+
Skip to content

Conversation

nh13
Copy link
Contributor

@nh13 nh13 commented Dec 14, 2021

In particular, this defines the output SAM to be unsorted BUT also query grouped. The latter is very important to explicitly define so downstream tools that don't make assumptions know that reads from the same template are grouped.

In particular, this defines the output SAM to be unsorted BUT also query grouped.  The latter is very important to explicitly define so downstream tools that don't make assumptions know that reads from the same template are grouped.
@lh3 lh3 merged commit ef52b4a into lh3:master Mar 6, 2022
@jmarshall
Copy link
Contributor

jmarshall commented Mar 7, 2022

If n_SQ is 0, this will print @SQ header lines before the @HD line.

(In fact this is really a pre-existing bug, as bwa mem -H '@HD\tVN:1.6' … would previously also have had the synthesised @SQ lines before the -H-supplied @HD header line.)

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

3 participants

点击 这是indexloc提供的php浏览器服务,不要输入任何密码和下载