segfault with CB_samTagOut w/o whitelist

[cnk113]

Hey Alex,

When I run any of my datasets with CB_samTagOut without a whitelist specified I run into a segfault when mapping starts.
When I specify a whitelist it works perfectly fine. I tried to track down the error but I couldn't pinpoint where it is.
I'm using the latest commit of STAR.

Best,
Chang

[alexdobin]

Hi Chang,

this looks like a bug. What was the command you were using?

Thanks!
Alex

[cnk113]

STAR --genomeDir $REFERENCE  --runThreadN 32 --soloType CB_samTagOut \
--readFilesIn $R1 $R3 $R2 --soloCBwhitelist $WL --soloCBmatchWLtype Exact \
--soloCBlen 18 --readFilesCommand zcat --outSAMattributes CR CY GX GN --peOverlapNbasesMin 10 \
--outSAMtype BAM SortedByCoordinate --soloFeatures Gene --soloStrand Unstranded \
--twopassMode Basic --outFilterMismatchNmax 20 --outFilterMismatchNoverLmax 0.1 --soloBarcodeReadLength 0

The only difference is setting --soloCBwhitelist None.
Always happens right when it prints starting mapping...
I have an external script to generate the WL since my barcodes are semi-random with degenerate bases, but this may be an issue for other users in the future.