@gmod/cram 4.0.9 → 5.0.0

package/dist/cramFile/slice/index.js

@@ -3,28 +3,25 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const errors_1 = require("../../errors");
-const getBits_1 = require("../codecs/getBits");
-const constants_1 = __importDefault(require("../constants"));
-const decodeRecord_1 = __importDefault(require("./decodeRecord"));
-const record_1 = __importDefault(require("../record"));
-const sectionParsers_1 = require("../sectionParsers");
-const util_1 = require("../util");
+const errors_ts_1 = require("../../errors.js");
+const getBits_ts_1 = require("../codecs/getBits.js");
+const constants_ts_1 = __importDefault(require("../constants.js"));
+const decodeRecord_ts_1 = __importDefault(require("./decodeRecord.js"));
+const record_ts_1 = __importDefault(require("../record.js"));
+const sectionParsers_ts_1 = require("../sectionParsers.js");
+const util_ts_1 = require("../util.js");
 /**
- * @private
- * Try to estimate the template length from a bunch of interrelated multi-segment reads.
- * @param {Array[CramRecord]} allRecords
- * @param {number} currentRecordNumber
- * @param {CramRecord} thisRecord
+ * Try to estimate the template length from a bunch of interrelated
+ * multi-segment reads.
  */
-function calculateMultiSegmentMatedTemplateLength(allRecords, currentRecordNumber, thisRecord) {
+function calculateMultiSegmentMatedTemplateLength(allRecords, _currentRecordNumber, thisRecord) {
     function getAllMatedRecords(startRecord) {
         const records = [startRecord];
         if (startRecord.mateRecordNumber !== undefined &&
             startRecord.mateRecordNumber >= 0) {
             const mateRecord = allRecords[startRecord.mateRecordNumber];
             if (!mateRecord) {
-                throw new errors_1.CramMalformedError('intra-slice mate record not found, this file seems malformed');
+                throw new errors_ts_1.CramMalformedError('intra-slice mate record not found, this file seems malformed');
             }
             records.push(...getAllMatedRecords(mateRecord));
         }
@@ -37,22 +34,20 @@ function calculateMultiSegmentMatedTemplateLength(allRecords, currentRecordNumbe
     if (estimatedTemplateLength >= 0) {
         matedRecords.forEach(r => {
             if (r.templateLength !== undefined) {
-                throw new errors_1.CramMalformedError('mate pair group has some members that have template lengths already, this file seems malformed');
+                throw new errors_ts_1.CramMalformedError('mate pair group has some members that have template lengths already, this file seems malformed');
             }
             r.templateLength = estimatedTemplateLength;
         });
     }
 }
 /**
- * @private
- * Attempt to calculate the `templateLength` for a pair of intra-slice paired reads.
- * Ported from htslib. Algorithm is imperfect.
- * @param {CramRecord} thisRecord
- * @param {CramRecord} mateRecord
+ * Attempt to calculate the `templateLength` for a pair of intra-slice paired
+ * reads. Ported from htslib. Algorithm is imperfect.
  */
 function calculateIntraSliceMatePairTemplateLength(thisRecord, mateRecord) {
-    // this just estimates the template length by using the simple (non-gapped) end coordinate of each
-    // read, because gapping in the alignment doesn't mean the template is longer or shorter
+    // this just estimates the template length by using the simple (non-gapped)
+    // end coordinate of each read, because gapping in the alignment doesn't mean
+    // the template is longer or shorter
