@gmod/cram 4.0.3 → 4.0.4

package/dist/htscodecs/byte_model.js

@@ -1,4 +1,7 @@
 "use strict";
+/* eslint-disable no-var */
+// @ts-nocheck
+Object.defineProperty(exports, "__esModule", { value: true });
 /*
  * Copyright (c) 2019 Genome Research Ltd.
  * Author(s): James Bonfield
@@ -36,25 +39,26 @@
 // compressed data.
 const MAX_FREQ = (1 << 16) - 17;
 const STEP = 16;
-module.exports = class ByteModel {
+class ByteModel {
     constructor(max_sym = 256) {
         this.total_freq = max_sym;
         this.max_sym = max_sym - 1;
-        this.S = new Array();
-        this.F = new Array();
-        for (var i = 0; i <= this.max_sym; i++) {
+        this.S = [];
+        this.F = [];
+        for (let i = 0; i <= this.max_sym; i++) {
             this.S[i] = i;
             this.F[i] = 1;
         }
     }
     ModelDecode(src, rc) {
         // Find symbol
-        var freq = rc.RangeGetFrequency(this.total_freq);
+        const freq = rc.RangeGetFrequency(this.total_freq);
         // Linear scan to find cumulative frequency 'freq'
-        var acc = 0;
-        var x = 0;
-        while (acc + this.F[x] <= freq)
+        let acc = 0;
+        let x = 0;
+        while (acc + this.F[x] <= freq) {
             acc += this.F[x++];
+        }
         //	for (var acc = 0; (acc += this.F[x]) <= freq; x++)
         //	    ;
         //	acc -= this.F[x];
@@ -63,12 +67,13 @@ module.exports = class ByteModel {
         // Update model
         this.F[x] += STEP;
         this.total_freq += STEP;
-        if (this.total_freq > MAX_FREQ)
+        if (this.total_freq > MAX_FREQ) {
             this.ModelRenormalise();
+        }
         // Keep symbols approximately frequency sorted
-        var sym = this.S[x];
+        const sym = this.S[x];
         if (x > 0 && this.F[x] > this.F[x - 1]) {
-            var tmp = this.F[x];
+            let tmp = this.F[x];
             this.F[x] = this.F[x - 1];
             this.F[x - 1] = tmp;
             tmp = this.S[x];
@@ -80,28 +85,30 @@ module.exports = class ByteModel {
     ModelRenormalise() {
         // Halve all the frequencies, being careful not to hit zero
         this.total_freq = 0;
-        for (var i = 0; i <= this.max_sym; i++) {
+        for (let i = 0; i <= this.max_sym; i++) {
             this.F[i] -= Math.floor(this.F[i] / 2);
             this.total_freq += this.F[i];
         }
     }
     ModelEncode(dst, rc, sym) {
         // Find cumulative frequency
-        var acc = 0;
-        for (var x = 0; this.S[x] != sym; x++)
+        let acc = 0;
+        for (var x = 0; this.S[x] != sym; x++) {
             acc += this.F[x];
+        }
         // Encode
         rc.RangeEncode(dst, acc, this.F[x], this.total_freq);
         // Update model
         this.F[x] += STEP;
         this.total_freq += STEP;
-        if (this.total_freq > MAX_FREQ)
+        if (this.total_freq > MAX_FREQ) {
             // FIXME x2
             this.ModelRenormalise();
+        }
         // Keep symbols approximately frequency sorted
         var sym = this.S[x];
         if (x > 0 && this.F[x] > this.F[x - 1]) {
-            var tmp = this.F[x];
+            let tmp = this.F[x];
             this.F[x] = this.F[x - 1];
             this.F[x - 1] = tmp;
             tmp = this.S[x];
@@ -109,5 +116,6 @@ module.exports = class ByteModel {
             this.S[x - 1] = tmp;
         }
     }
-};
+}
+exports.default = ByteModel;
 //# sourceMappingURL=byte_model.js.map

