@gmod/hic 1.2.0 → 1.2.1
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
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@@ -25,11 +25,26 @@ class NormalizationVector {
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// forever, and every call re-reads the same range from the file.
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const wanted = Math.min(end, this.nValues);
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if (!this.cache || start < this.cache.start || wanted > this.cache.end) {
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-
const adjustedStart = Math.max(0, start - 1000);
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const adjustedEnd = Math.min(this.nValues, end + 1000);
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// Clamped against `adjustedEnd`, and not merely against zero, or a window
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// starting past the vector produces a NEGATIVE `n` — and a negative read
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// length reaches the reader as `new Uint8Array(-8)`, a RangeError that
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// fails the whole fetch instead of the empty answer the caller below
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// already handles. The padding is what sets how far past is far enough:
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// more than 1000 bins, which at a fine binsize is not far at all.
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//
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// Reachable exactly where the comment above says: the assembly's refseq
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// is longer than the size the `.hic` recorded for that chromosome, so a
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// view of the tail of it asks for bins the vector never had.
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const adjustedStart = Math.min(Math.max(0, start - 1000), adjustedEnd);
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const startPosition = this.filePosition + adjustedStart * this.dataType;
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const n = adjustedEnd - adjustedStart;
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-
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// Nothing to read when the window is entirely past the vector, and on a
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// remote file a zero-length range request is still a round trip — one per
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// region pair, on every fetch, for as long as the view stays there.
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const data = n > 0
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? await this.file.read(startPosition, n * this.dataType)
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: new ArrayBuffer(0);
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const parser = new binary_ts_1.default(new DataView(data));
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const values = new Float64Array(n);
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for (let i = 0; i < n; i++) {
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"normalizationVector.js","sourceRoot":"","sources":["../src/normalizationVector.ts"],"names":[],"mappings":";;;;;AAAA,4DAAsC;AAItC,MAAM,MAAM,GAAG,CAAC,CAAA;AAEhB,MAAqB,mBAAmB;IAC9B,KAAK,CACqD;IAE1D,IAAI,CAAQ;IACZ,YAAY,CAAQ;IACpB,OAAO,CAAQ;IACf,QAAQ,CAAQ;IAExB,YACE,IAAY,EACZ,YAAoB,EACpB,OAAe,EACf,QAAgB;QAEhB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA;QAChC,IAAI,CAAC,OAAO,GAAG,OAAO,CAAA;QACtB,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAA;IAC1B,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,KAAa,EAAE,GAAW;QACxC,4EAA4E;QAC5E,0EAA0E;QAC1E,4EAA4E;QAC5E,0EAA0E;QAC1E,iEAAiE;QACjE,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,EAAE,IAAI,CAAC,OAAO,CAAC,CAAA;QAC1C,IAAI,CAAC,IAAI,CAAC,KAAK,IAAI,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,KAAK,IAAI,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,GAAG,EAAE,CAAC;YACvE,MAAM,
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+
{"version":3,"file":"normalizationVector.js","sourceRoot":"","sources":["../src/normalizationVector.ts"],"names":[],"mappings":";;;;;AAAA,4DAAsC;AAItC,MAAM,MAAM,GAAG,CAAC,CAAA;AAEhB,MAAqB,mBAAmB;IAC9B,KAAK,CACqD;IAE1D,IAAI,CAAQ;IACZ,YAAY,CAAQ;IACpB,OAAO,CAAQ;IACf,QAAQ,CAAQ;IAExB,YACE,IAAY,EACZ,YAAoB,EACpB,OAAe,EACf,QAAgB;QAEhB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA;QAChC,IAAI,CAAC,OAAO,GAAG,OAAO,CAAA;QACtB,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAA;IAC1B,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,KAAa,EAAE,GAAW;QACxC,4EAA4E;QAC5E,0EAA0E;QAC1E,4EAA4E;QAC5E,0EAA0E;QAC1E,iEAAiE;QACjE,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,EAAE,IAAI,CAAC,OAAO,CAAC,CAAA;QAC1C,IAAI,CAAC,IAAI,CAAC,KAAK,IAAI,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,KAAK,IAAI,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,GAAG,EAAE,CAAC;YACvE,MAAM,WAAW,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,OAAO,EAAE,GAAG,GAAG,IAAI,CAAC,CAAA;YACtD,0EAA0E;YAC1E,yEAAyE;YACzE,uEAAuE;YACvE,qEAAqE;YACrE,wEAAwE;YACxE,kEAAkE;YAClE,EAAE;YACF,wEAAwE;YACxE,wEAAwE;YACxE,6DAA6D;YAC7D,MAAM,aAAa,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,KAAK,GAAG,IAAI,CAAC,EAAE,WAAW,CAAC,CAAA;YACtE,MAAM,aAAa,GAAG,IAAI,CAAC,YAAY,GAAG,aAAa,GAAG,IAAI,CAAC,QAAQ,CAAA;YACvE,MAAM,CAAC,GAAG,WAAW,GAAG,aAAa,CAAA;YACrC,wEAAwE;YACxE,0EAA0E;YAC1E,oEAAoE;YACpE,MAAM,IAAI,GACR,CAAC,GAAG,CAAC;gBACH,CAAC,CAAC,