     const start = Math.min(thisRecord.alignmentStart, mateRecord.alignmentStart);
     const end = Math.max(thisRecord.alignmentStart + thisRecord.readLength - 1, mateRecord.alignmentStart + mateRecord.readLength - 1);
     const lengthEstimate = end - start + 1;
@@ -60,10 +55,9 @@ function calculateIntraSliceMatePairTemplateLength(thisRecord, mateRecord) {
     mateRecord.templateLength = lengthEstimate;
 }
 /**
- * @private establishes a mate-pair relationship between two records in the
- * same slice. CRAM compresses mate-pair relationships between records in the
- * same slice down into just one record having the index in the slice of its
- * mate
+ * establishes a mate-pair relationship between two records in the same slice.
+ * CRAM compresses mate-pair relationships between records in the same slice
+ * down into just one record having the index in the slice of its mate
  */
 function associateIntraSliceMate(allRecords, currentRecordNumber, thisRecord, mateRecord) {
     const complicatedMultiSegment = !!(mateRecord.mate ||
@@ -97,22 +91,22 @@ function associateIntraSliceMate(allRecords, currentRecordNumber, thisRecord, ma
     }
     // make sure the proper flags and cramFlags are set on both records
     // paired
-    thisRecord.flags |= constants_1.default.BAM_FPAIRED;
+    thisRecord.flags |= constants_ts_1.default.BAM_FPAIRED;
     // set mate unmapped if needed
-    if (mateRecord.flags & constants_1.default.BAM_FUNMAP) {
-        thisRecord.flags |= constants_1.default.BAM_FMUNMAP;
+    if (mateRecord.flags & constants_ts_1.default.BAM_FUNMAP) {
+        thisRecord.flags |= constants_ts_1.default.BAM_FMUNMAP;
         // thisRecord.templateLength = 0
     }
-    if (thisRecord.flags & constants_1.default.BAM_FUNMAP) {
+    if (thisRecord.flags & constants_ts_1.default.BAM_FUNMAP) {
         // thisRecord.templateLength = 0
-        mateRecord.flags |= constants_1.default.BAM_FMUNMAP;
+        mateRecord.flags |= constants_ts_1.default.BAM_FMUNMAP;
     }
     // set mate reversed if needed
-    if (mateRecord.flags & constants_1.default.BAM_FREVERSE) {
-        thisRecord.flags |= constants_1.default.BAM_FMREVERSE;
+    if (mateRecord.flags & constants_ts_1.default.BAM_FREVERSE) {
+        thisRecord.flags |= constants_ts_1.default.BAM_FMREVERSE;
     }
-    if (thisRecord.flags & constants_1.default.BAM_FREVERSE) {
-        mateRecord.flags |= constants_1.default.BAM_FMREVERSE;
+    if (thisRecord.flags & constants_ts_1.default.BAM_FREVERSE) {
+        mateRecord.flags |= constants_ts_1.default.BAM_FMREVERSE;
     }
     if (thisRecord.templateLength === undefined) {
         if (complicatedMultiSegment) {
@@ -137,19 +131,19 @@ class CramSlice {
     async getHeader() {
         // fetch and parse the slice header
         const { majorVersion } = await this.file.getDefinition();
-        const sectionParsers = (0, sectionParsers_1.getSectionParsers)(majorVersion);
+        const sectionParsers = (0, sectionParsers_ts_1.getSectionParsers)(majorVersion);
         const containerHeader = await this.container.getHeader();
         const header = await this.file.readBlock(containerHeader._endPosition + this.containerPosition);
         if (header.contentType === 'MAPPED_SLICE_HEADER') {
-            const content = (0, util_1.parseItem)(header.content, sectionParsers.cramMappedSliceHeader.parser, 0, containerHeader._endPosition);
+            const content = (0, util_ts_1.parseItem)(header.content, sectionParsers.cramMappedSliceHeader.parser, 0, containerHeader._endPosition);
