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output simulated identity with badread

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Heng Li
2026-04-14 12:49:35 -04:00
parent 4ca5a951ca
commit 37a650f58c
1 changed files with 4 additions and 3 deletions
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7
misc/paftools.js
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@@ -2424,8 +2424,8 @@ function paf_badread2fa(args)
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) {
var m, tag = '', a = null, is_fq = line[0] == '@'? true : false;
if (!/\schimera\s/.test(line) && (m = /\s(\S+),([+-])strand,(\d+)-(\d+).*read_identity=([0-9\.]+)%/.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]);
@@ -2433,6 +2433,7 @@ function paf_badread2fa(args)
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] ];
tag = "ri:f:" + m[5];
}
file.readline(buf);
var seq = buf.toString();
@@ -2441,7 +2442,7 @@ function paf_badread2fa(args)
file.readline(buf);
}
if (a != null) {
print(">" + a.join("!"));
print(">" + a.join("!"), tag);
print(seq);
} else ++n_discard;
++id;