Crash when generating a genomebam (Could I have a better error instead)

[detrout]

Hi I was getting a segmentation fault when trying to generate a genomebam,

the command was roughly:

kallisto quant -t 6 \
  -i mm10-M21_minimal-male/mm10-M21_minimal-male-kallisto-0.46.2.idx \
  -o 19906_A5 \
  --single \
  --fragment-length=1759.25 \
  --sd=1103.91175 \
  --genomebam \
  --gtf mm10-M21_minimal-male/mm10-M21_minimal-male.gtf  \
  19906_A5_GGACTCCT-CTCTCTAT_L001_R1_001.fastq.gz \
  19906_A5_GGACTCCT-CTCTCTAT_L002_R1_001.fastq.gz

I ran it in a debugger and found that I was triggering this assert in GeneModel.cpp:407

    assert(s +1 < line.size());
    assert(line[s+1] == ';');

I think the problem was I'd built my own gtf file and was treating the ; as a separator character and not a terminator, so I hadn't added the final ; and I think that violates the asserts.

Any chance you could add an error message about there being a malformed gtf file or missing ; to make life easier for other people with malformed files?

Thanks,

[detrout]

Making sure my gtf file had trailing ;s got past that crash, though now I have a crash in a different location.

[detrout]

Oh forgot to say I'm using kallisto 0.46.2 compiled from source.