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added sim2bed to convert simulated read names to BED

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Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
This commit is contained in:
Heng Li
2026-04-25 00:22:26 -04:00
co-authored by Claude Opus 4.5
parent f8381755f1
commit e5066c7976
1 changed files with 40 additions and 0 deletions
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misc/paftools.js
+40
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@@ -2348,6 +2348,44 @@ function paf_mason2fq(args)
buf2.destroy(); buf2.destroy();
} }
// convert Mason read names to BED
function paf_sim2bed(args)
{
if (args.length == 0) {
print("Usage: paftools.js sim2bed <sim.txt>");
exit(1);
}
var buf = new Bytes();
var file = new File(args[0]);
var seen = {};
while (file.readline(buf) >= 0) {
var line = buf.toString();
var t = line.split("!");
if (t.length < 5) continue;
var chr = t[1], st, en, strand;
if (t[2].indexOf("_") >= 0) { // mason paired-end
var pos = t[2].split("_");
var end = t[3].split("_");
var m = /^(.)(.)\/([12])$/.exec(t[4]);
if (m == null) continue;
strand = m[3] == "1" ? m[1] : m[2];
var read_no = parseInt(m[3]) - 1;
st = parseInt(pos[read_no]);
en = parseInt(end[read_no]);
} else { // badread/pbsim long reads
st = parseInt(t[2]);
en = parseInt(t[3]);
strand = t[4];
}
if (st > en) { var tmp = st; st = en; en = tmp; }
if (seen[line]) continue;
seen[line] = 1;
print([chr, st, en, line, 0, strand].join("\t"));
}
file.close();
buf.destroy();
}
// convert pbsim MAF to FASTQ // convert pbsim MAF to FASTQ
function paf_pbsim2fq(args) function paf_pbsim2fq(args)
{ {
@@ -3750,6 +3788,7 @@ function main(args)
print(" mapeval evaluate mapping accuracy using mason2/PBSIM-simulated FASTQ"); print(" mapeval evaluate mapping accuracy using mason2/PBSIM-simulated FASTQ");
print(" pafcmp compare two PAF files"); print(" pafcmp compare two PAF files");
print(" mason2fq convert mason2-simulated SAM to FASTQ"); print(" mason2fq convert mason2-simulated SAM to FASTQ");
print(" sim2bed convert mason2-simulated read names to BED");
print(" pbsim2fq convert PBSIM-simulated MAF to FASTQ"); print(" pbsim2fq convert PBSIM-simulated MAF to FASTQ");
print(" badread2fa convert Baderead FASTQ to FASTA"); print(" badread2fa convert Baderead FASTQ to FASTA");
print(" junceval evaluate splice junction consistency with known annotations"); print(" junceval evaluate splice junction consistency with known annotations");
@@ -3776,6 +3815,7 @@ function main(args)
else if (cmd == 'pafcmp') paf_pafcmp(args); else if (cmd == 'pafcmp') paf_pafcmp(args);
else if (cmd == 'bedcov') paf_bedcov(args); else if (cmd == 'bedcov') paf_bedcov(args);
else if (cmd == 'mason2fq') paf_mason2fq(args); else if (cmd == 'mason2fq') paf_mason2fq(args);
else if (cmd == 'sim2bed') paf_sim2bed(args);
else if (cmd == 'pbsim2fq') paf_pbsim2fq(args); else if (cmd == 'pbsim2fq') paf_pbsim2fq(args);
else if (cmd == 'badread2fa') paf_badread2fa(args); else if (cmd == 'badread2fa') paf_badread2fa(args);
else if (cmd == 'junceval') paf_junceval(args); else if (cmd == 'junceval') paf_junceval(args);