@gmod/bam 8.7.0 → 8.8.0

package/dist/index.d.ts

@@ -4,7 +4,7 @@ export { default as CSI } from './csi.ts';
 export { default as BamRecord } from './record.ts';
 export { default as HtsgetFile } from './htsget.ts';
 export { MISMATCH_DELETION, MISMATCH_HARD_CLIP, MISMATCH_INSERTION, MISMATCH_REF_SKIP, MISMATCH_SOFT_CLIP, MISMATCH_SUBST, forEachMismatchNumeric, } from './mismatches.ts';
-export { packReference } from './reference.ts';
+export { CHAR_CODE_FROM_NIBBLE, packReference, referenceNibble, } from './reference.ts';
 export type { NumericCigar } from './record.ts';
 export type { BamRecordClass, BamRecordLike, ReferenceSequenceFetcher, } from './bamFile.ts';
 export type { Mismatch, MismatchCallback, MismatchOptions, } from './mismatches.ts';

package/dist/index.js

@@ -3,7 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.packReference = exports.forEachMismatchNumeric = exports.MISMATCH_SUBST = exports.MISMATCH_SOFT_CLIP = exports.MISMATCH_REF_SKIP = exports.MISMATCH_INSERTION = exports.MISMATCH_HARD_CLIP = exports.MISMATCH_DELETION = exports.HtsgetFile = exports.BamRecord = exports.CSI = exports.BamFile = exports.DEFAULT_MAX_CACHE_BYTES = exports.DEFAULT_CACHE_IDLE_TIMEOUT_MS = exports.BAI = void 0;
+exports.referenceNibble = exports.packReference = exports.CHAR_CODE_FROM_NIBBLE = exports.forEachMismatchNumeric = exports.MISMATCH_SUBST = exports.MISMATCH_SOFT_CLIP = exports.MISMATCH_REF_SKIP = exports.MISMATCH_INSERTION = exports.MISMATCH_HARD_CLIP = exports.MISMATCH_DELETION = exports.HtsgetFile = exports.BamRecord = exports.CSI = exports.BamFile = exports.DEFAULT_MAX_CACHE_BYTES = exports.DEFAULT_CACHE_IDLE_TIMEOUT_MS = exports.BAI = void 0;
 var bai_ts_1 = require("./bai.js");
 Object.defineProperty(exports, "BAI", { enumerable: true, get: function () { return __importDefault(bai_ts_1).default; } });
 var bamFile_ts_1 = require("./bamFile.js");
@@ -28,6 +28,11 @@ Object.defineProperty(exports, "MISMATCH_REF_SKIP", { enumerable: true, get: fun
 Object.defineProperty(exports, "MISMATCH_SOFT_CLIP", { enumerable: true, get: function () { return mismatches_ts_1.MISMATCH_SOFT_CLIP; } });
