAA,CAAA,CAAA;QACH,CAAC;KAAA;IAED,YAAY;IACN,UAAU,CAAC,MAGhB;;YACC,MAAM,EAAE,KAAK,EAAE,GAAG,MAAM,CAAA;YACxB,MAAM,EAAE,MAAM,EAAE,KAAK,EAAE,EAAE,EAAE,GAAG,KAAK,CAAA;YACnC,OAAO,EAAE,IAAI,EAAE,MAAM,EAAE,UAAU,EAAE,IAAI,EAAE,UAAU,EAAE,IAAI,EAAE,KAAK,EAAE,EAAE,EAAE,CAAA;QACxE,CAAC;KAAA;IAEK,SAAS,CAAC,OAAiB,EAAE;;YACjC,MAAM,GAAG,GAAG,GAAG,IAAI,CAAC,OAAO,IAAI,IAAI,CAAC,OAAO,gCAAgC,CAAA;YAC3E,MAAM,MAAM,GAAG,MAAM,KAAK,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;YACrC,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE;gBACd,MAAM,IAAI,KAAK,CAAC,mBAAmB,MAAM,CAAC,UAAU,EAAE,CAAC,CAAA;aACxD;YACD,MAAM,IAAI,GAAG,MAAM,MAAM,CAAC,IAAI,EAAE,CAAA;YAChC,MAAM,KAAK,GAAG,MAAM,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YAElD,IAAI,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,KAAK,mBAAS,EAAE;gBACtC,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;aAClC;YACD,MAAM,OAAO,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;YAEpC,MAAM,UAAU,GAAG,KAAK,CAAC,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,CAAC,GAAG,OAAO,CAAC,CAAA;YACzD,MAAM,SAAS,GAAG,IAAA,qBAAe,EAAC,UAAU,CAAC,CAAA;YAE7C,oDAAoD;YACpD,+CAA+C;YAC/C,MAAM,QAAQ,GAAa,EAAE,CAAA;YAC7B,MAAM,QAAQ,GAA2B,EAAE,CAAA;YAC3C,MAAM,OAAO,GAAG,SAAS,CAAC,MAAM,CAAC,CAAC,CAAkB,EAAE,EAAE,CAAC,CAAC,CAAC,GAAG,KAAK,IAAI,CAAC,CAAA;YACxE,OAAO,CAAC,OAAO,CAAC,CAAC,MAA8B,EAAE,KAAa,EAAE,EAAE;gBAChE,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,IAAgB,EAAE,EAAE;oBACvC,IAAI,IAAI,CAAC,GAAG,KAAK,IAAI,EAAE;wBACrB,uBAAuB;wBACvB,MAAM,OAAO,GAAG,IAAI,CAAC,KAAK,CAAA;wBAC1B,QAAQ,CAAC,OAAO,CAAC,GAAG,KAAK,CAAA;wBACzB,QAAQ,CAAC,KAAK,CAAC,GAAG,OAAO,CAAA;qBAC1B;gBACH,CAAC,CAAC,CAAA;YACJ,CAAC,CAAC,CAAA;YACF,IAAI,CAAC,UAAU,GAAG,QAAQ,CAAA;YAC1B,IAAI,CAAC,UAAU,GAAG,QAAQ,CAAA;YAC1B,OAAO,SAAS,CAAA;QAClB,CAAC;KAAA;CACF;AA/FD,6BA+FC"}
+{"version":3,"file":"htsget.js","sourceRoot":"","sources":["../src/htsget.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,2DAA6C;AAC7C,mCAA+B;AAE/B,qDAA8C;AAE9C,+BAAuC;AAMvC,SAAe,MAAM,CAAC,GAAkB,EAAE,IAA0B;;QAClE,MAAM,GAAG,GAAG,MAAM,OAAO,CAAC,GAAG,CAC3B,GAAG,CAAC,GAAG,CAAC,CAAM,KAAK,EAAC,EAAE;YACpB,MAAM,EAAE,GAAG,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;YAC9B,IAAI,GAAG,CAAC,UAAU,CAAC,OAAO,CAAC,EAAE,CAAC;gBAC5B,OAAO,eAAM,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,QAAQ,CAAC,CAAA;YACjD,CAAC;iBAAM,CAAC;gBACN,+DAA+D;gBAC/D,mBAAmB;gBACnB,4DAA4D;gBAC5D,MAAM,EAAE,OAAO,KAAc,OAAO,EAAhB,IAAI,UAAK,OAAO,EAA9B,WAAoB,CAAU,CAAA;gBACpC,MAAM,GAAG,GAAG,MAAM,KAAK,CAAC,GAAG,kCACtB,IAAI,KACP,OAAO,kCAAO,IAAI,aAAJ,IAAI,uBAAJ,IAAI,CAAE,OAAO,GAAK,IAAI,KACpC,CAAA;gBACF,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC;oBACZ,MAAM,IAAI,KAAK,CACb,QAAQ,GAAG,CAAC,MAAM,aAAa,GAAG,KAAK,MAAM,GAAG,CAAC,IAAI,EAAE,EAAE,CAC1D,CAAA;gBACH,CAAC;gBACD,OAAO,eAAM,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,WAAW,EAAE,CAAC,CAAA;YAC7C,CAAC;QACH,CAAC,CAAA,CAAC,CACH,CAAA;QAED,OAAO,eAAM,CAAC,MAAM,CAAC,MAAM,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,IAAA,uBAAK,EAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAA;IACrE,CAAC;CAAA;AAED,MAAqB,UAAW,SAAQ,iBAAO;IAK7C,YAAY,IAA0C;QACpD,KAAK,CAAC,EAAE,MAAM,EAAE,IAAI,EAAE,CAAC,CAAA;QACvB,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;QAC3B,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;IAC7B,CAAC;IAEM,qBAAqB,CAC1B,GAAW,EACX,GAAW,EACX,GAAW,EACX,IAAc;;;YAEd,MAAM,IAAI,GAAG,GAAG,IAAI,CAAC,OAAO,IAAI,IAAI,CAAC,OAAO,EAAE,CAAA;YAC9C,MAAM,GAAG,GAAG,GAAG,IAAI,kBAAkB,GAAG,UAAU,GAAG,QAAQ,GAAG,aAAa,CAAA;YAC7E,MAAM,KAAK,GAAG,MAAA,IAAI,CAAC,UAAU,0CAAG,GAAG,CAAC,CAAA;YACpC,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;gBACxB,oBAAM,EAAE,CAAA,CAAA;YACV,CAAC;iBAAM,CAAC;gBACN,MAAM,MAAM,GAAG,cAAM,KAAK,CAAC,GAAG,oBAAO,IAAI,EAAG,CAAA,CAAA;gBAC5C,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE,CAAC;oBACf,MAAM,IAAI,KAAK,CACb,QAAQ,MAAM,CAAC,MAAM,aAAa,GAAG,KAAK,cAAM,MAAM,CAAC,IAAI,EAAE,CAAA,EAAE,CAChE,CAAA;gBACH,CAAC;gBACD,MAAM,IAAI,GAAG,cAAM,MAAM,CAAC,IAAI,EAAE,CAAA,CAAA;gBAChC,MAAM,KAAK,GAAG,cAAM,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA,CAAA;gBAE3D,cAAA,KAAK,CAAC,CAAC,iBAAA,cAAA,IAAI,CAAC,mBAAmB,CAC7B;oBACE,sCAAsC;oBACtC;wBACE,MAAM,EAAE,KAAK;wBACb,YAAY,EAAE,SAAS;wBACvB,GAAG,EAAE,CAAC;wBACN,SAAS;4BACP,OAAO,CAAC,CAAA;wBACV,CAAC;wBACD,cAAc;4BACZ,OAAO,GAAG,GAAG,IAAI,GAAG,IAAI,GAAG,EAAE,CAAA;wBAC/B,CAAC;wBACD,WAAW;4BACT,OAAO,CAAC,CAAA;wBACV,CAAC;wBACD,IAAI,EAAE;4BACJ,YAAY,EAAE,CAAC;4BACf,aAAa,EAAE,CAAC;4BAChB,SAAS,EAAE,GAAG,EAAE,CAAC,CAAC;yBACnB;wBACD,IAAI,EAAE;4BACJ,YAAY,EAAE,MAAM,CAAC,gBAAgB;4BACrC,aAAa,EAAE,CAAC;4BAChB,SAAS,EAAE,GAAG,EAAE,CAAC,CAAC;yBACnB;wBACD,QAAQ;4BACN,OAAO,GAAG,GAAG,IAAI,GAAG,IAAI,GAAG,EAAE,CAAA;wBAC/B,CAAC;qBACF;iBACF,EACD,KAAK,EACL,GAAG,EACH,GAAG,EACH,IAAI,CACL,CAAA,CAAA,CAAA,CAAA;YACH,CAAC;;KACF;IAEK,UAAU,CAAC,EAAE,KAAK,EAAoC;;YAC1D,IAAI,CAAC,KAAK,CAAC,MAAM,EAAE,CAAC;gBAClB,MAAM,IAAI,KAAK,CAAC,iCAAiC,CAAC,CAAA;YACpD,CAAC;YACD,OAAO,EAAE,IAAI,EAAE,KAAK,CAAC,MAAM,EAAE,UAAU,EAAE,EAAE,EAAE,UAAU,EAAE,EAAE,EAAE,KAAK,EAAE,CAAA;QACtE,CAAC;KAAA;IAEK,SAAS,CAAC,OAAiB,EAAE;;YACjC,MAAM,GAAG,GAAG,GAAG,IAAI,CAAC,OAAO,IAAI,IAAI,CAAC,OAAO,gCAAgC,CAAA;YAC3E,MAAM,MAAM,GAAG,MAAM,KAAK,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;YACrC,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE,CAAC;gBACf,MAAM,IAAI,KAAK,CACb,QAAQ,MAAM,CAAC,MAAM,aAAa,GAAG,KAAK,MAAM,MAAM,CAAC,IAAI,EAAE,EAAE,CAChE,CAAA;YACH,CAAC;YACD,MAAM,IAAI,GAAG,MAAM,MAAM,CAAC,IAAI,EAAE,CAAA;YAChC,MAAM,KAAK,GAAG,MAAM,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YAElD,IAAI,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,KAAK,mBAAS,EAAE,CAAC;gBACvC,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;YACnC,CAAC;YACD,MAAM,OAAO,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;YACpC,MAAM,UAAU,GAAG,KAAK,CAAC,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,CAAC,GAAG,OAAO,CAAC,CAAA;YACzD,MAAM,SAAS,GAAG,IAAA,qBAAe,EAAC,UAAU,CAAC,CAAA;YAE7C,oDAAoD;YACpD,+CAA+C;YAC/C,MAAM,QAAQ,GAA0C,EAAE,CAAA;YAC1D,MAAM,QAAQ,GAA2B,EAAE,CAAA;YAC3C,MAAM,OAAO,GAAG,SAAS,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,KAAK,IAAI,CAAC,CAAA;YACrD,KAAK,MAAM,CAAC,KAAK,EAAE,MAAM,CAAC,IAAI,OAAO,CAAC,OAAO,EAAE,EAAE,CAAC;gBAChD,IAAI,OAAO,GAAG,EAAE,CAAA;gBAChB,IAAI,MAAM,GAAG,CAAC,CAAA;gBACd,KAAK,MAAM,IAAI,IAAI,MAAM,CAAC,IAAI,EAAE,CAAC;oBAC/B,IAAI,IAAI,CAAC,GAAG,KAAK,IAAI,EAAE,CAAC;wBACtB,OAAO,GAAG,IAAI,CAAC,KAAK,CAAA;oBACtB,CAAC;yBAAM,IAAI,IAAI,CAAC,GAAG,KAAK,IAAI,EAAE,CAAC;wBAC7B,MAAM,GAAG,CAAC,IAAI,CAAC,KAAK,CAAA;oBACtB,CAAC;gBACH,CAAC;gBACD,QAAQ,CAAC,OAAO,CAAC,GAAG,KAAK,CAAA;gBACzB,QAAQ,CAAC,KAAK,CAAC,GAAG,EAAE,OAAO,EAAE,MAAM,EAAE,CAAA;YACvC,CAAC;YACD,IAAI,CAAC,UAAU,GAAG,QAAQ,CAAA;YAC1B,IAAI,CAAC,UAAU,GAAG,QAAQ,CAAA;YAC1B,OAAO,SAAS,CAAA;QAClB,CAAC;KAAA;CACF;AAtHD,6BAsHC"}

