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added first-only and all-primary modes to eval

This commit is contained in:
Heng Li 2017-07-26 19:32:26 -04:00
parent 9f728dd96a
commit 8b08a2ec41
1 changed files with 24 additions and 6 deletions
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30
misc/pbsim-eval.js
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@ -37,9 +37,10 @@ var getopt = function(args, ostr) {
} }
var c, max_mapq = 60, mode = 0, err_out_q = 256, print_err = false, ovlp_ratio = 0.333; var c, max_mapq = 60, mode = 0, err_out_q = 256, print_err = false, ovlp_ratio = 0.333;
while ((c = getopt(arguments, "Q:r:")) != null) { while ((c = getopt(arguments, "Q:r:m:")) != null) {
if (c == 'Q') err_out_q = parseInt(getopt.arg), print_err = true; if (c == 'Q') err_out_q = parseInt(getopt.arg), print_err = true;
else if (c == 'r') ovlp_ratio = parseFloat(getopt.arg); else if (c == 'r') ovlp_ratio = parseFloat(getopt.arg);
else if (c == 'm') mode = parseInt(getopt.arg);
} }
var file = arguments.length == getopt.ind? new File() : new File(arguments[getopt.ind]); var file = arguments.length == getopt.ind? new File() : new File(arguments[getopt.ind]);
@ -68,16 +69,20 @@ function is_correct(s, b)
function count_err(qname, a, tot, err, mode) function count_err(qname, a, tot, err, mode)
{ {
var s = qname.split("!"); var s = qname.split("!");
if (a.length == 0) return;
if (s.length < 5 || (s[4] != '+' && s[4] != '-')) if (s.length < 5 || (s[4] != '+' && s[4] != '-'))
throw Error("Failed to parse pbsim2fa read names '" + qname + "'"); throw Error("Failed to parse pbsim2fa read names '" + qname + "'");
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
if (mode == 0) { // longest only if (mode == 0 || mode == 1) { // longest only or first only
var max = 0, max_i = -1; var max_i = 0;
for (var i = 0; i < a.length; ++i) if (mode == 0) {
if (a[i][2] - a[i][1] > max) var max = 0;
max = a[i][2] - a[i][1], max_i = i; for (var i = 0; i < a.length; ++i)
if (a[i][2] - a[i][1] > max)
max = a[i][2] - a[i][1], max_i = i;
}
var mapq = a[max_i][4]; var mapq = a[max_i][4];
++tot[mapq]; ++tot[mapq];
if (!is_correct(s, a[max_i])) { if (!is_correct(s, a[max_i])) {
@ -85,6 +90,19 @@ function count_err(qname, a, tot, err, mode)
print('E', qname, a[max_i].join("\t")); print('E', qname, a[max_i].join("\t"));
++err[mapq]; ++err[mapq];
} }
} else if (mode == 2) { // all primary mode
var max_err_mapq = -1, max_mapq = 0, max_err_i = -1;
for (var i = 0; i < a.length; ++i) {
max_mapq = max_mapq > a[i][4]? max_mapq : a[i][4];
if (!is_correct(s, a[i]))
if (a[i][4] > max_err_mapq)
max_err_mapq = a[i][4], max_err_i = i;
}
if (max_err_mapq >= 0) {
++tot[max_err_mapq], ++err[max_err_mapq];
if (max_err_mapq >= err_out_q)
print('E', qname, a[max_err_i].join("\t"));
} else ++tot[max_mapq];
} }
} }