package/dist/htscodecs/byte_model.js.map

@@ -1 +1 @@
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+{"version":3,"file":"byte_model.js","sourceRoot":"","sources":["../../src/htscodecs/byte_model.ts"],"names":[],"mappings":";AAAA,2BAA2B;AAC3B,cAAc;;AAEd;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA+BG;AAEH,qEAAqE;AACrE,gEAAgE;AAChE,mBAAmB;AAEnB,MAAM,QAAQ,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,GAAG,EAAE,CAAA;AAC/B,MAAM,IAAI,GAAG,EAAE,CAAA;AAEf,MAAqB,SAAS;IAC5B,YAAY,OAAO,GAAG,GAAG;QACvB,IAAI,CAAC,UAAU,GAAG,OAAO,CAAA;QACzB,IAAI,CAAC,OAAO,GAAG,OAAO,GAAG,CAAC,CAAA;QAC1B,IAAI,CAAC,CAAC,GAAG,EAAE,CAAA;QACX,IAAI,CAAC,CAAC,GAAG,EAAE,CAAA;QAEX,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,IAAI,IAAI,CAAC,OAAO,EAAE,CAAC,EAAE,EAAE,CAAC;YACvC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA;YACb,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA;QACf,CAAC;IACH,CAAC;IAED,WAAW,CAAC,GAAG,EAAE,EAAE;QACjB,cAAc;QACd,MAAM,IAAI,GAAG,EAAE,CAAC,iBAAiB,CAAC,IAAI,CAAC,UAAU,CAAC,CAAA;QAElD,kDAAkD;QAClD,IAAI,GAAG,GAAG,CAAC,CAAA;QACX,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,OAAO,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,IAAI,EAAE,CAAC;YAC/B,GAAG,IAAI,IAAI,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAA;QACpB,CAAC;QAED,qDAAqD;QACrD,QAAQ;QACR,oBAAoB;QAEpB,qBAAqB;QACrB,EAAE,CAAC,WAAW,CAAC,GAAG,EAAE,GAAG,EAAE,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,UAAU,CAAC,CAAA;QAEpD,eAAe;QACf,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,IAAI,CAAA;QACjB,IAAI,CAAC,UAAU,IAAI,IAAI,CAAA;QACvB,IAAI,IAAI,CAAC,UAAU,GAAG,QAAQ,EAAE,CAAC;YAC/B,IAAI,CAAC,gBAAgB,EAAE,CAAA;QACzB,CAAC;QAED,8CAA8C;QAC9C,MAAM,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QACrB,IAAI,CAAC,GAAG,CAAC,IAAI,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC;YACvC,IAAI,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;YACnB,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;YACzB,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;YAEnB,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;YACf,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;YACzB,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;QACrB,CAAC;QAED,OAAO,GAAG,CAAA;IACZ,CAAC;IAED,gBAAgB;QACd,2DAA2D;QAC3D,IAAI,CAAC,UAAU,GAAG,CAAC,CAAA;QACnB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,IAAI,IAAI,CAAC,OAAO,EAAE,CAAC,EAAE,EAAE,CAAC;YACvC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;YACtC,IAAI,CAAC,UAAU,IAAI,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QAC9B,CAAC;IACH,CAAC;IAED,WAAW,CAAC,GAAG,EAAE,EAAE,EAAE,GAAG;QACtB,4BAA4B;QAC5B,IAAI,GAAG,GAAG,CAAC,CAAA;QACX,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,GAAG,EAAE,CAAC,EAAE,EAAE,CAAC;YACtC,GAAG,IAAI,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QAClB,CAAC;QAED,SAAS;QACT,EAAE,CAAC,WAAW,CAAC,GAAG,EAAE,GAAG,EAAE,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,UAAU,CAAC,CAAA;QAEpD,eAAe;QACf,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,IAAI,CAAA;QACjB,IAAI,CAAC,UAAU,IAAI,IAAI,CAAA;QACvB,IAAI,IAAI,CAAC,UAAU,GAAG,QAAQ,EAAE,CAAC;YAC/B,WAAW;YACX,IAAI,CAAC,gBAAgB,EAAE,CAAA;QACzB,CAAC;QAED,8CAA8C;QAC9C,IAAI,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QACnB,IAAI,CAAC,GAAG,CAAC,IAAI,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC;YACvC,IAAI,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;YACnB,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;YACzB,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;YAEnB,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;YACf,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;YACzB,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;QACrB,CAAC;IACH,CAAC;CACF;AA5FD,4BA4FC"}