             return { ...header, parsedContent: content };
         }
         else if (header.contentType === 'UNMAPPED_SLICE_HEADER') {
-            const content = (0, util_1.parseItem)(header.content, sectionParsers.cramUnmappedSliceHeader.parser, 0, containerHeader._endPosition);
+            const content = (0, util_ts_1.parseItem)(header.content, sectionParsers.cramUnmappedSliceHeader.parser, 0, containerHeader._endPosition);
             return { ...header, parsedContent: content };
         }
         else {
-            throw new errors_1.CramMalformedError(`error reading slice header block, invalid content type ${header.contentType}`);
+            throw new errors_ts_1.CramMalformedError(`error reading slice header block, invalid content type ${header.contentType}`);
         }
     }
     // memoize
@@ -189,7 +183,7 @@ class CramSlice {
         // read the slice header
         const decoder = new TextDecoder('utf8');
         const sliceHeader = (await this.getHeader()).parsedContent;
-        if (!(0, sectionParsers_1.isMappedSliceHeader)(sliceHeader)) {
+        if (!(0, sectionParsers_ts_1.isMappedSliceHeader)(sliceHeader)) {
             throw new Error('slice header not mapped');
         }
         if (sliceHeader.refSeqId < 0) {
@@ -202,7 +196,7 @@ class CramSlice {
         if (sliceHeader.refBaseBlockId >= 0) {
             const refBlock = await this.getBlockByContentId(sliceHeader.refBaseBlockId);
             if (!refBlock) {
-                throw new errors_1.CramMalformedError('embedded reference specified, but reference block does not exist');
+                throw new errors_ts_1.CramMalformedError('embedded reference specified, but reference block does not exist');
             }
             // TODO: we do not read anything named 'span'
             // if (sliceHeader.span > refBlock.uncompressedSize) {
@@ -224,7 +218,7 @@ class CramSlice {
             }
             const seq = await this.file.fetchReferenceSequenceCallback(sliceHeader.refSeqId, sliceHeader.refSeqStart, sliceHeader.refSeqStart + sliceHeader.refSeqSpan - 1);
             if (seq.length !== sliceHeader.refSeqSpan) {
-                throw new errors_1.CramArgumentError('seqFetch callback returned a reference sequence of the wrong length');
+                throw new errors_ts_1.CramArgumentError('seqFetch callback returned a reference sequence of the wrong length');
             }
             return {
                 seq,
@@ -249,18 +243,18 @@ class CramSlice {
         // check MD5 of reference if available
         if (majorVersion > 1 &&
             this.file.options.checkSequenceMD5 &&
-            (0, sectionParsers_1.isMappedSliceHeader)(sliceHeader.parsedContent) &&
+            (0, sectionParsers_ts_1.isMappedSliceHeader)(sliceHeader.parsedContent) &&
             sliceHeader.parsedContent.refSeqId >= 0 &&
             sliceHeader.parsedContent.md5?.join('') !== '0000000000000000') {
             const refRegion = await this.getReferenceRegion();
             if (refRegion) {
                 const { seq, start, end } = refRegion;
-                const seqMd5 = (0, util_1.sequenceMD5)(seq);
+                const seqMd5 = (0, util_ts_1.sequenceMD5)(seq);
                 const storedMd5 = sliceHeader.parsedContent.md5
                     ?.map(byte => (byte < 16 ? '0' : '') + byte.toString(16))
                     .join('');
                 if (seqMd5 !== storedMd5) {