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,aAAa,EAAE,CAAC,GAAG,IAAI,CAAC,QAAQ,CAAC;gBACxD,CAAC,CAAC,IAAI,WAAW,CAAC,CAAC,CAAC,CAAA;YACxB,MAAM,MAAM,GAAG,IAAI,mBAAY,CAAC,IAAI,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAA;YACnD,MAAM,MAAM,GAAG,IAAI,YAAY,CAAC,CAAC,CAAC,CAAA;YAClC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;gBAC3B,MAAM,CAAC,CAAC,CAAC;oBACP,IAAI,CAAC,QAAQ,KAAK,MAAM,CAAC,CAAC,CAAC,MAAM,CAAC,SAAS,EAAE,CAAC,CAAC,CAAC,MAAM,CAAC,QAAQ,EAAE,CAAA;YACrE,CAAC;YACD,IAAI,CAAC,KAAK,GAAG,EAAE,KAAK,EAAE,aAAa,EAAE,GAAG,EAAE,WAAW,EAAE,MAAM,EAAE,CAAA;QACjE,CAAC;QAED,4EAA4E;QAC5E,sEAAsE;QACtE,wEAAwE;QACxE,2EAA2E;QAC3E,iCAAiC;QACjC,MAAM,UAAU,GAAG,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,KAAK,CAAA;QAC3C,OAAO,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,QAAQ,CAAC,UAAU,EAAE,UAAU,GAAG,CAAC,GAAG,GAAG,KAAK,CAAC,CAAC,CAAA;IAC3E,CAAC;CACF;AAnED,sCAmEC"}
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@@ -20,11 +20,26 @@ export default class NormalizationVector {
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// forever, and every call re-reads the same range from the file.
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const wanted = Math.min(end, this.nValues);
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if (!this.cache || start < this.cache.start || wanted > this.cache.end) {
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const adjustedStart = Math.max(0, start - 1000);
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const adjustedEnd = Math.min(this.nValues, end + 1000);
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// Clamped against `adjustedEnd`, and not merely against zero, or a window
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// starting past the vector produces a NEGATIVE `n` — and a negative read
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// length reaches the reader as `new Uint8Array(-8)`, a RangeError that
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// fails the whole fetch instead of the empty answer the caller below
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// already handles. The padding is what sets how far past is far enough:
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// more than 1000 bins, which at a fine binsize is not far at all.
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//
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// Reachable exactly where the comment above says: the assembly's refseq
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// is longer than the size the `.hic` recorded for that chromosome, so a
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// view of the tail of it asks for bins the vector never had.
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const adjustedStart = Math.min(Math.max(0, start - 1000), adjustedEnd);
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const startPosition = this.filePosition + adjustedStart * this.dataType;
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const n = adjustedEnd - adjustedStart;
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-
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+
// Nothing to read when the window is entirely past the vector, and on a
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// remote file a zero-length range request is still a round trip — one per
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// region pair, on every fetch, for as long as the view stays there.
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const data = n > 0
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? await this.file.read(startPosition, n * this.dataType)
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: new ArrayBuffer(0);
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const parser = new BinaryParser(new DataView(data));
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const values = new Float64Array(n);
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for (let i = 0; i < n; i++) {
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"normalizationVector.js","sourceRoot":"","sources":["../src/normalizationVector.ts"],"names":[],"mappings":"AAAA,OAAO,YAAY,MAAM,aAAa,CAAA;AAItC,MAAM,MAAM,GAAG,CAAC,CAAA;AAEhB,MAAM,CAAC,OAAO,OAAO,mBAAmB;IAC9B,KAAK,CACqD;IAE1D,IAAI,CAAQ;IACZ,YAAY,CAAQ;IACpB,OAAO,CAAQ;IACf,QAAQ,CAAQ;IAExB,YACE,IAAY,EACZ,YAAoB,EACpB,OAAe,EACf,QAAgB;QAEhB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA;QAChC,IAAI,CAAC,OAAO,GAAG,OAAO,CAAA;QACtB,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAA;IAC1B,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,KAAa,EAAE,GAAW;QACxC,4EAA4E;QAC5E,0EAA0E;QAC1E,4EAA4E;QAC5E,0EAA0E;QAC1E,iEAAiE;QACjE,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,EAAE,IAAI,CAAC,OAAO,CAAC,CAAA;QAC1C,IAAI,CAAC,IAAI,CAAC,KAAK,IAAI,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,KAAK,IAAI,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,GAAG,EAAE,CAAC;YACvE,MAAM,
