bartender_extractor: src/bartender_extractor.cpp:126: int main(int, char**): Assertion `dir == 0 || dir == -1 || dir == 1' failed.

[mt...@sanger.ac.uk]

Hi,

First of all, thanks for developing the tool and the test datasets and scripts.

I am exploring the feasibility of using it in a MultiParalell Report Assay (MPRA) where our reads are a composition of three barcodes separated by constant sequences. I have created a toy example but it fails running through the bartender_extractor step. I have tried different direction options but the result is the same in all of them:

$ bartender_extractor_com -f Patterns.fq -o Patterns_extracted -q ? -p GTGAT[11]TTGGG[10]GTGAT[10] -m 2 --direction=forward -u 36,46

Running bartender extractor

forward

bartender_extractor Patterns.fq Patterns_extracted 63 "(GTGA.|GTG.T|GT.AT|G.GAT|.TGAT)([ATCGN]{11})(TTGGG)([ATCGN]{10})(GTGAT)([ATCGN]{10})" GTGAT  6 1 36 46

bartender_extractor: src/bartender_extractor.cpp:126: int main(int, char**): Assertion `dir == 0 || dir == -1 || dir == 1' failed.

$ bartender_extractor_com -f Patterns.fq -o Patterns_extracted -q ? -p GTGAT[11]TTGGG[10]GTGAT[10] -m 2 --direction=both -u 36,46

Running bartender extractor

both

bartender_extractor Patterns.fq Patterns_extracted 63 "(GTGA.|GTG.T|GT.AT|G.GAT|.TGAT)([ATCGN]{11})(TTGGG)([ATCGN]{10})(GTGAT)([ATCGN]{10})" GTGAT  6 0 36 46

bartender_extractor: src/bartender_extractor.cpp:126: int main(int, char**): Assertion `dir == 0 || dir == -1 || dir == 1' failed.

$ bartender_extractor_com -f Patterns.fq -o Patterns_extracted -q ? -p GTGAT[11]TTGGG[10]GTGAT[10] -m 2 --direction=rc -u 36,46

Running bartender extractor

rc

bartender_extractor Patterns.fq Patterns_extracted 63 "(GTGA.|GTG.T|GT.AT|G.GAT|.TGAT)([ATCGN]{11})(TTGGG)([ATCGN]{10})(GTGAT)([ATCGN]{10})" GTGAT  6 -1 36 46

bartender_extractor: src/bartender_extractor.cpp:126: int main(int, char**): Assertion `dir == 0 || dir == -1 || dir == 1' failed.

Can you please help me? I am happy to provide the toy file. Best regards,

gcc version: 8.1.0

bartender version: bartender-1.1