repcred failure with empty sequence_alignment

[bcorrie]

When running on repertoire_id=5f21e817e1adeb2edc126144 on covid19-1.ireceptor.org, I get:

Rendering book in directory '.'

processing file: _main.Rmd
Quitting from lines 389-444 (_main.Rmd) 
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'XStringSet': The column sequence_alignment contains no data
Calls: tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted

Sure enough, this repertoire has this field empty, but it is a nullable field in the standard, so repcred should probably be more robust if this is not available. Not sure which reports this would effect...

[bcorrie]

Also occurs on study_id = IR-Binder-000001, repertoire_id = 5efbc7325f94cb6215deecfc

[bcorrie]

PRJNA381394, subject B00_CLL_05_10x failed with this error as well... repertoire_id = 12, ipa5.ireceptor.org

[ssnn-airr]

I updated the code to skip the part of the code that needs sequence_alignment if there is no sequence_alignment data. I added 5000 sequences of PRJNA381394, subject B00_CLL_05_10x to the tests and seems to work. Can you please update your container and try again?

[bcorrie]

Repcred ran fine on the previous problem data sets:

subject_id=B00_CLL_05_10x repertoire_id=5efbc7325f94cb6215deecfc repertoire_id=5f21e817e1adeb2edc126144

So it looks like this problem is fixed...