seqkit amplicon minus strand co-ordinates count from end

[ZacharyArdern]

Describe your issue

when using seqkit amplicon, if the primers extract a negative strand feature, the co-ordinates given (with BED format) are counted from the end of the chromosome/contig. I think this is not the expected/intended behaviour, and is not the behaviour of seqkit locate. e.g.:

seqkit amplicon --bed -t dna -F ATGGAGATGTTGTCTGGAGCCG -R VTAYASRCRYYTAAGYTTCGCW test.txt ;

seqkit locate -d -p ATGGAGATGTTGTCTGGAGCCG test.txt ;

Thank you!

test.txt

[shenwei356]

Yes, you're right. It's a bug, and I've just fixed it, please help to test it. Thanks for reporting.

• seqkit_linux_amd64.tar.gz
• seqkit_darwin_arm64.tar.gz
• seqkit_darwin_amd64.tar.gz

echo -ne ">s\nATGGAGATGTTGTCTGGAGCCG\n"  \
    | seqkit stats 
file  format  type  num_seqs  sum_len  min_len  avg_len  max_len
-     FASTA   DNA          1       22       22       22       22

echo -ne ">s\nATGGAGATGTTGTCTGGAGCCG\n"  \
    | seqkit amplicon -F TGGAG -R GGCTCC -I --bed
s       1       21      .       0       +       TGGAGATGTTGTCTGGAGCC

echo -ne ">s\nATGGAGATGTTGTCTGGAGCCG\n"  \
    | seqkit amplicon -F GGCTCC -R TGGAG -I --bed
s       1       21      .       0       -       GGCTCCAGACAACATCTCCA

[ZacharyArdern]

Thanks for the quick fix! I've tested it and it appears to have the correct behaviour now