package/dist/htscodecs/fqzcomp.d.ts

@@ -1 +1 @@
-export function decode(src: any, q_lens: any): Uint8Array<any> | undefined;
+export declare function decode(src: Uint8Array, q_lens: any): Uint8Array<ArrayBuffer> | undefined;

package/dist/htscodecs/fqzcomp.js

@@ -1,4 +1,11 @@
 "use strict";
+/* eslint-disable no-var */
+// @ts-nocheck
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.decode = decode;
 /*
  * Copyright (c) 2019 Genome Research Ltd.
  * Author(s): James Bonfield
@@ -31,42 +38,44 @@
  * (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 = require('./iostream');
-const ByteModel = require('./byte_model');
-const RangeCoder = require('./arith_sh');
-//----------------------------------------------------------------------
+const arith_sh_1 = __importDefault(require("./arith_sh"));
+const byte_model_1 = __importDefault(require("./byte_model"));
+const iostream_1 = __importDefault(require("./iostream"));
+// ----------------------------------------------------------------------
 // Main arithmetic entry function: decodes a compressed src and
 // returns the uncompressed buffer.
 function read_array(src, tab, size) {
-    var j = 0; // array value
-    var z = 0; // array index: tab[j]
-    var last = -1;
+    let j = 0; // array value
+    let z = 0; // array index: tab[j]
+    let last = -1;
     // Remove first level of run-length encoding
-    var R = new Array(1024); // runs
+    const R = new Array(1024); // runs
     while (z < size) {
-        var run = src.ReadByte();
+        const run = src.ReadByte();
         R[j++] = run;
         z += run;
         if (run == last) {
-            var copy = src.ReadByte();
+            let copy = src.ReadByte();
             z += run * copy;
-            while (copy--)
+            while (copy--) {
                 R[j++] = run;
+            }
         }
         last = run;
     }
     // Now expand runs in R to tab, noting 255 is max run
-    var i = 0;
+    let i = 0;
     j = 0;
     z = 0;
     while (z < size) {
-        var run_len = 0;
+        let run_len = 0;
         do {
             var part = R[j++];
             run_len += part;
         } while (part == 255);
-        while (run_len--)
+        while (run_len--) {
             tab[z++] = i;
+        }
         i++;
     }
 }
@@ -83,11 +92,12 @@ const GFLAG_HAVE_STAB = 2;
 const GFLAG_DO_REV = 4;
 // Compute a new context from our current state and qual q
 function fqz_update_ctx(params, state, q) {
-    var last = params.context;
+    let last = params.context;
     state.qctx = (state.qctx << params.qshift) + params.qtab[q]; // >>> 0
     last += (state.qctx & ((1 << params.qbits) - 1)) << params.qloc; // >>> 0
-    if (params.do_pos)
+    if (params.do_pos) {
         last += params.ptab[Math.min(state.p, 1023)] << params.ploc;
+    }
     if (params.do_delta) {
         last += params.dtab[Math.min(state.delta, 255)] << params.dloc;
         // Is it better to use q here or qtab[q]?
@@ -96,13 +106,14 @@ function fqz_update_ctx(params, state, q) {
         state.delta += state.prevq != q ? 1 : 0;
         state.prevq = q;
     }
-    if (params.do_sel)
+    if (params.do_sel) {
         last += state.s << params.sloc;
+    }
     state.p--;
     return last & 0xffff;
 }
 function decode_fqz_single_param(src) {
-    var p = {}; // params
+    const p = {}; // params
     // Load FQZ parameters
     p.context = src.ReadUint16();
     p.pflags = src.ReadByte();
@@ -114,7 +125,7 @@ function decode_fqz_single_param(src) {
     p.do_delta = p.pflags & FLAG_DTAB;
     p.do_qtab = p.pflags & FLAG_QTAB;
     p.max_sym = src.ReadByte();
-    var x = src.ReadByte();
+    let x = src.ReadByte();
     p.qbits = x >> 4;
     p.qshift = x & 15;
     x = src.ReadByte();
@@ -126,13 +137,15 @@ function decode_fqz_single_param(src) {
     // Qual map, eg to "unbin" Illumina qualities
     p.qmap = new Array(256);
     if (p.pflags & FLAG_QMAP) {
-        for (var i = 0; i < p.max_sym; i++)
+        for (var i = 0; i < p.max_sym; i++) {
             p.qmap[i] = src.ReadByte();
+        }
     }
     else {
         // Useful optimisation to speed up main loop
-        for (var i = 0; i < 256; i++)
