Read names & tags are lost when vg surject is run with the -S parameter

[minkinaa]

1. What were you trying to do?

I am trying to run vg surject with the -S parameter (issue also occurs with -P, I believe). These are transcript reads which have been injected into the graph via vg inject to generate a gam.

2. What did you want to happen?

Output a surjected file on a given assembly with deletions interpreted as splicing events.

3. What actually happened?

vg surject finished without error, but read names are lost in the output. The first column of the bam is empty, followed by a tab, followed by the flag column. Tags are not being transferred over from the injected bam either (as they do when vg surject is run without -S). The command works as expected all around when run without any additional parameters.

4. If you got a line like Stack trace path: /somewhere/on/your/computer/stacktrace.txt, please copy-paste the contents of that file here:

No errors indicated during the run.

5. What data and command can the vg dev team use to make the problem happen?

vg surject -S -x HG02074_PS00977_PacBio.full_all_chrs.gbz -b HG02074_shared.gam -n GRCh38 > output.bam

I will email a link to a public s3 bucket that holds these input files to Adam.

6. What does running vg version say?

vg version v1.70.0 "Zebedassi"
Compiled with g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 on Linux
Linked against libstd++ 20230528
Using HTSlib headers 101990, library 1.19.1-29-g3cfe8769
Built by anovak@courtyard.gi.ucsc.edu

[minkinaa]

Small update as I work with these outputs further -- curiously, this isn't totally consistent behavior. The occasional read will retain its read name and the associated tags in a file where most reads don't.

EDIT: Aah, looks like it's just the unmapped reads that do retain read names + tags.