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IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS\n * BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN\n * ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN\n * CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE\n * SOFTWARE.\n */\n\nexport function paf_delta2paf(buffer: Buffer) {\n let rname = ''\n let qname = ''\n let qs = 0\n let qe = 0\n let rs = 0\n let re = 0\n let strand = 0\n let NM = 0\n let cigar = [] as number[]\n let x = 0\n let y = 0\n let seen_gt = false\n\n const records = []\n const regex = new RegExp(/^>(\\S+)\\s+(\\S+)\\s+(\\d+)\\s+(\\d+)/)\n\n let blockStart = 0\n let i = 0\n while (blockStart < buffer.length) {\n const n = buffer.indexOf('\\n', blockStart)\n if (n === -1) {\n break\n }\n const b = buffer.subarray(blockStart, n)\n const line = (decoder?.decode(b) || b.toString()).trim()\n blockStart = n + 1\n i++\n if (line) {\n const m = regex.exec(line)\n if (m !== null) {\n rname = m[1]!\n qname = m[2]!\n seen_gt = true\n continue\n }\n if (!seen_gt) {\n continue\n }\n const t = line.split(' ')\n if (t.length === 7) {\n const t0 = +t[0]!\n const t1 = +t[1]!\n const t2 = +t[2]!\n const t3 = +t[3]!\n const t4 = +t[4]!\n strand = (t0 < t1 && t2 < t3) || (t0 > t1 && t2 > t3) ? 1 : -1\n rs = +(t0 < t1 ? t0 : t1) - 1\n re = +(t1 > t0 ? t1 : t0)\n qs = +(t2 < t3 ? t2 : t3) - 1\n qe = +(t3 > t2 ? t3 : t2)\n x = y = 0\n NM = t4\n cigar = []\n } else if (t.length === 1) {\n const d = +t[0]!\n if (d === 0) {\n let blen = 0\n const cigar_str = []\n\n if (re - rs - x !== qe - qs - y) {\n throw new Error(`inconsistent alignment on line ${i}`)\n }\n cigar.push((re - rs - x) << 4)\n for (const entry of cigar) {\n const rlen = entry >> 4\n blen += rlen\n cigar_str.push(rlen + 'MID'.charAt(cigar[i]! & 0xf))\n }\n\n records.push({\n qname,\n qstart: qs,\n qend: qe,\n tname: rname,\n tstart: rs,\n tend: re,\n strand,\n extra: {\n numMatches: blen - NM,\n blockLen: blen,\n mappingQual: 0,\n NM,\n cg: cigar_str.join(''),\n },\n })\n } else if (d > 0) {\n const l = d - 1\n x += l + 1\n y += l\n if (l > 0) {\n cigar.push(l << 4)\n }\n\n if (cigar.length > 0 && (cigar[cigar.length - 1]! & 0xf) === 2) {\n cigar[cigar.length - 1]! += 1 << 4\n } else {\n cigar.push((1 << 4) | 2)\n } // deletion\n } else {\n const l = -d - 1\n x += l\n y += l + 1\n if (l > 0) {\n cigar.push(l << 4)\n }\n\n if (cigar.length > 0 && (cigar[cigar.length - 1]! & 0xf) === 1) {\n cigar[cigar.length - 1]! += 1 << 4\n } else {\n cigar.push((1 << 4) | 1)\n } // insertion\n }\n }\n }\n }\n return records\n}\n","import { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { openLocation } from '@jbrowse/core/util/io'\nimport { unzip } from '@gmod/bgzf-filehandle'\nimport { isGzip } from '@jbrowse/core/util'\nimport type { Buffer } from 'buffer'\n// locals\nimport PAFAdapter from '../PAFAdapter/PAFAdapter'\nimport { paf_delta2paf } from './util'\n\nexport default class DeltaAdapter extends PAFAdapter {\n async setupPre(opts?: BaseOptions) {\n const loc = openLocation(this.getConf('deltaLocation'), this.pluginManager)\n const buffer = (await loc.readFile(opts)) as Buffer\n const buf = isGzip(buffer) ? await unzip(buffer) : buffer\n return paf_delta2paf(buf)\n }\n}\n"],"names":["decoder","TextDecoder","undefined","DeltaAdapter","PAFAdapter","setupPre","opts","loc","openLocation","this","getConf","pluginManager","buffer","readFile","rname","qname","qs","qe","rs","re","strand","NM","cigar","x","y","seen_gt","records","regex","RegExp","blockStart","i","length","n","indexOf","b","subarray","line","decode","toString","trim","m","exec","t","split","t0","t1","t2","t3","d","blen","cigar_str","Error","push","entry","rlen","charAt","qstart","qend","tname","tstart","tend","extra","numMatches","blockLen","mappingQual","cg","join","l","paf_delta2paf","isGzip","unzip"],"sourceRoot":""}
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