INNER CODE UNIT · JavaScript

pafmerge

lh3/miniasm · misc/paftop.js:62

function pafmerge(a, max_gap)
{
	for (var i = 1; i < a.length; ++i) {
		var ai = a[i];
		for (var j = 0; j < i; ++j) {
			var aj = a[j];
			if (aj[4] != ai[4] || aj[5] != ai[5]) continue; // diff strand or chr
			var ts = [ai[7], aj[7]], te = [ai[8], aj[8]];
			var qs = [ai[2], aj[2]], qe = [ai[3], aj[3]];
			if (qs[0] > qs[1]) {
				qs = [aj[2], ai[2]], qe = [aj[3], ai[3]];
				ts = [aj[7], ai[7]], te = [aj[8], ai[8]];
				if (ai[4] == '-') {
					ts = [aj[6] - aj[8], ai[6] - ai[8]];
					te = [aj[6] - aj[7], ai[6] - ai[7]];
				}
			} else {
				if (ai[4] == '-') {

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