SHM Output Issue

[immuno-git]

Hello, I have been trying to use the Immune_repertoire portion of the RIMA pipeline to calculate SHM statistics for TRUST4 output mouse data (that has not otherwise been processed through the RIMA pipeline).

Rscript src/immune_repertoire/trust4_bcr_process.R --cdr3 C1.processed.txt -s test -o out

However, when I run trust4_bcr_process.R, the program fails with

[1] "Saving SHM results ..."
Error in if (is.na(sample_bcr_cluster)) { : the condition has length > 1
Execution halted

Commenting out that section of the code shown below allows it to run to completion, but I am worried about the effect on the validity of the data analysis.

} else if (is.na(sample_bcr_cluster)) {
ss.ratio <- NULL

Do you have any suggestions for fixing this?

Also, what is the actual statistic being calculated for the SHMRatio output? I am trying to make sure I understand what the values being outputted mean.

Thank you for your time and help, and happy holidays.