You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Added merging of headers when using the sfm command with a directory
containing multiple files as input.
The merging respects the requirements outlined in the SAM spec:
- order of sequence dictionaries is kept
- read group identifiers are made unique if needed + optional rg tags of
reads are updated accordingly
- program line identifiers are made unique if needed + optional pg tags
of reads are updated accordingly
- comment lines are merged
- the sorting order is set to Unknown
If elprep cannot merge while guaranteeing the above constraints, an
error is produced.
Various bug fixes and extensions:
* Added --tmp-path option for sfm.
* Fixed /dev/stdin and /dev/stdout for sfm.
* Added a command for merging intermediate metrics files.
* Fixed detection of directory path names in sfm.