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convert badread output to evaluation format

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This commit is contained in:
Heng Li
2026-04-13 23:43:11 -04:00
parent e2542e6425
commit ca6f4dc5e2
1 changed files with 47 additions and 0 deletions
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47
misc/paftools.js
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@@ -2405,6 +2405,52 @@ function paf_pbsim2fq(args)
buf2.destroy();
}
function paf_badread2fa(args)
{
if (args.length < 2) {
print("Usage: paftools.js badread2fa <ref.fa.fai> <badread.fq>");
exit(1);
}
var len = {}, file, buf = new Bytes();
file = new File(args[0]);
while (file.readline(buf) >= 0) {
var t = buf.toString().split("\t");
len[t[0]] = parseInt(t[1]);
}
file.close();
var id = 0, n_discard = 0;
file = new File(args[1]);
while (file.readline(buf) >= 0) {
var line = buf.toString();
var m, a = null, is_fq = line[0] == '@'? true : false;
if (!/\schimera\s/.test(line) && (m = /\s(\S+),([+-])strand,(\d+)-(\d+)/.exec(line)) != null) {
if (len[m[1]] == null) throw Error("failed to find the contig length of " + m[1]);
m[3] = parseInt(m[3]);
m[4] = parseInt(m[4]);
if (m[2] == '+')
a = [ "S" + (id+1), m[1], m[3], m[4], m[2] ];
else
a = [ "S" + (id+1), m[1], len[m[1]] - m[4], len[m[1]] - m[3], m[2] ];
}
file.readline(buf);
var seq = buf.toString();
if (is_fq) {
file.readline(buf);
file.readline(buf);
}
if (a != null) {
print(">" + a.join("!"));
print(seq);
} else ++n_discard;
++id;
}
file.close();
buf.destroy();
warn("WARNING: discarded " + n_discard + " reads");
}
function paf_junceval(args)
{
var c, l_fuzzy = 0, print_ovlp = false, print_err_only = false, first_only = false, chr_only = false, aa = false, is_bed = false;
@@ -3729,6 +3775,7 @@ function main(args)
else if (cmd == 'bedcov') paf_bedcov(args);
else if (cmd == 'mason2fq') paf_mason2fq(args);
else if (cmd == 'pbsim2fq') paf_pbsim2fq(args);
else if (cmd == 'badread2fa') paf_badread2fa(args);
else if (cmd == 'junceval') paf_junceval(args);
else if (cmd == 'exoneval') paf_exoneval(args);
else if (cmd == 'ov-eval') paf_ov_eval(args);