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r871: print erroneous genes

This commit is contained in:
Heng Li 2018-11-04 20:37:06 -05:00
parent 57ec73ec6c
commit e46cbb7d84
1 changed files with 30 additions and 13 deletions
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43
misc/paftools.js
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@ -1,6 +1,6 @@
#!/usr/bin/env k8
var paftools_version = '2.13-r870-dirty';
var paftools_version = '2.13-r871-dirty';
/*****************************
***** Library functions *****
@ -772,8 +772,11 @@ function paf_asmstat(args)
function paf_asmgene(args)
{
var c, opt = { min_cov:0.99, min_iden:0.99 };
while ((c = getopt(args, "")) != null);
var c, opt = { min_cov:0.99, min_iden:0.99 }, print_err = false;
while ((c = getopt(args, "i:c:e")) != null)
if (c == 'i') opt.min_iden = parseFloat(getopt.arg);
else if (c == 'c') opt.min_cov = parseFloat(getopt.arg);
else if (c == 'e') print_err = true;
var n_fn = args.length - getopt.ind;
if (n_fn < 2) {
@ -810,7 +813,7 @@ function paf_asmgene(args)
}
var buf = new Bytes();
var gene = {}, header = ["Metric"];
var gene = {}, header = [], refpos = {};
for (var i = getopt.ind; i < args.length; ++i) {
var fn = args[i];
var label = fn.replace(/.paf(.gz)?$/, "");
@ -819,6 +822,7 @@ function paf_asmgene(args)
while (file.readline(buf) >= 0) {
var t = buf.toString().split("\t");
var ql = parseInt(t[1]), qs = parseInt(t[2]), qe = parseInt(t[3]), mlen = parseInt(t[9]), blen = parseInt(t[10]), mapq = parseInt(t[11]);
if (i == getopt.ind) refpos[t[0]] = [t[0], t[5], t[7], t[8]].join("\t");
if (gene[t[0]] == null) gene[t[0]] = [];
if (a.length && t[0] != a[0][0]) {
gene[t[0]][i - getopt.ind] = process_query(opt, a);
@ -841,18 +845,31 @@ function paf_asmgene(args)
for (var g in gene) {
if (gene[g][0] == null || gene[g][0][0] != 1) continue;
for (var i = 0; i < n_fn; ++i) {
if (gene[g][i] == null) rst[4][i]++;
else if (gene[g][i][0] == 1) rst[0][i]++;
else if (gene[g][i][0] > 1) rst[1][i]++;
else if (gene[g][i][1] >= opt.min_cov) rst[2][i]++;
else if (gene[g][i][1] >= 0.5) rst[3][i]++;
else if (gene[g][i][1] >= 0.1) rst[4][i]++;
else rst[5][i]++;
if (gene[g][i] == null) {
rst[4][i]++;
if (print_err) print('M', header[i], refpos[g]);
} else if (gene[g][i][0] == 1) rst[0][i]++;
else if (gene[g][i][0] > 1) {
rst[1][i]++;
if (print_err) print('D', header[i], refpos[g]);
} else if (gene[g][i][1] >= opt.min_cov) {
rst[2][i]++;
if (print_err) print('F', header[i], refpos[g]);
} else if (gene[g][i][1] >= 0.5) {
rst[3][i]++;
if (print_err) print('5', header[i], refpos[g]);
} else if (gene[g][i][1] >= 0.1) {
rst[4][i]++;
if (print_err) print('1', header[i], refpos[g]);
} else {
rst[5][i]++;
if (print_err) print('0', header[i], refpos[g]);
}
}
}
print(header.join("\t"));
print('H', 'Metric', header.join("\t"));
for (var k = 0; k < rst.length; ++k) {
print(col1[k], rst[k].join("\t"));
print('X', col1[k], rst[k].join("\t"));
}
buf.destroy();
}