package/dist/index.d.ts

@@ -1,6 +1,5 @@
-import BAI from './bai';
-import CSI from './csi';
-import BamFile from './bamFile';
-import HtsgetFile from './htsget';
-import BamRecord from './record';
-export { BAI, CSI, BamFile, BamRecord, HtsgetFile };
+export { default as BAI } from './bai';
+export { default as BamFile } from './bamFile';
+export { default as CSI } from './csi';
+export { default as BamRecord } from './record';
+export { default as HtsgetFile } from './htsget';

package/dist/index.js

@@ -3,15 +3,15 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.HtsgetFile = exports.BamRecord = exports.BamFile = exports.CSI = exports.BAI = void 0;
-const bai_1 = __importDefault(require("./bai"));
-exports.BAI = bai_1.default;
-const csi_1 = __importDefault(require("./csi"));
-exports.CSI = csi_1.default;
-const bamFile_1 = __importDefault(require("./bamFile"));
-exports.BamFile = bamFile_1.default;
-const htsget_1 = __importDefault(require("./htsget"));
-exports.HtsgetFile = htsget_1.default;
-const record_1 = __importDefault(require("./record"));
-exports.BamRecord = record_1.default;
+exports.HtsgetFile = exports.BamRecord = exports.CSI = exports.BamFile = exports.BAI = void 0;
+var bai_1 = require("./bai");
+Object.defineProperty(exports, "BAI", { enumerable: true, get: function () { return __importDefault(bai_1).default; } });
+var bamFile_1 = require("./bamFile");
+Object.defineProperty(exports, "BamFile", { enumerable: true, get: function () { return __importDefault(bamFile_1).default; } });
+var csi_1 = require("./csi");
+Object.defineProperty(exports, "CSI", { enumerable: true, get: function () { return __importDefault(csi_1).default; } });
+var record_1 = require("./record");
+Object.defineProperty(exports, "BamRecord", { enumerable: true, get: function () { return __importDefault(record_1).default; } });
+var htsget_1 = require("./htsget");
+Object.defineProperty(exports, "HtsgetFile", { enumerable: true, get: function () { return __importDefault(htsget_1).default; } });
 //# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;AAAA,gDAAuB;AAMd,cANF,aAAG,CAME;AALZ,gDAAuB;AAKT,cALP,aAAG,CAKO;AAJjB,wDAA+B;AAIZ,kBAJZ,iBAAO,CAIY;AAH1B,sDAAiC;AAGM,qBAHhC,gBAAU,CAGgC;AAFjD,sDAAgC;AAEJ,oBAFrB,gBAAS,CAEqB"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;AAAA,6BAAsC;AAA7B,2GAAA,OAAO,OAAO;AACvB,qCAA8C;AAArC,mHAAA,OAAO,OAAW;AAC3B,6BAAsC;AAA7B,2GAAA,OAAO,OAAO;AACvB,mCAA+C;AAAtC,oHAAA,OAAO,OAAa;AAC7B,mCAAgD;AAAvC,qHAAA,OAAO,OAAc"}

package/dist/indexFile.d.ts

@@ -1,11 +1,9 @@
 import { GenericFilehandle } from 'generic-filehandle';
-import VirtualOffset from './virtualOffset';
 import Chunk from './chunk';
 import { BaseOpts } from './util';
 export default abstract class IndexFile {
     filehandle: GenericFilehandle;
     renameRefSeq: (s: string) => string;
-    setupP?: Promise<any>;
     /**
      * @param {filehandle} filehandle
      * @param {function} [renameRefSeqs]
@@ -15,14 +13,10 @@ export default abstract class IndexFile {
         renameRefSeq?: (a: string) => string;
     });
     abstract lineCount(refId: number): Promise<number>;
-    protected abstract _parse(opts?: BaseOpts): Promise<any>;
     abstract indexCov(refId: number, start?: number, end?: number): Promise<{
         start: number;
         end: number;
         score: number;
     }[]>;
     abstract blocksForRange(chrId: number, start: number, end: number, opts?: BaseOpts): Promise<Chunk[]>;
-    _findFirstData(data: any, virtualOffset: VirtualOffset): void;
-    parse(opts?: BaseOpts): Promise<any>;
-    hasRefSeq(seqId: number, opts?: BaseOpts): Promise<boolean>;
 }

