Soft clip disappeared after CallMolecularConsensusReads

[jonghwanyoon]

hello

When calling Molecular consensus reads using fgbio's CallMolecularConsensusReads, the soft clip disappears.
I went through CorrectUmis, GroupReadsByUmi, CallMolecularConsensusReads, alignment on a bam file mapped with raw fastq, and noticed that the soft clips disappeared on important singleton reads.

Given the presence of soft clips in the bam file resulting from GroupReadsByUmi, it seems that the issue is in CallMolecularConsensusReads.

I only gave CallMolecularConsensusReads the java option and the --min-reads=1 parameter.
There doesn't seem to be any parameter associated with CallMolecularConsensusReads (I could be wrong)
This is the same in 2.1.1, when collapsing between chromosomes became possible, and in 2.4.0, the current latest version.

Although it is a singleton read, it is an important read that represents a clinically meaningful fusion, so I don't want the soft clips to disappear.
May I request your opinion on this issue?

Thank you!