-            p.qmap[i] = i; // NOP
+        for (var i = 0; i < 256; i++) {
+            p.qmap[i] = i;
+        } // NOP
     }
     // Read tables
     p.qtab = new Array(1024);
@@ -141,78 +154,82 @@ function decode_fqz_single_param(src) {
     }
     else {
         // Useful optimisation to speed up main loop
-        for (var i = 0; i < 256; i++)
-            p.qtab[i] = i; // NOP
+        for (var i = 0; i < 256; i++) {
+            p.qtab[i] = i;
+        } // NOP
     }
     p.ptab = new Array(1024);
-    if (p.pflags & FLAG_PTAB)
+    if (p.pflags & FLAG_PTAB) {
         read_array(src, p.ptab, 1024);
+    }
     p.dtab = new Array(256);
-    if (p.pflags & FLAG_DTAB)
+    if (p.pflags & FLAG_DTAB) {
         read_array(src, p.dtab, 256);
+    }
     return p;
 }
 function decode_fqz_params(src) {
-    var gparams = {
+    const gparams = {
         max_sym: 0,
     };
     // Check fqz format version
-    var vers = src.ReadByte();
+    const vers = src.ReadByte();
     if (vers != 5) {
         console.error('Invalid FQZComp version number');
         return;
     }
-    var gflags = src.ReadByte();
-    var nparam = gflags & GFLAG_MULTI_PARAM ? src.ReadByte() : 1;
-    var max_sel = gflags.nparam > 1 ? gflags.nparam - 1 : 0; // Note max_sel, not num_sel
-    var stab = new Array(256);
+    const gflags = src.ReadByte();
+    const nparam = gflags & GFLAG_MULTI_PARAM ? src.ReadByte() : 1;
+    let max_sel = gflags.nparam > 1 ? gflags.nparam - 1 : 0; // Note max_sel, not num_sel
+    const stab = new Array(256);
     if (gflags & GFLAG_HAVE_STAB) {
         max_sel = src.ReadByte();
         read_array(src, stab, 256);
     }
     else {
-        for (var i = 0; i < nparam; i++)
+        for (var i = 0; i < nparam; i++) {
             stab[i] = i;
-        for (; i < 256; i++)
+        }
+        for (; i < 256; i++) {
             stab[i] = nparam - 1;
+        }
     }
     gparams.do_rev = gflags & GFLAG_DO_REV;
     gparams.stab = stab;
     gparams.max_sel = max_sel;
     gparams.params = new Array(gparams.nparam);
-    for (var p = 0; p < nparam; p++) {
+    for (let p = 0; p < nparam; p++) {
         gparams.params[p] = decode_fqz_single_param(src);
-        if (gparams.max_sym < gparams.params[p].max_sym)
+        if (gparams.max_sym < gparams.params[p].max_sym) {
             gparams.max_sym = gparams.params[p].max_sym;
+        }
     }
     return gparams;
 }
 function fqz_create_models(gparams) {
-    var model = {};
+    const model = {};
     model.qual = new Array(1 << 16);
-    for (var i = 0; i < 1 << 16; i++)
-        model.qual[i] = new ByteModel(gparams.max_sym + 1); // +1 as max value not num. values
+    for (var i = 0; i < 1 << 16; i++) {
+        model.qual[i] = new byte_model_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 ByteModel(256);
-    model.rev = new ByteModel(2);
-    model.dup = new ByteModel(2);
-    if (gparams.max_sel > 0)
-        model.sel = new ByteModel(gparams.max_sel + 1); // +1 as max value not num. values
+    for (var i = 0; i < 4; i++) {
+        model.len[i] = new byte_model_1.default(256);
+    }
+    model.rev = new byte_model_1.default(2);
+    model.dup = new byte_model_1.default(2);
+    if (gparams.max_sel > 0) {
+        model.sel = new byte_model_1.default(gparams.max_sel + 1);
+    } // +1 as max value not num. values
     return model;
 }
 // Initialise a new record, updating state.
 // Returns 1 if dup, otherwise 0
 function decode_fqz_new_record(src, rc, gparams, model, state, rev) {
     // Parameter selector
-    if (gparams.max_sel > 0) {
-        state.s = model.sel.ModelDecode(src, rc);
-    }
-    else {
-        state.s = 0;
-    }
+    state.s = gparams.max_sel > 0 ? model.sel.ModelDecode(src, rc) : 0;
     state.x = gparams.stab[state.s];
-    var params = gparams.params[state.x];
+    const params = gparams.params[state.x];
     // Reset contexts at the start of each new record
     if (params.fixed_len >= 0) {
         // Not fixed or fixed but first record
@@ -220,19 +237,22 @@ function decode_fqz_new_record(src, rc, gparams, model, state, rev) {
         len |= model.len[1].ModelDecode(src, rc) << 8;