package/dist/indexFile.js

@@ -1,13 +1,4 @@
 "use strict";
-var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
-    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
-    return new (P || (P = Promise))(function (resolve, reject) {
-        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
-        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
-        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
-        step((generator = generator.apply(thisArg, _arguments || [])).next());
-    });
-};
 Object.defineProperty(exports, "__esModule", { value: true });
 class IndexFile {
     /**
@@ -18,32 +9,6 @@ class IndexFile {
         this.filehandle = filehandle;
         this.renameRefSeq = renameRefSeq;
     }
-    _findFirstData(data, virtualOffset) {
-        const currentFdl = data.firstDataLine;
-        if (currentFdl) {
-            data.firstDataLine =
-                currentFdl.compareTo(virtualOffset) > 0 ? virtualOffset : currentFdl;
-        }
-        else {
-            data.firstDataLine = virtualOffset;
-        }
-    }
-    parse(opts = {}) {
-        return __awaiter(this, void 0, void 0, function* () {
-            if (!this.setupP) {
-                this.setupP = this._parse(opts).catch(e => {
-                    this.setupP = undefined;
-                    throw e;
-                });
-            }
-            return this.setupP;
-        });
-    }
-    hasRefSeq(seqId, opts = {}) {
-        return __awaiter(this, void 0, void 0, function* () {
-            return !!((yield this.parse(opts)).indices[seqId] || {}).binIndex;
-        });
-    }
 }
 exports.default = IndexFile;
 //# sourceMappingURL=indexFile.js.map

package/dist/indexFile.js.map

@@ -1 +1 @@
-{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":";;;;;;;;;;;AAKA,MAA8B,SAAS;IAKrC;;;OAGG;IACH,YAAY,EACV,UAAU,EACV,YAAY,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,GAIhC;QACC,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;QAC5B,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA;IAClC,CAAC;IAgBD,cAAc,CAAC,IAAS,EAAE,aAA4B;QACpD,MAAM,UAAU,GAAG,IAAI,CAAC,aAAa,CAAA;QACrC,IAAI,UAAU,EAAE;YACd,IAAI,CAAC,aAAa;gBAChB,UAAU,CAAC,SAAS,CAAC,aAAa,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,aAAa,CAAC,CAAC,CAAC,UAAU,CAAA;SACvE;aAAM;YACL,IAAI,CAAC,aAAa,GAAG,aAAa,CAAA;SACnC;IACH,CAAC;IAEK,KAAK,CAAC,OAAiB,EAAE;;YAC7B,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE;gBAChB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;oBACxC,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;oBACvB,MAAM,CAAC,CAAA;gBACT,CAAC,CAAC,CAAA;aACH;YACD,OAAO,IAAI,CAAC,MAAM,CAAA;QACpB,CAAC;KAAA;IAEK,SAAS,CAAC,KAAa,EAAE,OAAiB,EAAE;;YAChD,OAAO,CAAC,CAAC,CAAC,CAAC,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,OAAO,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC,QAAQ,CAAA;QACnE,CAAC;KAAA;CACF;AAzDD,4BAyDC"}
+{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":";;AAIA,MAA8B,SAAS;IAIrC;;;OAGG;IACH,YAAY,EACV,UAAU,EACV,YAAY,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,GAIhC;QACC,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;QAC5B,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA;IAClC,CAAC;CAcF;AA/BD,4BA+BC"}

