From 29ebf1ddb0dadc47b0ffff3df977d854625513fb Mon Sep 17 00:00:00 2001 From: Hasindu Gamaarachchi Date: Mon, 9 Sep 2024 23:25:42 +1000 Subject: [PATCH] Update commands.md --- _docs/commands.md | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/_docs/commands.md b/_docs/commands.md index 4e9c9c3e..939095dd 100644 --- a/_docs/commands.md +++ b/_docs/commands.md @@ -242,8 +242,10 @@ Align nanopore events to reference k-mers (optimised nanopolish eventalign). Not Write output in PAF format. Introduced in f5c v1.3. Output explained in https://hasindu2008.github.io/f5c/docs/output. * `--sam`: Write the alignment output in SAM format instead of tsv. -* `--sam-out-version INT` - Sam output version (set 1 to revert to old nanopolish style format) [default: 2]. Introduced in f5c v1.3. New SAM output is explained in https://hasindu2008.github.io/f5c/docs/output. +* `--sam-out-version INT`: + Sam output version (set 1 to revert to old nanopolish style format) [default: 2]. Introduced in f5c v1.3. New SAM output is explained in https://hasindu2008.github.io/f5c/docs/output. +* ` --m6anet`: + Write output in m6anet format. Introduced in f5c v1.5. * `--print-read-names`: Print read IDs instead of indexes. * `--scale-events`: