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Hi, I was wondering what is the format of barcode file and the supposed parameter of "--barcode_place" for illumina PE reads. Thank you!

Hi developers!

Thanks for making defastq, it's super fast and easy to use. However, as I was comparing to a previous result with a different tool, I realised there is a bug when the option --allowed-mismatches set to 2.

I'm adding a minimal working example here of a set of fastq files that have 1 read in them and an index file with just one barcode in it. The reads contains the barcode with 1 mismatch. When I run defastq with --allowed-mismatches 1, it works as expected and the read is demultiplexed. However, when I run with --allowed-mismatches 2, the read ens up in undecoded.R2.fastq.gz.

Code:

/g/scb/zaugg/claringb/scz_CRISPR_screen/tools/defastq \
 -1 test_reads.R1.fastq.gz \
 -2 test_reads.R2.fastq.gz \
 -b read2 \
 -s 27 \
 -l 11 \
 -i test_barcodes.csv \
 -o mismatch2 \
 -a 2 \
 -n 8

/g/scb/zaugg/claringb/scz_CRISPR_screen/tools/defastq \
 -1 test_reads.R1.fastq.gz \
 -2 test_reads.R2.fastq.gz \
 -b read2 \
 -s 27 \
 -l 11 \
 -i test_barcodes.csv \
 -o mismatch1 \
 -a 1 \
 -n 8

Could you look into what's going on here?
Thanks, Annique

test_barcodes.csv
test_reads.R1.fastq.gz
test_reads.R2.fastq.gz