single strand mapping --for-only option

[DepledgeLab]

The MiniMap 2.1 documentation makes mention of a --for-only option which is super helpful in mapping to transcriptomes. However, this option does not appear to be recognised by any recent versions of minimap2.

Can you reinstate it?

[yupenghe]

I also have an issue with the "--for-only" and "--rev-only" options. When I add either "--for-only" or "--rev-only" option, minimap2 just freezes in some cases even if it only involves 25 reads and a tiny genome reference. I attached the data and command to reproduce the error.

Commands are in the run.sh file. To run this test example, simply do sh run.sh.

minimap2.tar.gz

[lh3]

Thanks a lot for the example. I believe the bug has been fixed. It was introduced by a faster merging algorithm specific to short reads. For v2.10, you can add option --heap-sort=no to use the default merging algorithm. It is not affected by this bug.

[yupenghe]

Thanks! It is solved.