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changed the way mapq is counted

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Heng Li
2017-07-26 14:20:31 -04:00
parent bd33bed455
commit 323293fbda
1 changed files with 4 additions and 7 deletions
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misc/pbsim-eval.js
+4 -7
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@@ -72,20 +72,17 @@ function count_err(qname, a, tot, err, mode)
s[2] = parseInt(s[2]); s[2] = parseInt(s[2]);
s[3] = parseInt(s[3]); s[3] = parseInt(s[3]);
s.shift(); // skip pbsim orginal read name s.shift(); // skip pbsim orginal read name
var max_mapq = 0;
for (var i = 0; i < a.length; ++i)
if (a[i][4] > max_mapq)
max_mapq = a[i][4];
++tot[max_mapq];
if (mode == 0) { // longest only if (mode == 0) { // longest only
var max = 0, max_i = -1; var max = 0, max_i = -1;
for (var i = 0; i < a.length; ++i) for (var i = 0; i < a.length; ++i)
if (a[i][2] - a[i][1] > max) if (a[i][2] - a[i][1] > max)
max = a[i][2] - a[i][1], max_i = i; max = a[i][2] - a[i][1], max_i = i;
var mapq = a[max_i][4];
++tot[mapq];
if (!is_correct(s, a[max_i])) { if (!is_correct(s, a[max_i])) {
if (max_mapq >= err_out_q) if (mapq >= err_out_q)
print('E', qname, a[max_i].join("\t")); print('E', qname, a[max_i].join("\t"));
++err[max_mapq]; ++err[mapq];
} }
} }
} }