From 4ca5a951caf7255fc0e9abffdad649d809d86ec6 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Mon, 13 Apr 2026 23:52:07 -0400
Subject: [PATCH] command line help

---
 misc/paftools.js | 1 +
 1 file changed, 1 insertion(+)

diff --git a/misc/paftools.js b/misc/paftools.js
index 578ddea..d148849 100755
--- a/misc/paftools.js
+++ b/misc/paftools.js
@@ -3750,6 +3750,7 @@ function main(args)
 		print("  pafcmp     compare two PAF files");
 		print("  mason2fq   convert mason2-simulated SAM to FASTQ");
 		print("  pbsim2fq   convert PBSIM-simulated MAF to FASTQ");
+		print("  badread2fa convert Baderead FASTQ to FASTA");
 		print("  junceval   evaluate splice junction consistency with known annotations");
 		print("  exoneval   evaluate exon-level consistency with known annotations");
 		print("  ov-eval    evaluate read overlap sensitivity using read-to-ref mapping");