         len |= model.len[2].ModelDecode(src, rc) << 16;
         len |= model.len[3].ModelDecode(src, rc) << 24;
-        if (params.fixed_len > 0)
+        if (params.fixed_len > 0) {
             params.fixed_len = -len;
+        }
     }
     else {
         len = -params.fixed_len;
     }
     state.len = len;
-    if (gparams.do_rev)
+    if (gparams.do_rev) {
         rev[state.rec] = model.rev.ModelDecode(src, rc);
+    }
     state.is_dup = 0;
     if (params.pflags & FLAG_DEDUP) {
-        if (model.dup.ModelDecode(src, rc))
+        if (model.dup.ModelDecode(src, rc)) {
             state.is_dup = 1;
+        }
     }
     state.p = len; // number of remaining bytes in this record
     state.delta = 0;
@@ -242,20 +262,21 @@ function decode_fqz_new_record(src, rc, gparams, model, state, rev) {
 }
 function decode_fqz(src, q_lens) {
     // Decode parameter block
-    var n_out = src.ReadUint7();
-    var gparams = decode_fqz_params(src);
-    if (!gparams)
+    const n_out = src.ReadUint7();
+    const gparams = decode_fqz_params(src);
+    if (!gparams) {
         return;
+    }
     var params = gparams.params;
-    var rev = new Array(q_lens.length);
+    const rev = new Array(q_lens.length);
     // Create initial models
-    var model = fqz_create_models(gparams);
+    const model = fqz_create_models(gparams);
     // Create our entropy encoder and output buffers
-    var rc = new RangeCoder(src);
+    const rc = new arith_sh_1.default(src);
     rc.RangeStartDecode(src);
-    var output = new Uint8Array(n_out);
+    const output = new Uint8Array(n_out);
     // Internal FQZ state
-    var state = {
+    const state = {
         qctx: 0, // Qual-only sub-context
         prevq: 0, // Previous quality value
         delta: 0, // Running delta (q vs prevq)
@@ -267,15 +288,16 @@ function decode_fqz(src, q_lens) {
         rec: 0, // Record number
     };
     // The main decode loop itself
-    var i = 0; // position in output buffer
+    let i = 0; // position in output buffer
     while (i < n_out) {
         if (state.p == 0) {
             decode_fqz_new_record(src, rc, gparams, model, state, rev);
             if (state.is_dup > 0) {
                 if (model.dup.ModelDecode(src, rc)) {
                     // Duplicate of last line
-                    for (var x = 0; x < len; x++)
+                    for (let x = 0; x < len; x++) {
                         output[i + x] = output[i + x - state.len];
+                    }
                     i += state.len;
                     state.p = 0;
                     continue;
@@ -286,27 +308,28 @@ function decode_fqz(src, q_lens) {
             var last = params.context;
         }
         // Decode the current quality (possibly mapped via qmap)
-        var Q = model.qual[last].ModelDecode(src, rc);
-        //if (params.do_qmap)
+        const Q = model.qual[last].ModelDecode(src, rc);
+        // if (params.do_qmap)
         //    output[i++] = params.qmap[Q];
-        //else
+        // else
         //    output[i++] = Q
         output[i++] = params.qmap[Q]; // optimised version of above
         last = fqz_update_ctx(params, state, Q);
     }
-    if (gparams.do_rev)
+    if (gparams.do_rev) {
         reverse_qualities(output, n_out, rev, q_lens);
+    }
     return output;
 }
 function reverse_qualities(qual, qual_len, rev, len) {
-    var rec = 0;
-    var i = 0;
+    let rec = 0;
+    let i = 0;
     while (i < qual_len) {
         if (rev[rec]) {
-            var j = 0;
-            var k = len[rec] - 1;
+            let j = 0;
+            let k = len[rec] - 1;
             while (j < k) {
-                var tmp = qual[i + j];
+                const tmp = qual[i + j];
                 qual[i + j] = qual[i + k];
                 qual[i + k] = tmp;
                 j++;
@@ -317,9 +340,7 @@ function reverse_qualities(qual, qual_len, rev, len) {
     }
 }
 function decode(src, q_lens) {
-    var stream = new IOStream(src);
-    //var n_out = stream.ReadUint32(); stream.ReadUint32(); // move to main
+    const stream = new iostream_1.default(src);
     return decode_fqz(stream, q_lens);
 }
-module.exports = { decode };
 //# sourceMappingURL=fqzcomp.js.map

