The -b option of "junctions extract" doesn't work

[NaotoKubota]

Hi, thank you for the development of such a great tool!

I executed junctions extract with the option -b to get junction read counts for each cell from a standard 10x scRNA-seq bam file:

regtools junctions extract \
-s XS \
-b ./filtered_feature_bc_matrix/barcodes.tsv.gz \
-o ./test.junc \
./possorted_genome_bam.bam

barcode.tsv.gz is a file generated by cellranger mapping:

$ zcat ./filtered_feature_bc_matrix/barcodes.tsv.gz | head
TACCCACCAGCTGTTA-1
GAATCACAGTATAACG-1
AGAACCTTCATGACAC-1
TTTGGTTGTCGTCGGT-1
TCGCAGGAGGTTATAG-1
GGGCTCAGTCGACTGC-1
TCACAAGTCTACGCAA-1
TCTCACGTCTTCCACG-1
ATTTCTGGTTGACGGA-1
ACGTTCCTCGAAGCAG-1

But I found the output file (test.junc) was the same as the file generated without the -b option.
Besides the barcode file was overwritten like below:

$ head ./filtered_feature_bc_matrix/barcodes.tsv.gz
1	CTCTGGTAGGTGCCAA-1:1
1	CTCCAACAGGATACCG-1:1
1	AGCTTCCTCCCTCTAG-1:1
2	CCCATTGCATCACCAA-1:1,AGCTTCCTCCCTCTAG-1:2
4	AGCTTCCTCCCTCTAG-1:3,TAAGCGTAGCATGCAG-1:1,GCCAGGTTCGACGAGA-1:1,GTCATTTTCCGCAGTG-1:1
1	ACTGTCCTCTGATGGT-1:1
6	ACTGTCCTCTGATGGT-1:1,GCTTCACGTTCTAAGC-1:1,AAAGAACGTACTAAGA-1:1,AGTGACTTCTTACGGA-1:1,TCTTCCTGTGCTATTG-1:1,ATCTCTATCGGCACTG-1:1
1	GTCACGGAGCAAGCCA-1:1
1	ATGACCAAGTAAATGC-1:1
1	ATTCATCCAACGACTT-1:1

The log says the barcode file was correctly taken as an argument:

Program:        regtools
Version:        1.0.0
Minimum junction anchor length: 8
Minimum intron length: 70
Maximum intron length: 500000
Alignment: ./possorted_genome_bam.bam
Output file: ./test.junc
Barcode file: ./filtered_feature_bc_matrix/barcodes.tsv.gz

I am not sure my script is totally correct but I would appreciate if you could fix the bug and also provide an example of output files when executing with the -b option.

Thank you,

[NaotoKubota]

I just noticed that -b option specifies an output file of junction read counts for each barcode! Sorry for confusing you guys.