-                    throw new errors_1.CramMalformedError(`MD5 checksum reference mismatch for ref ${sliceHeader.parsedContent.refSeqId} pos ${start}..${end}. recorded MD5: ${storedMd5}, calculated MD5: ${seqMd5}`);
+                    throw new errors_ts_1.CramMalformedError(`MD5 checksum reference mismatch for ref ${sliceHeader.parsedContent.refSeqId} pos ${start}..${end}. recorded MD5: ${storedMd5}, calculated MD5: ${seqMd5}`);
                 }
             }
         }
@@ -270,7 +264,7 @@ class CramSlice {
         // data block
         const coreDataBlock = await this.getCoreDataBlock();
         const cursors = {
-            lastAlignmentStart: (0, sectionParsers_1.isMappedSliceHeader)(sliceHeader.parsedContent)
+            lastAlignmentStart: (0, sectionParsers_ts_1.isMappedSliceHeader)(sliceHeader.parsedContent)
                 ? sliceHeader.parsedContent.refSeqStart
                 : 0,
             coreBlock: { bitPosition: 7, bytePosition: 0 },
@@ -289,15 +283,15 @@ class CramSlice {
         const decodeDataSeries = (dataSeriesName) => {
             const codec = compressionScheme.getCodecForDataSeries(dataSeriesName);
             if (!codec) {
-                throw new errors_1.CramMalformedError(`no codec defined for ${dataSeriesName} data series`);
+                throw new errors_ts_1.CramMalformedError(`no codec defined for ${dataSeriesName} data series`);
             }
             return codec.decode(this, coreDataBlock, blocksByContentId, cursors);
         };
         const records = new Array(sliceHeader.parsedContent.numRecords);
         for (let i = 0; i < records.length; i += 1) {
             try {
-                const init = (0, decodeRecord_1.default)(this, decodeDataSeries, compressionScheme, sliceHeader, coreDataBlock, blocksByContentId, cursors, majorVersion, i);
-                records[i] = new record_1.default({
+                const init = (0, decodeRecord_ts_1.default)(this, decodeDataSeries, compressionScheme, sliceHeader, coreDataBlock, blocksByContentId, cursors, majorVersion, i);
+                records[i] = new record_ts_1.default({
                     ...init,
                     uniqueId: sliceHeader.contentPosition +
                         sliceHeader.parsedContent.recordCounter +
@@ -306,7 +300,7 @@ class CramSlice {
                 });
             }
             catch (e) {
-                if (e instanceof getBits_1.CramBufferOverrunError) {
+                if (e instanceof getBits_ts_1.CramBufferOverrunError) {
                     console.warn('read attempted beyond end of buffer, file seems truncated.');
                     break;
                 }
@@ -347,7 +341,7 @@ class CramSlice {
         // if we can fetch reference sequence, add the reference sequence to the records
         if (records.length && this.file.fetchReferenceSequenceCallback) {
             const sliceHeader = await this.getHeader();
-            if ((0, sectionParsers_1.isMappedSliceHeader)(sliceHeader.parsedContent) &&
+            if ((0, sectionParsers_ts_1.isMappedSliceHeader)(sliceHeader.parsedContent) &&
                 (sliceHeader.parsedContent.refSeqId >= 0 || // single-ref slice
                     sliceHeader.parsedContent.refSeqId === -2) // multi-ref slice
             ) {
@@ -408,6 +402,6 @@ class CramSlice {
 exports.default = CramSlice;
 // memoize several methods in the class for performance
 'getHeader getBlocks _getBlocksContentIdIndex'.split(' ').forEach(method => {
-    (0, util_1.tinyMemoize)(CramSlice, method);
+    (0, util_ts_1.tinyMemoize)(CramSlice, method);
 });
 //# sourceMappingURL=index.js.map