package/dist/nullIndex.d.ts

@@ -0,0 +1,7 @@
+import IndexFile from './indexFile';
+export default class NullIndex extends IndexFile {
+    lineCount(): Promise<any>;
+    protected _parse(): Promise<any>;
+    indexCov(): Promise<any>;
+    blocksForRange(): Promise<any>;
+}

package/dist/nullIndex.js

@@ -0,0 +1,33 @@
+"use strict";
+var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
+    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
+    return new (P || (P = Promise))(function (resolve, reject) {
+        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
+        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
+        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
+        step((generator = generator.apply(thisArg, _arguments || [])).next());
+    });
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const indexFile_1 = __importDefault(require("./indexFile"));
+class NullIndex extends indexFile_1.default {
+    lineCount() {
+        throw new Error('never called');
+    }
+    _parse() {
+        throw new Error('never called');
+    }
+    indexCov() {
+        return __awaiter(this, void 0, void 0, function* () {
+            throw new Error('never called');
+        });
+    }
+    blocksForRange() {
+        throw new Error('never called');
+    }
+}
+exports.default = NullIndex;
+//# sourceMappingURL=nullIndex.js.map

package/dist/nullIndex.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"nullIndex.js","sourceRoot":"","sources":["../src/nullIndex.ts"],"names":[],"mappings":";;;;;;;;;;;;;;AAAA,4DAAmC;AAEnC,MAAqB,SAAU,SAAQ,mBAAS;IACvC,SAAS;QACd,MAAM,IAAI,KAAK,CAAC,cAAc,CAAC,CAAA;IACjC,CAAC;IACS,MAAM;QACd,MAAM,IAAI,KAAK,CAAC,cAAc,CAAC,CAAA;IACjC,CAAC;IAEY,QAAQ;;YACnB,MAAM,IAAI,KAAK,CAAC,cAAc,CAAC,CAAA;QACjC,CAAC;KAAA;IAEM,cAAc;QACnB,MAAM,IAAI,KAAK,CAAC,cAAc,CAAC,CAAA;IACjC,CAAC;CACF;AAfD,4BAeC"}

package/dist/record.d.ts

@@ -17,7 +17,7 @@ export default class BamRecord {
     seq_id(): number;
     _get(field: string): any;
     _tags(): string[];
-    parent(): undefined;
+    parent(): void;
     children(): any;
     id(): number;
     /**
@@ -75,7 +75,7 @@ export default class BamRecord {
     _seq_bytes(): number;
     getReadBases(): string;
     seq(): string;
-    getPairOrientation(): string | null;
+    getPairOrientation(): string;
     _bin_mq_nl(): number;
     _flag_nc(): number;
     seq_length(): number;

