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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
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11
misc/exon-eval.js
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@ -123,11 +123,12 @@ Interval.find_ovlp = function(a, st, en)
* Main function * * Main function *
*****************/ *****************/
var c, l_fuzzy = 10, min_ov_ratio = 0.95, print_err = false; var c, l_fuzzy = 10, min_ov_ratio = 0.95, print_err = false, print_corr = false;
while ((c = getopt(arguments, "l:r:e")) != null) { while ((c = getopt(arguments, "l:r:ec")) != null) {
if (c == 'l') l_fuzzy = parseInt(getopt.arg); if (c == 'l') l_fuzzy = parseInt(getopt.arg);
else if (c == 'r') min_ov_ratio = parseFloat(getopt.arg); else if (c == 'r') min_ov_ratio = parseFloat(getopt.arg);
else if (c == 'e') print_err = true; else if (c == 'e') print_err = true;
else if (c == 'c') print_corr = true;
} }
if (arguments.length - getopt.ind < 2) { if (arguments.length - getopt.ind < 2) {
@ -224,14 +225,14 @@ while (file.readline(buf) >= 0) {
} }
if (hit) break; if (hit) break;
} }
if (!hit && print_err) { if ((print_err && !hit) || (print_corr && hit)) {
var x = '['; var x = '[';
for (var j = 0; j < o.length; ++j) { for (var j = 0; j < o.length; ++j) {
if (j) x += ', '; if (j) x += ', ';
x += '(' + o[j][0] + "," + o[j][1] + ')'; x += '(' + o[j][0] + "," + o[j][1] + ')';
} }
x += ']'; 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; } else ++n_novel;
} }
@ -242,7 +243,7 @@ file.close();
buf.destroy(); buf.destroy();
if (!print_err) { if (!print_err && !print_corr) {
print("Number of unmapped reads: " + n_unmapped); print("Number of unmapped reads: " + n_unmapped);
print("Number of mapped reads: " + n_mapped); print("Number of mapped reads: " + n_mapped);
print("Number of mapped exons: " + n_exon); print("Number of mapped exons: " + n_exon);