package/dist/cramFile/slice/index.js.map

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package/dist/htscodecs/arith_gen.d.ts

@@ -1,4 +1,4 @@
-import IOStream from './iostream';
+import IOStream from './iostream.ts';
 export default class RangeCoderGen {
     stream: IOStream;
     decode(src: Uint8Array): Uint8Array<any>;

package/dist/htscodecs/arith_gen.js

@@ -37,10 +37,10 @@ Object.defineProperty(exports, "__esModule", { value: true });
  * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
  * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
-const seek_bzip_1 = __importDefault(require("seek-bzip"));
-const arith_sh_1 = __importDefault(require("./arith_sh"));
-const byte_model_1 = __importDefault(require("./byte_model"));
-const iostream_1 = __importDefault(require("./iostream"));
+const index_ts_1 = require("../seek-bzip/index.js");
+const arith_sh_ts_1 = __importDefault(require("./arith_sh.js"));
+const byte_model_ts_1 = __importDefault(require("./byte_model.js"));
+const iostream_ts_1 = __importDefault(require("./iostream.js"));
 const ARITH_ORDER = 1;
 const ARITH_EXT = 4;
 const ARITH_STRIPE = 8;
@@ -50,7 +50,7 @@ const ARITH_RLE = 64;
 const ARITH_PACK = 128;
 class RangeCoderGen {
     decode(src) {
-        this.stream = new iostream_1.default(src);
+        this.stream = new iostream_ts_1.default(src);
         return this.decodeStream(this.stream);
     }
     decodeStream(stream, n_out = 0) {
@@ -101,8 +101,8 @@ class RangeCoderGen {
         if (max_sym == 0) {
             max_sym = 256;
         }
-        const byte_model = new byte_model_1.default(max_sym);
-        const rc = new arith_sh_1.default(stream);
+        const byte_model = new byte_model_ts_1.default(max_sym);
+        const rc = new arith_sh_ts_1.default(stream);
         rc.RangeStartDecode(stream);
         for (let i = 0; i < n_out; i++) {
             output[i] = byte_model.ModelDecode(stream, rc);
@@ -119,9 +119,9 @@ class RangeCoderGen {
         }
         const byte_model = new Array(max_sym);
         for (var i = 0; i < max_sym; i++) {
-            byte_model[i] = new byte_model_1.default(max_sym);
+            byte_model[i] = new byte_model_ts_1.default(max_sym);
         }
-        const rc = new arith_sh_1.default(stream);
+        const rc = new arith_sh_ts_1.default(stream);
         rc.RangeStartDecode(stream);
         let last = 0;
         for (var i = 0; i < n_out; i++) {
@@ -133,7 +133,7 @@ class RangeCoderGen {
     // ----------------------------------------------------------------------
     // External codec
     decodeExt(stream, n_out) {
-        return seek_bzip_1.default.decode(stream.buf.slice(stream.pos));
+        return (0, index_ts_1.decode)(stream.buf.slice(stream.pos));
     }
     // ----------------------------------------------------------------------
     // Order-0 RLE codec
@@ -143,12 +143,12 @@ class RangeCoderGen {
         if (max_sym == 0) {
             max_sym = 256;
         }
-        const model_lit = new byte_model_1.default(max_sym);
+        const model_lit = new byte_model_ts_1.default(max_sym);
         const model_run = new Array(258);
         for (var i = 0; i <= 257; i++) {
-            model_run[i] = new byte_model_1.default(4);
+            model_run[i] = new byte_model_ts_1.default(4);
         }
-        const rc = new arith_sh_1.default(stream);
+        const rc = new arith_sh_ts_1.default(stream);
         rc.RangeStartDecode(stream);
         var i = 0;
         while (i < n_out) {
@@ -178,13 +178,13 @@ class RangeCoderGen {
         }
         const model_lit = new Array(max_sym);
         for (var i = 0; i < max_sym; i++) {
-            model_lit[i] = new byte_model_1.default(max_sym);
+            model_lit[i] = new byte_model_ts_1.default(max_sym);
         }
         const model_run = new Array(258);
         for (var i = 0; i <= 257; i++) {
-            model_run[i] = new byte_model_1.default(4);
+            model_run[i] = new byte_model_ts_1.default(4);
         }
-        const rc = new arith_sh_1.default(stream);
+        const rc = new arith_sh_ts_1.default(stream);
         rc.RangeStartDecode(stream);
         let last = 0;
         var i = 0;
@@ -263,7 +263,7 @@ class RangeCoderGen {
     }
     // Compute M array and return meta-data stream
     packMeta(src) {
-        const stream = new iostream_1.default('', 0, 1024);
+        const stream = new iostream_ts_1.default('', 0, 1024);
         // Count symbols
         const M = new Array(256);
         for (var i = 0; i < src.length; i++) {

package/dist/htscodecs/arith_gen.js.map

@@ -1 +1 @@
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package/dist/htscodecs/fqzcomp.js