 Object.defineProperty(exports, "MISMATCH_SUBST", { enumerable: true, get: function () { return mismatches_ts_1.MISMATCH_SUBST; } });
 Object.defineProperty(exports, "forEachMismatchNumeric", { enumerable: true, get: function () { return mismatches_ts_1.forEachMismatchNumeric; } });
+// `referenceNibble` and `CHAR_CODE_FROM_NIBBLE` are what read a base back out
+// of a packed region — a consumer that holds one otherwise has no way to see
+// what is in it, which makes a binding untestable from the outside.
 var reference_ts_1 = require("./reference.js");
+Object.defineProperty(exports, "CHAR_CODE_FROM_NIBBLE", { enumerable: true, get: function () { return reference_ts_1.CHAR_CODE_FROM_NIBBLE; } });
 Object.defineProperty(exports, "packReference", { enumerable: true, get: function () { return reference_ts_1.packReference; } });
+Object.defineProperty(exports, "referenceNibble", { enumerable: true, get: function () { return reference_ts_1.referenceNibble; } });
 //# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;AAAA,mCAAyC;AAAhC,8GAAA,OAAO,OAAO;AACvB,2CAIqB;AAHnB,2HAAA,6BAA6B,OAAA;AAC7B,qHAAA,uBAAuB,OAAA;AACvB,sHAAA,OAAO,OAAW;AAEpB,mCAAyC;AAAhC,8GAAA,OAAO,OAAO;AACvB,yCAAkD;AAAzC,uHAAA,OAAO,OAAa;AAC7B,yCAAmD;AAA1C,wHAAA,OAAO,OAAc;AAE9B,0EAA0E;AAC1E,+EAA+E;AAC/E,2EAA2E;AAC3E,2BAA2B;AAC3B,iDAQwB;AAPtB,kHAAA,iBAAiB,OAAA;AACjB,mHAAA,kBAAkB,OAAA;AAClB,mHAAA,kBAAkB,OAAA;AAClB,kHAAA,iBAAiB,OAAA;AACjB,mHAAA,kBAAkB,OAAA;AAClB,+GAAA,cAAc,OAAA;AACd,uHAAA,sBAAsB,OAAA;AAExB,+CAA8C;AAArC,6GAAA,aAAa,OAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;AAAA,mCAAyC;AAAhC,8GAAA,OAAO,OAAO;AACvB,2CAIqB;AAHnB,2HAAA,6BAA6B,OAAA;AAC7B,qHAAA,uBAAuB,OAAA;AACvB,sHAAA,OAAO,OAAW;AAEpB,mCAAyC;AAAhC,8GAAA,OAAO,OAAO;AACvB,yCAAkD;AAAzC,uHAAA,OAAO,OAAa;AAC7B,yCAAmD;AAA1C,wHAAA,OAAO,OAAc;AAE9B,0EAA0E;AAC1E,+EAA+E;AAC/E,2EAA2E;AAC3E,2BAA2B;AAC3B,iDAQwB;AAPtB,kHAAA,iBAAiB,OAAA;AACjB,mHAAA,kBAAkB,OAAA;AAClB,mHAAA,kBAAkB,OAAA;AAClB,kHAAA,iBAAiB,OAAA;AACjB,mHAAA,kBAAkB,OAAA;AAClB,+GAAA,cAAc,OAAA;AACd,uHAAA,sBAAsB,OAAA;AAExB,8EAA8E;AAC9E,6EAA6E;AAC7E,oEAAoE;AACpE,+CAIuB;AAHrB,qHAAA,qBAAqB,OAAA;AACrB,6GAAA,aAAa,OAAA;AACb,+GAAA,eAAe,OAAA"}

