bustools linker produces wrong output

[mkabza]

Hi,

I tried to use bustools linker today to analyze combinatorial barcoding data and I encountered some really weird behavior. It can be demonstrated using the following code (current binary release, output.bus file from test/ directory, tested on Ubuntu 18.04):

./bustools text -p output.bus | head

TTCCCAGGTGTGAAAT CCTCTTATAG 14 1
TTCCCAGGTGTGAAAT CCTCTTATAG 17 1
TTCCCAGGTGTGAAAT CCTCTTATAG 10 1
ATCTGCCAGCTCAACT CACAGGTAAG 10 1
AGCTTGACAGAGTGTG TTAATAGCCA 13 1
AATCCAGGTCACTGGC GCTTTTGTCA 10 1
AATCCAGGTCACTGGC GCTTTTGTCA 10 1
AATCCAGGTCACTGGC GCTTTTGTCA 1 1
AGCTTGACAGAGTGTG TTAATAGCCA 10 1
AATCCAGGTCACTGGC GCTTTTGTCA 10 1

./bustools linker -p -s 0 -e 1 output.bus | ./bustools text -p - | head

TAGGCTCGGGCGAAT CCTCTTATAG 14 1
TAGGCTCGGGCGAAT CCTCTTATAG 17 1
TAGGCTCGGGCGAAT CCTCTTATAG 10 1
ACCCTGCTACACAGA CACAGGTAAG 10 1
TACTCGCCGGTGGGC TTAATAGCCA 13 1
CAAGCTCGACGCGAT GCTTTTGTCA 10 1
CAAGCTCGACGCGAT GCTTTTGTCA 10 1
CAAGCTCGACGCGAT GCTTTTGTCA 1 1
TACTCGCCGGTGGGC TTAATAGCCA 10 1
CAAGCTCGACGCGAT GCTTTTGTCA 10 1

The command is supposed to remove the first base of the barcode; instead it introduces multiple changes to the barcode sequence