@@ -38,9 +38,9 @@ exports.decode = decode;
  * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
  * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
-const arith_sh_1 = __importDefault(require("./arith_sh"));
-const byte_model_1 = __importDefault(require("./byte_model"));
-const iostream_1 = __importDefault(require("./iostream"));
+const arith_sh_ts_1 = __importDefault(require("./arith_sh.js"));
+const byte_model_ts_1 = __importDefault(require("./byte_model.js"));
+const iostream_ts_1 = __importDefault(require("./iostream.js"));
 // ----------------------------------------------------------------------
 // Main arithmetic entry function: decodes a compressed src and
 // returns the uncompressed buffer.
@@ -210,16 +210,16 @@ function fqz_create_models(gparams) {
     const model = {};
     model.qual = new Array(1 << 16);
     for (var i = 0; i < 1 << 16; i++) {
-        model.qual[i] = new byte_model_1.default(gparams.max_sym + 1);
+        model.qual[i] = new byte_model_ts_1.default(gparams.max_sym + 1);
     } // +1 as max value not num. values
     model.len = new Array(4);
     for (var i = 0; i < 4; i++) {
-        model.len[i] = new byte_model_1.default(256);
+        model.len[i] = new byte_model_ts_1.default(256);
     }
-    model.rev = new byte_model_1.default(2);
-    model.dup = new byte_model_1.default(2);
+    model.rev = new byte_model_ts_1.default(2);
+    model.dup = new byte_model_ts_1.default(2);
     if (gparams.max_sel > 0) {
-        model.sel = new byte_model_1.default(gparams.max_sel + 1);
+        model.sel = new byte_model_ts_1.default(gparams.max_sel + 1);
     } // +1 as max value not num. values
     return model;
 }
@@ -272,7 +272,7 @@ function decode_fqz(src, q_lens) {
     // Create initial models
     const model = fqz_create_models(gparams);
     // Create our entropy encoder and output buffers
-    const rc = new arith_sh_1.default(src);
+    const rc = new arith_sh_ts_1.default(src);
     rc.RangeStartDecode(src);
     const output = new Uint8Array(n_out);
     // Internal FQZ state
@@ -340,7 +340,7 @@ function reverse_qualities(qual, qual_len, rev, len) {
     }
 }
 function decode(src, q_lens) {
-    const stream = new iostream_1.default(src);
+    const stream = new iostream_ts_1.default(src);
     return decode_fqz(stream, q_lens);
 }
 //# sourceMappingURL=fqzcomp.js.map

package/dist/htscodecs/fqzcomp.js.map

@@ -1 +1 @@
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package/dist/htscodecs/index.js

@@ -79,11 +79,11 @@ exports.tok3_uncompress = tok3_uncompress;
 // the CRAM 3.1 codecs.
 // This JavaScript file is not part of the reference implementation
 // and is simply and interface to get a consistent interface for cram-js.
-const arith_gen_1 = __importDefault(require("./arith_gen"));
-const fqzcomp = __importStar(require("./fqzcomp"));
-const r4x8 = __importStar(require("./rans"));
-const r4x16 = __importStar(require("./rans4x16"));
-const tok3 = __importStar(require("./tok3"));
+const arith_gen_ts_1 = __importDefault(require("./arith_gen.js"));
+const fqzcomp = __importStar(require("./fqzcomp.js"));
+const r4x8 = __importStar(require("./rans.js"));
+const r4x16 = __importStar(require("./rans4x16.js"));
+const tok3 = __importStar(require("./tok3.js"));
 function r4x8_uncompress(inputBuffer) {
     return r4x8.decode(inputBuffer);
 }
@@ -93,7 +93,7 @@ function r4x16_uncompress(inputBuffer) {
 function arith_uncompress(inputBuffer) {
     // fix by @cmdcolin for CRAM 3.1
     // xref https://github.com/jkbonfield/htscodecs/pull/1/files
-    return new arith_gen_1.default().decode(inputBuffer);
+    return new arith_gen_ts_1.default().decode(inputBuffer);
 }
 function fqzcomp_uncompress(inputBuffer) {
     const q_lens = [];