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{"version":3,"file":"normalizationVector.js","sourceRoot":"","sources":["../src/normalizationVector.ts"],"names":[],"mappings":"AAAA,OAAO,YAAY,MAAM,aAAa,CAAA;AAItC,MAAM,MAAM,GAAG,CAAC,CAAA;AAEhB,MAAM,CAAC,OAAO,OAAO,mBAAmB;IAC9B,KAAK,CACqD;IAE1D,IAAI,CAAQ;IACZ,YAAY,CAAQ;IACpB,OAAO,CAAQ;IACf,QAAQ,CAAQ;IAExB,YACE,IAAY,EACZ,YAAoB,EACpB,OAAe,EACf,QAAgB;QAEhB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA;QAChC,IAAI,CAAC,OAAO,GAAG,OAAO,CAAA;QACtB,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAA;IAC1B,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,KAAa,EAAE,GAAW;QACxC,4EAA4E;QAC5E,0EAA0E;QAC1E,4EAA4E;QAC5E,0EAA0E;QAC1E,iEAAiE;QACjE,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,EAAE,IAAI,CAAC,OAAO,CAAC,CAAA;QAC1C,IAAI,CAAC,IAAI,CAAC,KAAK,IAAI,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,KAAK,IAAI,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,GAAG,EAAE,CAAC;YACvE,MAAM,WAAW,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,OAAO,EAAE,GAAG,GAAG,IAAI,CAAC,CAAA;YACtD,0EAA0E;YAC1E,yEAAyE;YACzE,uEAAuE;YACvE,qEAAqE;YACrE,wEAAwE;YACxE,kEAAkE;YAClE,EAAE;YACF,wEAAwE;YACxE,wEAAwE;YACxE,6DAA6D;YAC7D,MAAM,aAAa,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,KAAK,GAAG,IAAI,CAAC,EAAE,WAAW,CAAC,CAAA;YACtE,MAAM,aAAa,GAAG,IAAI,CAAC,YAAY,GAAG,aAAa,GAAG,IAAI,CAAC,QAAQ,CAAA;YACvE,MAAM,CAAC,GAAG,WAAW,GAAG,aAAa,CAAA;YACrC,wEAAwE;YACxE,0EAA0E;YAC1E,oEAAoE;YACpE,MAAM,IAAI,GACR,CAAC,GAAG,CAAC;gBACH,CAAC,CAAC,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,aAAa,EAAE,CAAC,GAAG,IAAI,CAAC,QAAQ,CAAC;gBACxD,CAAC,CAAC,IAAI,WAAW,CAAC,CAAC,CAAC,CAAA;YACxB,MAAM,MAAM,GAAG,IAAI,YAAY,CAAC,IAAI,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAA;YACnD,MAAM,MAAM,GAAG,IAAI,YAAY,CAAC,CAAC,CAAC,CAAA;YAClC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;gBAC3B,MAAM,CAAC,CAAC,CAAC;oBACP,IAAI,CAAC,QAAQ,KAAK,MAAM,CAAC,CAAC,CAAC,MAAM,CAAC,SAAS,EAAE,CAAC,CAAC,CAAC,MAAM,CAAC,QAAQ,EAAE,CAAA;YACrE,CAAC;YACD,IAAI,CAAC,KAAK,GAAG,EAAE,KAAK,EAAE,aAAa,EAAE,GAAG,EAAE,WAAW,EAAE,MAAM,EAAE,CAAA;QACjE,CAAC;QAED,4EAA4E;QAC5E,sEAAsE;QACtE,wEAAwE;QACxE,2EAA2E;QAC3E,iCAAiC;QACjC,MAAM,UAAU,GAAG,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,KAAK,CAAA;QAC3C,OAAO,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,QAAQ,CAAC,UAAU,EAAE,UAAU,GAAG,CAAC,GAAG,GAAG,KAAK,CAAC,CAAC,CAAA;IAC3E,CAAC;CACF"}
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package/package.json
CHANGED
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@@ -33,11 +33,27 @@ export default class NormalizationVector {
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// forever, and every call re-reads the same range from the file.
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const wanted = Math.min(end, this.nValues)
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if (!this.cache || start < this.cache.start || wanted > this.cache.end) {
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-
const adjustedStart = Math.max(0, start - 1000)
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const adjustedEnd = Math.min(this.nValues, end + 1000)
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// Clamped against `adjustedEnd`, and not merely against zero, or a window
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38
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+
// starting past the vector produces a NEGATIVE `n` — and a negative read
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39
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+
// length reaches the reader as `new Uint8Array(-8)`, a RangeError that
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40
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+
// fails the whole fetch instead of the empty answer the caller below
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41
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+
// already handles. The padding is what sets how far past is far enough:
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42
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+
// more than 1000 bins, which at a fine binsize is not far at all.
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43
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//
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44
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+
// Reachable exactly where the comment above says: the assembly's refseq
|
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45
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+
// is longer than the size the `.hic` recorded for that chromosome, so a
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46
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+
// view of the tail of it asks for bins the vector never had.
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47
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const adjustedStart = Math.min(Math.max(0, start - 1000), adjustedEnd)
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const startPosition = this.filePosition + adjustedStart * this.dataType
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const n = adjustedEnd - adjustedStart
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-
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+
// Nothing to read when the window is entirely past the vector, and on a
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+
// remote file a zero-length range request is still a round trip — one per
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// region pair, on every fetch, for as long as the view stays there.
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const data =
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n > 0
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? await this.file.read(startPosition, n * this.dataType)
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: new ArrayBuffer(0)
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const parser = new BinaryParser(new DataView(data))
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const values = new Float64Array(n)
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for (let i = 0; i < n; i++) {
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