@gmod/cram
Version:
read CRAM files with pure Javascript
60 lines • 2.18 kB
JavaScript
import CramCodec from "./_base.js";
import { CramBufferOverrunError, CramUnimplementedError } from "../../errors.js";
export default class GammaCodec extends CramCodec {
constructor(parameters, dataType) {
super(parameters, dataType);
if (this.dataType !== 'int') {
throw new CramUnimplementedError(`${this.dataType} decoding not yet implemented by GAMMA codec`);
}
}
decode(_slice, coreDataBlock, _blocksByContentId, cursors) {
return decodeGammaInline(coreDataBlock.content, cursors.coreBlock, this.parameters.offset);
}
}
/**
* Optimized gamma decoder with inlined bit reading.
* Avoids function call overhead by inlining the getBits logic.
*/
function decodeGammaInline(data, cursor, offset) {
let { bytePosition, bitPosition } = cursor;
let length = 1;
// Count leading zeros (each 0 bit increases length). A truncated core block
// reads as zeros forever, so guard against running off the end.
// eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
while (true) {
if (bytePosition >= data.length) {
throw new CramBufferOverrunError('read beyond end of core block; file seems truncated');
}
const bit = (data[bytePosition] >> bitPosition) & 1;
bitPosition -= 1;
if (bitPosition < 0) {
bytePosition += 1;
bitPosition = 7;
}
if (bit === 1) {
break;
}
length += 1;
}
// Now read (length - 1) more bits for the value
let readBits = 0;
const bitsToRead = length - 1;
if (bitsToRead > 0) {
// Optimized multi-bit read
for (let i = 0; i < bitsToRead; i++) {
readBits <<= 1;
readBits |= (data[bytePosition] >> bitPosition) & 1;
bitPosition -= 1;
if (bitPosition < 0) {
bytePosition += 1;
bitPosition = 7;
}
}
}
// Update cursor
cursor.bytePosition = bytePosition;
cursor.bitPosition = bitPosition;
const value = readBits | (1 << (length - 1));
return value - offset;
}
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