package/dist/record.js

@@ -3,7 +3,6 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-/* eslint-disable @typescript-eslint/no-empty-function */
 const constants_1 = __importDefault(require("./constants"));
 const SEQRET_DECODER = '=ACMGRSVTWYHKDBN'.split('');
 const CIGAR_DECODER = 'MIDNSHP=X???????'.split('');
@@ -62,11 +61,11 @@ class BamRecord {
             tags.push('next_segment_position', 'pair_orientation');
         }
         tags = tags.concat(this._tagList || []);
-        Object.keys(this.data).forEach(k => {
+        for (const k of Object.keys(this.data)) {
             if (k[0] !== '_' && k !== 'next_seq_id') {
                 tags.push(k);
             }
-        });
+        }
         const seen = {};
         return tags.filter(t => {
             if ((t in this.data && this.data[t] === undefined) ||
@@ -81,7 +80,7 @@ class BamRecord {
         });
     }
     parent() {
-        return undefined;
+        return;
     }
     children() {
         return this.get('subfeatures');
@@ -106,7 +105,7 @@ class BamRecord {
     }
     qualRaw() {
         if (this.isSegmentUnmapped()) {
-            return undefined;
+            return;
         }
         const { start, byteArray } = this.bytes;
         const p = start +
@@ -122,7 +121,7 @@ class BamRecord {
     }
     multi_segment_next_segment_strand() {
         if (this.isMateUnmapped()) {
-            return undefined;
+            return;
         }
         return this.isMateReverseComplemented() ? -1 : 1;
     }
@@ -143,7 +142,7 @@ class BamRecord {
         // called, we already know that we have no such tag, because
         // it would already have been cached.
         if (this._allTagsParsed) {
-            return undefined;
+            return;
         }
         const { byteArray, start } = this.bytes;
         let p = this._tagOffset ||
@@ -162,40 +161,48 @@ class BamRecord {
             p += 3;
             let value;
             switch (type) {
-                case 'A':
+                case 'A': {
                     value = String.fromCharCode(byteArray[p]);
                     p += 1;
                     break;
-                case 'i':
+                }
+                case 'i': {
                     value = byteArray.readInt32LE(p);
                     p += 4;
                     break;
-                case 'I':
+                }
+                case 'I': {
                     value = byteArray.readUInt32LE(p);
                     p += 4;
                     break;
-                case 'c':
+                }
+                case 'c': {
                     value = byteArray.readInt8(p);
                     p += 1;
                     break;
-                case 'C':
+                }
+                case 'C': {
                     value = byteArray.readUInt8(p);
                     p += 1;
                     break;
-                case 's':
+                }
+                case 's': {
                     value = byteArray.readInt16LE(p);
                     p += 2;
                     break;
-                case 'S':
+                }
+                case 'S': {
                     value = byteArray.readUInt16LE(p);
                     p += 2;
                     break;
-                case 'f':
+                }
+                case 'f': {
                     value = byteArray.readFloatLE(p);
                     p += 4;
                     break;
+                }
                 case 'Z':
-                case 'H':
+                case 'H': {
                     value = '';
                     while (p <= blockEnd) {
                         const cc = byteArray[p++];
@@ -207,6 +214,7 @@ class BamRecord {
                         }
                     }
                     break;
+                }
                 case 'B': {
                     value = '';
                     const cc = byteArray[p++];
@@ -300,10 +308,11 @@ class BamRecord {
                     }
                     break;
                 }
-                default:
+                default: {
                     console.warn(`Unknown BAM tag type '${type}', tags may be incomplete`);
                     value = undefined;
-                    p = blockEnd; // stop parsing tags
+                    p = blockEnd;
+                } // stop parsing tags
             }
             this._tagOffset = p;
             this._tagList.push(tag);
@@ -313,7 +322,7 @@ class BamRecord {
             this.data[lcTag] = value;
         }
         this._allTagsParsed = true;
-        return undefined;
+        return;
     }
     _parseAllTags() {
         this._parseTag('');
@@ -324,7 +333,7 @@ class BamRecord {
         cigar
             .match(/\d+\D/g)
             //@ts-ignore
-            .map(op => [op.match(/\D/)[0].toUpperCase(), parseInt(op, 10)]));
+            .map(op => [op.match(/\D/)[0].toUpperCase(), Number.parseInt(op, 10)]));
     }
     /**
      * @returns {boolean} true if the read is paired, regardless of whether both segments are mapped
@@ -378,7 +387,7 @@ class BamRecord {
     }
     cigar() {
         if (this.isSegmentUnmapped()) {
-            return undefined;
+            return;
         }
         const { byteArray, start } = this.bytes;
         const numCigarOps = this.get('_n_cigar_op');
@@ -497,7 +506,7 @@ class BamRecord {
             }
             return tmp.join('');
         }
-        return null;
+        return '';
     }
     _bin_mq_nl() {
         return this.bytes.byteArray.readInt32LE(this.bytes.start + 12);
@@ -519,13 +528,13 @@ class BamRecord {
     }
     toJSON() {
         const data = {};
-        Object.keys(this).forEach(k => {
+        for (const k of Object.keys(this)) {
             if (k.charAt(0) === '_' || k === 'bytes') {
-                return;
+                continue;
             }
             //@ts-ignore
             data[k] = this[k];
-        });
+        }
         return data;
     }
 }

package/dist/record.js.map

@@ -1 +1 @@
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package/dist/sam.js