package/dist/htscodecs/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/htscodecs/index.ts"],"names":[],"mappings":";AAAA,cAAc;AACd,EAAE;AACF;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA+BG;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAcH,0CAEC;AAED,4CAEC;AAED,4CAIC;AAED,gDAGC;AAED,0CAIC;AAnCD,oEAAoE;AACpE,uBAAuB;AAEvB,mEAAmE;AACnE,yEAAyE;AAEzE,4DAA+B;AAC/B,mDAAoC;AACpC,6CAA8B;AAC9B,kDAAmC;AACnC,6CAA8B;AAE9B,SAAgB,eAAe,CAAC,WAAuB;IACrD,OAAO,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,CAAA;AACjC,CAAC;AAED,SAAgB,gBAAgB,CAAC,WAAuB;IACtD,OAAO,KAAK,CAAC,MAAM,CAAC,WAAW,CAAC,CAAA;AAClC,CAAC;AAED,SAAgB,gBAAgB,CAAC,WAAuB;IACtD,gCAAgC;IAChC,4DAA4D;IAC5D,OAAO,IAAI,mBAAK,EAAE,CAAC,MAAM,CAAC,WAAW,CAAC,CAAA;AACxC,CAAC;AAED,SAAgB,kBAAkB,CAAC,WAAuB;IACxD,MAAM,MAAM,GAAG,EAAE,CAAA;IACjB,OAAO,OAAO,CAAC,MAAM,CAAC,WAAW,EAAE,MAAM,CAAC,CAAA;AAC5C,CAAC;AAED,SAAgB,eAAe,CAAC,WAAuB;IACrD,2CAA2C;IAC3C,MAAM,GAAG,GAAG,IAAI,CAAC,MAAM,CAAC,WAAW,EAAE,CAAC,EAAE,IAAI,CAAC,CAAA;IAC7C,OAAO,UAAU,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,CAAC,MAAM,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;AAC7E,CAAC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/htscodecs/index.ts"],"names":[],"mappings":";AAAA,cAAc;AACd,EAAE;AACF;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA+BG;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAcH,0CAEC;AAED,4CAEC;AAED,4CAIC;AAED,gDAGC;AAED,0CAIC;AAnCD,oEAAoE;AACpE,uBAAuB;AAEvB,mEAAmE;AACnE,yEAAyE;AAEzE,kEAAkC;AAClC,sDAAuC;AACvC,gDAAiC;AACjC,qDAAsC;AACtC,gDAAiC;AAEjC,SAAgB,eAAe,CAAC,WAAuB;IACrD,OAAO,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,CAAA;AACjC,CAAC;AAED,SAAgB,gBAAgB,CAAC,WAAuB;IACtD,OAAO,KAAK,CAAC,MAAM,CAAC,WAAW,CAAC,CAAA;AAClC,CAAC;AAED,SAAgB,gBAAgB,CAAC,WAAuB;IACtD,gCAAgC;IAChC,4DAA4D;IAC5D,OAAO,IAAI,sBAAK,EAAE,CAAC,MAAM,CAAC,WAAW,CAAC,CAAA;AACxC,CAAC;AAED,SAAgB,kBAAkB,CAAC,WAAuB;IACxD,MAAM,MAAM,GAAG,EAAE,CAAA;IACjB,OAAO,OAAO,CAAC,MAAM,CAAC,WAAW,EAAE,MAAM,CAAC,CAAA;AAC5C,CAAC;AAED,SAAgB,eAAe,CAAC,WAAuB;IACrD,2CAA2C;IAC3C,MAAM,GAAG,GAAG,IAAI,CAAC,MAAM,CAAC,WAAW,EAAE,CAAC,EAAE,IAAI,CAAC,CAAA;IAC7C,OAAO,UAAU,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,CAAC,MAAM,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;AAC7E,CAAC"}

package/dist/htscodecs/rans.js

@@ -38,7 +38,7 @@ exports.decode = decode;
  * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
  * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
-const iostream_1 = __importDefault(require("./iostream"));
+const iostream_ts_1 = __importDefault(require("./iostream.js"));
 // ----------------------------------------------------------------------
 // rANS primitives itself
 //
@@ -80,7 +80,7 @@ function RansRenorm(src, R) {
 // Main rANS entry function: decodes a compressed src and
 // returns the uncompressed buffer.
 function decode(src) {
-    const stream = new iostream_1.default(src);
+    const stream = new iostream_ts_1.default(src);
     const order = stream.ReadByte();
     const n_in = stream.ReadUint32();
     const n_out = stream.ReadUint32();