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Merge branch 'dev' into tex

This commit is contained in:
Heng Li 2017-08-01 13:53:16 -04:00
parent d933a263d7 8b1e36c609
commit 0c563e1868
1 changed files with 15 additions and 6 deletions
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21
misc/pbsim-eval.js
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@ -36,11 +36,12 @@ var getopt = function(args, ostr) {
return optopt; return optopt;
} }
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 = 0.1, cap_short_mapq = false;
while ((c = getopt(arguments, "Q:r:m:")) != null) { while ((c = getopt(arguments, "Q:r:m:c")) != 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); else if (c == 'm') mode = parseInt(getopt.arg);
else if (c == 'c') cap_short_mapq = true;
} }
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]);
@ -77,11 +78,11 @@ function count_err(qname, a, tot, err, mode)
s.shift(); // skip pbsim orginal read name s.shift(); // skip pbsim orginal read name
if (mode == 0 || mode == 1) { // longest only or first only if (mode == 0 || mode == 1) { // longest only or first only
var max_i = 0; var max_i = 0;
if (mode == 0) { if (mode == 0) { // longest only
var max = 0; var max = 0;
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][5] > max)
max = a[i][2] - a[i][1], max_i = i; max = a[i][5], max_i = i;
} }
var mapq = a[max_i][4]; var mapq = a[max_i][4];
++tot[mapq]; ++tot[mapq];
@ -92,6 +93,14 @@ function count_err(qname, a, tot, err, mode)
} }
} else if (mode == 2) { // all primary mode } else if (mode == 2) { // all primary mode
var max_err_mapq = -1, max_mapq = 0, max_err_i = -1; var max_err_mapq = -1, max_mapq = 0, max_err_i = -1;
if (cap_short_mapq) {
var max = 0, max_q = 0;
for (var i = 0; i < a.length; ++i)
if (a[i][5] > max)
max = a[i][5], max_q = a[i][4];
for (var i = 0; i < a.length; ++i)
a[i][4] = max_q < a[i][4]? max_q : a[i][4];
}
for (var i = 0; i < a.length; ++i) { for (var i = 0; i < a.length; ++i) {
max_mapq = max_mapq > a[i][4]? max_mapq : a[i][4]; max_mapq = max_mapq > a[i][4]? max_mapq : a[i][4];
if (!is_correct(s, a[i])) if (!is_correct(s, a[i]))
@ -121,7 +130,7 @@ while (file.readline(buf) >= 0) {
continue; continue;
var mapq = parseInt(t[11]); var mapq = parseInt(t[11]);
if (mapq > max_mapq) mapq = max_mapq; if (mapq > max_mapq) mapq = max_mapq;
a.push([t[5], parseInt(t[7]), parseInt(t[8]), t[4], mapq]); a.push([t[5], parseInt(t[7]), parseInt(t[8]), t[4], mapq, parseInt(t[9])]);
} }
} }
} }