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

minor tuning to the matching rules

This commit is contained in:
Heng Li 2017-08-19 16:21:49 +08:00
parent 8058c85b72
commit 5ed2faf270
1 changed files with 16 additions and 19 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

35
misc/exon-eval.js
View File

@ -123,7 +123,7 @@ Interval.find_ovlp = function(a, st, en)
* Main function *
*****************/
var c, l_fuzzy = 10, min_ov_ratio = 0.95, print_ovlp = false, print_err_only = false, first_only = false;
var c, l_fuzzy = 0, min_ov_ratio = 0.95, print_ovlp = false, print_err_only = false, first_only = false;
while ((c = getopt(arguments, "l:r:ep1")) != null) {
if (c == 'l') l_fuzzy = parseInt(getopt.arg);
else if (c == 'r') min_ov_ratio = parseFloat(getopt.arg);
@ -168,7 +168,7 @@ var n_ext_hit = 0, n_int_hit = 0, n_sgl_hit = 0;
file = new File(arguments[getopt.ind+1]);
var last_qname = null;
var re_cigar = /(\d+)([MIDNSH])/g;
var re_cigar = /(\d+)([MIDNSHX=])/g;
while (file.readline(buf) >= 0) {
var m, t = buf.toString().split("\t");
if (t[0].charAt(0) == '@') continue;
@ -190,7 +190,7 @@ while (file.readline(buf) >= 0) {
exon.push([exon_st, en]);
en += len;
exon_st = en;
} else if (op == 'M' || op == 'D') en += len;
} else if (op == 'M' || op == 'X' || op == '=' || op == 'D') en += len;
}
exon.push([exon_st, en]);
n_exon += exon.length;
@ -212,22 +212,19 @@ while (file.readline(buf) >= 0) {
var l1 = o[j][1] - o[j][0];
var min = l0 < l1? l0 : l1;
var ov_ratio = ol / min;
if (ov_ratio >= min_ov_ratio) {
var st_diff = exon[i][0] - o[j][0];
var en_diff = exon[i][1] - o[j][1];
if (st_diff < 0) st_diff = -st_diff;
if (en_diff < 0) en_diff = -en_diff;
if (i == 0 && exon.length == 1) {
++n_sgl_hit, hit = true;
} else if (i == 0) {
if (en_diff <= l_fuzzy) ++n_ext_hit, hit = true;
} else if (i == exon.length - 1) {
if (st_diff <= l_fuzzy) ++n_ext_hit, hit = true;
} else {
//if (en_diff <= l_fuzzy && st_diff <= l_fuzzy && ol / span >= min_ov_ratio)
if (en_diff + st_diff <= l_fuzzy || ol / span >= min_ov_ratio)
++n_int_hit, hit = true;
}
var st_diff = exon[i][0] - o[j][0];
var en_diff = exon[i][1] - o[j][1];
if (st_diff < 0) st_diff = -st_diff;
if (en_diff < 0) en_diff = -en_diff;
if (i == 0 && exon.length == 1) {
if (ov_ratio >= min_ov_ratio) ++n_sgl_hit, hit = true;
} else if (i == 0) {
if (en_diff <= l_fuzzy) ++n_ext_hit, hit = true;
} else if (i == exon.length - 1) {
if (st_diff <= l_fuzzy) ++n_ext_hit, hit = true;
} else {
if (en_diff + st_diff <= l_fuzzy)
++n_int_hit, hit = true;
}
if (hit) break;
}