genomic-reader/dist/bigwig/encodeBigBed.js

A Typescript library for reading BigWig, BigBed, 2bit, and Bam files. Capable of streaming. For use in the browser or on Node.js.

"use strict";
Object.defineProperty(exports, "__esModule", { value: true });
exports.parseBigBedIdrPeak = exports.parseBigBedTssPeak = exports.parseBigBedMethyl = exports.parseBigBedBroadPeak = exports.parseBigBedNarrowPeak = void 0;
exports.parseBigBedNarrowPeak = function (chrom, startBase, endBase, rest) {
    const entry = {
        chr: chrom,
        start: startBase,
        end: endBase
    };
    let tokens = rest.split("\t");
    if (tokens.length > 0) {
        entry.name = tokens[0];
    }
    if (tokens.length > 1) {
        entry.score = parseFloat(tokens[1]);
    }
    if (tokens.length > 2) {
        entry.strand = tokens[2];
    }
    if (tokens.length > 3) {
        entry.signalValue = parseInt(tokens[3]);
    }
    if (tokens.length > 4) {
        entry.pValue = parseInt(tokens[4]);
    }
    if (tokens.length > 5) {
        entry.qValue = parseInt(tokens[5]);
    }
    if (tokens.length > 6) {
        entry.peak = parseInt(tokens[6]);
    }
    return entry;
};
exports.parseBigBedBroadPeak = function (chrom, startBase, endBase, rest) {
    const entry = {
        chr: chrom,
        start: startBase,
        end: endBase
    };
    let tokens = rest.split("\t");
    if (tokens.length > 0) {
        entry.name = tokens[0];
    }
    if (tokens.length > 1) {
        entry.score = parseFloat(tokens[1]);
    }
    if (tokens.length > 2) {
        entry.strand = tokens[2];
    }
    if (tokens.length > 3) {
        entry.signalValue = parseInt(tokens[3]);
    }
    if (tokens.length > 4) {
        entry.pValue = parseInt(tokens[4]);
    }
    if (tokens.length > 5) {
        entry.qValue = parseInt(tokens[5]);
    }
    return entry;
};
exports.parseBigBedMethyl = function (chrom, startBase, endBase, rest) {
    const entry = {
        chr: chrom,
        start: startBase,
        end: endBase
    };
    let tokens = rest.split("\t");
    if (tokens.length > 0) {
        entry.name = tokens[0];
    }
    if (tokens.length > 1) {
        entry.score = parseInt(tokens[1]);
    }
    if (tokens.length > 2) {
        entry.strand = tokens[2];
    }
    if (tokens.length > 3) {
        entry.thickStart = parseInt(tokens[3]);
    }
    if (tokens.length > 4) {
        entry.thickEnd = parseInt(tokens[4]);
    }
    if (tokens.length > 5) {
        entry.reserved = parseInt(tokens[5]);
    }
    if (tokens.length > 6) {
        entry.readCount = parseInt(tokens[6]);
    }
    if (tokens.length > 7) {
        entry.percentMeth = parseInt(tokens[7]);
    }
    return entry;
};
exports.parseBigBedTssPeak = function (chrom, startBase, endBase, rest) {
    const entry = {
        chr: chrom,
        start: startBase,
        end: endBase
    };
    let tokens = rest.split("\t");
    if (tokens.length > 0) {
        entry.name = tokens[0];
    }
    if (tokens.length > 1) {
        entry.score = parseFloat(tokens[1]);
    }
    if (tokens.length > 2) {
        entry.strand = tokens[2];
    }
    if (tokens.length > 3) {
        entry.count = parseFloat(tokens[3]);
    }
    if (tokens.length > 4) {
        entry.gene_id = tokens[4];
    }
    if (tokens.length > 5) {
        entry.gene_name = tokens[5];
    }
    if (tokens.length > 6) {
        entry.tss_id = tokens[6];
    }
    if (tokens.length > 7) {
        entry.peak_cov = tokens[7];
    }
    return entry;
};
exports.parseBigBedIdrPeak = function (chrom, startBase, endBase, rest) {
    const entry = {
        chr: chrom,
        start: startBase,
        end: endBase
    };
    let tokens = rest.split("\t");
    if (tokens.length > 0) {
        entry.name = tokens[0];
    }
    if (tokens.length > 1) {
        entry.score = parseInt(tokens[1]);
    }
    if (tokens.length > 2) {
        entry.strand = tokens[2];
    }
    if (tokens.length > 3) {
        entry.localIDR = parseFloat(tokens[3]);
    }
    if (tokens.length > 4) {
        entry.globalIDR = parseFloat(tokens[4]);
    }
    if (tokens.length > 5) {
        entry.rep1_chromStart = parseInt(tokens[5]);
    }
    if (tokens.length > 6) {
        entry.rep1_chromEnd = parseInt(tokens[6]);
    }
    if (tokens.length > 7) {
        entry.rep1_count = parseFloat(tokens[7]);
    }
    if (tokens.length > 8) {
        entry.rep2_chromStart = parseInt(tokens[8]);
    }
    if (tokens.length > 9) {
        entry.rep2_chromEnd = parseInt(tokens[9]);
    }
    if (tokens.length > 10) {
        entry.rep2_chromEnd = parseFloat(tokens[10]);
    }
    return entry;
};
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