@@ -4,16 +4,20 @@ exports.parseHeaderText = void 0;
 function parseHeaderText(text) {
     const lines = text.split(/\r?\n/);
     const data = [];
-    lines.forEach(line => {
+    for (const line of lines) {
         const [tag, ...fields] = line.split(/\t/);
-        const parsedFields = fields.map(f => {
-            const [fieldTag, value] = f.split(':', 2);
-            return { tag: fieldTag, value };
-        });
         if (tag) {
-            data.push({ tag: tag.substr(1), data: parsedFields });
+            data.push({
+                tag: tag.slice(1),
+                data: fields.map(f => {
+                    const r = f.indexOf(':');
+                    const fieldTag = f.slice(0, r);
+                    const value = f.slice(r + 1);
+                    return { tag: fieldTag, value };
+                }),
+            });
         }
-    });
+    }
     return data;
 }
 exports.parseHeaderText = parseHeaderText;

package/dist/sam.js.map

@@ -1 +1 @@
-{"version":3,"file":"sam.js","sourceRoot":"","sources":["../src/sam.ts"],"names":[],"mappings":";;;AAAA,SAAgB,eAAe,CAAC,IAAY;IAC1C,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA;IACjC,MAAM,IAAI,GAA8D,EAAE,CAAA;IAC1E,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE;QACnB,MAAM,CAAC,GAAG,EAAE,GAAG,MAAM,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACzC,MAAM,YAAY,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE;YAClC,MAAM,CAAC,QAAQ,EAAE,KAAK,CAAC,GAAG,CAAC,CAAC,KAAK,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;YACzC,OAAO,EAAE,GAAG,EAAE,QAAQ,EAAE,KAAK,EAAE,CAAA;QACjC,CAAC,CAAC,CAAA;QACF,IAAI,GAAG,EAAE;YACP,IAAI,CAAC,IAAI,CAAC,EAAE,GAAG,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,IAAI,EAAE,YAAY,EAAE,CAAC,CAAA;SACtD;IACH,CAAC,CAAC,CAAA;IACF,OAAO,IAAI,CAAA;AACb,CAAC;AAdD,0CAcC"}
+{"version":3,"file":"sam.js","sourceRoot":"","sources":["../src/sam.ts"],"names":[],"mappings":";;;AAAA,SAAgB,eAAe,CAAC,IAAY;IAC1C,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA;IACjC,MAAM,IAAI,GAA8D,EAAE,CAAA;IAC1E,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;QACzB,MAAM,CAAC,GAAG,EAAE,GAAG,MAAM,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACzC,IAAI,GAAG,EAAE,CAAC;YACR,IAAI,CAAC,IAAI,CAAC;gBACR,GAAG,EAAE,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC;gBACjB,IAAI,EAAE,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE;oBACnB,MAAM,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;oBACxB,MAAM,QAAQ,GAAG,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;oBAC9B,MAAM,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;oBAC5B,OAAO,EAAE,GAAG,EAAE,QAAQ,EAAE,KAAK,EAAE,CAAA;gBACjC,CAAC,CAAC;aACH,CAAC,CAAA;QACJ,CAAC;IACH,CAAC;IACD,OAAO,IAAI,CAAA;AACb,CAAC;AAlBD,0CAkBC"}

package/dist/util.d.ts

@@ -1,3 +1,5 @@
+/// <reference types="node" />
+import Long from 'long';
 import Chunk from './chunk';
 import VirtualOffset from './virtualOffset';
 export declare function timeout(ms: number): Promise<unknown>;
@@ -32,4 +34,14 @@ export interface BaseOpts {
     signal?: AbortSignal;
 }
 export declare function makeOpts(obj?: AbortSignal | BaseOpts): BaseOpts;
-export declare function optimizeChunks(chunks: Chunk[], lowest: VirtualOffset): Chunk[];
+export declare function optimizeChunks(chunks: Chunk[], lowest?: VirtualOffset): Chunk[];
+export declare function parsePseudoBin(bytes: Buffer, offset: number): {
+    lineCount: number;
+};
+export declare function findFirstData(firstDataLine: VirtualOffset | undefined, virtualOffset: VirtualOffset): VirtualOffset;
+export declare function parseNameBytes(namesBytes: Buffer, renameRefSeq?: (arg: string) => string): {
+    refNameToId: {
+        [key: string]: number;
+    };
+    refIdToName: string[];
+};