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r980: support auNGA

This commit is contained in:
Heng Li 2020-04-10 21:36:59 -04:00
parent 0a5e386359
commit 50775362bb
1 changed files with 25 additions and 5 deletions
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30
misc/paftools.js
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@ -1,6 +1,6 @@
#!/usr/bin/env k8 #!/usr/bin/env k8
var paftools_version = '2.17-r979-dirty'; var paftools_version = '2.17-r980-dirty';
/***************************** /*****************************
***** Library functions ***** ***** Library functions *****
@ -640,6 +640,23 @@ function paf_asmstat(args)
} }
} }
function AUN(lens, tot) {
lens.sort(function(a,b) { return b - a; });
if (tot == null) {
tot = 0;
for (var k = 0; k < lens.length; ++k)
tot += lens[k];
}
var x = 0, y = 0;
for (var k = 0; k < lens.length; ++k) {
var l = x + lens[k] <= tot? lens[k] : tot - x;
x += lens[k];
y += l * (l / tot);
if (x >= tot) break;
}
return y.toFixed(0);
}
function count_bp(bp, min_blen, min_gap) { function count_bp(bp, min_blen, min_gap) {
var n_bp = 0; var n_bp = 0;
for (var k = 0; k < bp.length; ++k) for (var k = 0; k < bp.length; ++k)
@ -660,7 +677,7 @@ function paf_asmstat(args)
return (NM - n_gaps + n_gapo) / (n_M + n_gapo); return (NM - n_gaps + n_gapo) / (n_M + n_gapo);
} }
var labels = ['Length', 'l_cov', 'Rcov', 'Rdup', 'Qcov', 'NG75', 'NG50', 'NGA50', '#breaks', 'bp(' + min_seg_len + ',0)', 'bp(' + min_seg_len + ',10k)']; var labels = ['Length', 'l_cov', 'Rcov', 'Rdup', 'Qcov', 'NG75', 'NG50', 'NGA50', 'AUNGA', '#breaks', 'bp(' + min_seg_len + ',0)', 'bp(' + min_seg_len + ',10k)'];
var rst = []; var rst = [];
for (var i = 0; i < labels.length; ++i) for (var i = 0; i < labels.length; ++i)
rst[i] = []; rst[i] = [];
@ -763,10 +780,13 @@ function paf_asmstat(args)
// compute NGA50 // compute NGA50
rst[7][i] = N50(qblock_len, ref_len, 0.5); rst[7][i] = N50(qblock_len, ref_len, 0.5);
// compute AUNGA
rst[8][i] = AUN(qblock_len, ref_len);
// compute break points // compute break points
rst[8][i] = n_breaks; rst[9][i] = n_breaks;
rst[9][i] = count_bp(bp, 500, 0); rst[10][i] = count_bp(bp, 500, 0);
rst[10][i] = count_bp(bp, 500, 10000); rst[11][i] = count_bp(bp, 500, 10000);
// nb-plot; NOT USED // nb-plot; NOT USED
/* /*