package/dist/htscodecs/fqzcomp.js.map

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package/dist/htscodecs/index.d.ts

@@ -1,5 +1,5 @@
-export function r4x8_uncompress(inputBuffer: any, outputBuffer: any): Uint8Array<any>;
-export function r4x16_uncompress(inputBuffer: any): any;
-export function arith_uncompress(inputBuffer: any): Uint8Array<any>;
-export function fqzcomp_uncompress(inputBuffer: any): Uint8Array<any> | undefined;
-export function tok3_uncompress(inputBuffer: any): Uint8Array<ArrayBuffer>;
+export declare function r4x8_uncompress(inputBuffer: Uint8Array): Uint8Array<any>;
+export declare function r4x16_uncompress(inputBuffer: Uint8Array): any;
+export declare function arith_uncompress(inputBuffer: Uint8Array): Uint8Array<any>;
+export declare function fqzcomp_uncompress(inputBuffer: Uint8Array): Uint8Array<ArrayBuffer> | undefined;
+export declare function tok3_uncompress(inputBuffer: Uint8Array): Uint8Array<ArrayBuffer>;

package/dist/htscodecs/index.js

@@ -1,4 +1,6 @@
 "use strict";
+// @ts-nocheck
+//
 /*
  * Copyright (c) 2020 Genome Research Ltd.
  * Author(s): James Bonfield
@@ -31,16 +33,58 @@
  * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
  * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.r4x8_uncompress = r4x8_uncompress;
+exports.r4x16_uncompress = r4x16_uncompress;
+exports.arith_uncompress = arith_uncompress;
+exports.fqzcomp_uncompress = fqzcomp_uncompress;
+exports.tok3_uncompress = tok3_uncompress;
 // This is an interface to the htscodecs reference implementation of
 // 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.
-var r4x8 = require('./rans');
-var r4x16 = require('./rans4x16');
-var arith = require('./arith_gen');
-var fqzcomp = require('./fqzcomp');
-var tok3 = require('./tok3');
-function r4x8_uncompress(inputBuffer, outputBuffer) {
+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"));
+function r4x8_uncompress(inputBuffer) {
     return r4x8.decode(inputBuffer);
 }
 function r4x16_uncompress(inputBuffer) {
@@ -49,22 +93,15 @@ 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().decode(inputBuffer);
+    return new arith_gen_1.default().decode(inputBuffer);
 }
 function fqzcomp_uncompress(inputBuffer) {
-    var q_lens = new Array();
+    const q_lens = [];
     return fqzcomp.decode(inputBuffer, q_lens);
 }
 function tok3_uncompress(inputBuffer) {
     // Returns in string form instead of buffer
-    var out = tok3.decode(inputBuffer, 0, '\0');
+    const out = tok3.decode(inputBuffer, 0, '\0');
     return Uint8Array.from(Array.from(out).map(letter => letter.charCodeAt(0)));
 }
-module.exports = {
-    r4x8_uncompress: r4x8_uncompress,
-    r4x16_uncompress: r4x16_uncompress,
-    arith_uncompress: arith_uncompress,
-    fqzcomp_uncompress: fqzcomp_uncompress,
-    tok3_uncompress: tok3_uncompress,
-};
 //# sourceMappingURL=index.js.map