zzh
/
minimap2
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

option to print correct exons

This commit is contained in:
Heng Li 2017-08-11 17:50:21 -04:00
parent 0c1760bc86
commit 30b8cb4672
1 changed files with 6 additions and 5 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

11
misc/exon-eval.js
View File

@ -123,11 +123,12 @@ Interval.find_ovlp = function(a, st, en)
* Main function *
*****************/
var c, l_fuzzy = 10, min_ov_ratio = 0.95, print_err = false;
while ((c = getopt(arguments, "l:r:e")) != null) {
var c, l_fuzzy = 10, min_ov_ratio = 0.95, print_err = false, print_corr = false;
while ((c = getopt(arguments, "l:r:ec")) != null) {
if (c == 'l') l_fuzzy = parseInt(getopt.arg);
else if (c == 'r') min_ov_ratio = parseFloat(getopt.arg);
else if (c == 'e') print_err = true;
else if (c == 'c') print_corr = true;
}
if (arguments.length - getopt.ind < 2) {
@ -224,14 +225,14 @@ while (file.readline(buf) >= 0) {
}
if (hit) break;
}
if (!hit && print_err) {
if ((print_err && !hit) || (print_corr && hit)) {
var x = '[';
for (var j = 0; j < o.length; ++j) {
if (j) x += ', ';
x += '(' + o[j][0] + "," + o[j][1] + ')';
}
x += ']';
print(t[0], i+1, exon[i][0], exon[i][1], x);
print(t[0], i+1, t[2], exon[i][0], exon[i][1], x);
}
} else ++n_novel;
}
@ -242,7 +243,7 @@ file.close();
buf.destroy();
if (!print_err) {
if (!print_err && !print_corr) {
print("Number of unmapped reads: " + n_unmapped);
print("Number of mapped reads: " + n_mapped);
print("Number of mapped exons: " + n_exon);