package/esm/index.d.ts

@@ -4,7 +4,7 @@ export { default as CSI } from './csi.ts';
 export { default as BamRecord } from './record.ts';
 export { default as HtsgetFile } from './htsget.ts';
 export { MISMATCH_DELETION, MISMATCH_HARD_CLIP, MISMATCH_INSERTION, MISMATCH_REF_SKIP, MISMATCH_SOFT_CLIP, MISMATCH_SUBST, forEachMismatchNumeric, } from './mismatches.ts';
-export { packReference } from './reference.ts';
+export { CHAR_CODE_FROM_NIBBLE, packReference, referenceNibble, } from './reference.ts';
 export type { NumericCigar } from './record.ts';
 export type { BamRecordClass, BamRecordLike, ReferenceSequenceFetcher, } from './bamFile.ts';
 export type { Mismatch, MismatchCallback, MismatchOptions, } from './mismatches.ts';

package/esm/index.js

@@ -8,5 +8,8 @@ export { default as HtsgetFile } from "./htsget.js";
 // arrays without a record around them — a SAM parser, or a worker that was
 // posted the typed arrays.
 export { MISMATCH_DELETION, MISMATCH_HARD_CLIP, MISMATCH_INSERTION, MISMATCH_REF_SKIP, MISMATCH_SOFT_CLIP, MISMATCH_SUBST, forEachMismatchNumeric, } from "./mismatches.js";
-export { packReference } from "./reference.js";
+// `referenceNibble` and `CHAR_CODE_FROM_NIBBLE` are what read a base back out
+// of a packed region — a consumer that holds one otherwise has no way to see
+// what is in it, which makes a binding untestable from the outside.
+export { CHAR_CODE_FROM_NIBBLE, packReference, referenceNibble, } from "./reference.js";
 //# sourceMappingURL=index.js.map

package/esm/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,GAAG,EAAE,MAAM,UAAU,CAAA;AACzC,OAAO,EACL,6BAA6B,EAC7B,uBAAuB,EACvB,OAAO,IAAI,OAAO,GACnB,MAAM,cAAc,CAAA;AACrB,OAAO,EAAE,OAAO,IAAI,GAAG,EAAE,MAAM,UAAU,CAAA;AACzC,OAAO,EAAE,OAAO,IAAI,SAAS,EAAE,MAAM,aAAa,CAAA;AAClD,OAAO,EAAE,OAAO,IAAI,UAAU,EAAE,MAAM,aAAa,CAAA;AAEnD,0EAA0E;AAC1E,+EAA+E;AAC/E,2EAA2E;AAC3E,2BAA2B;AAC3B,OAAO,EACL,iBAAiB,EACjB,kBAAkB,EAClB,kBAAkB,EAClB,iBAAiB,EACjB,kBAAkB,EAClB,cAAc,EACd,sBAAsB,GACvB,MAAM,iBAAiB,CAAA;AACxB,OAAO,EAAE,aAAa,EAAE,MAAM,gBAAgB,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,GAAG,EAAE,MAAM,UAAU,CAAA;AACzC,OAAO,EACL,6BAA6B,EAC7B,uBAAuB,EACvB,OAAO,IAAI,OAAO,GACnB,MAAM,cAAc,CAAA;AACrB,OAAO,EAAE,OAAO,IAAI,GAAG,EAAE,MAAM,UAAU,CAAA;AACzC,OAAO,EAAE,OAAO,IAAI,SAAS,EAAE,MAAM,aAAa,CAAA;AAClD,OAAO,EAAE,OAAO,IAAI,UAAU,EAAE,MAAM,aAAa,CAAA;AAEnD,0EAA0E;AAC1E,+EAA+E;AAC/E,2EAA2E;AAC3E,2BAA2B;AAC3B,OAAO,EACL,iBAAiB,EACjB,kBAAkB,EAClB,kBAAkB,EAClB,iBAAiB,EACjB,kBAAkB,EAClB,cAAc,EACd,sBAAsB,GACvB,MAAM,iBAAiB,CAAA;AACxB,8EAA8E;AAC9E,6EAA6E;AAC7E,oEAAoE;AACpE,OAAO,EACL,qBAAqB,EACrB,aAAa,EACb,eAAe,GAChB,MAAM,gBAAgB,CAAA"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/bam",
-  "version": "8.7.0",
+  "version": "8.8.0",
   "packageManager": "pnpm@11.15.1",
   "description": "Parser for BAM and BAM index (bai) files",
   "license": "MIT",

package/src/index.ts

@@ -21,7 +21,14 @@ export {
   MISMATCH_SUBST,
   forEachMismatchNumeric,
 } from './mismatches.ts'
-export { packReference } from './reference.ts'
+// `referenceNibble` and `CHAR_CODE_FROM_NIBBLE` are what read a base back out
+// of a packed region — a consumer that holds one otherwise has no way to see
+// what is in it, which makes a binding untestable from the outside.
+export {
+  CHAR_CODE_FROM_NIBBLE,
+  packReference,
+  referenceNibble,
+} from './reference.ts'
 
 export type { NumericCigar } from './record.ts'
 export type {