How to keep pairing status in BAM output when also providing index FASTQs

[clintval]

When I run splitcode on a pair of FASTQs I correctly get pairing status in the BAM output:

$ splitcode \
    --nFastqs 2 \
    --out-bam \
    --pipe \
    r1.fastq.gz \
    r2.fastq.gz \
    | samtools view | head -n2
A01000:460:XXXXXX:1:2101:10004:10081	77	*	0	0	*	*     	0	0	ACGT	,:FF
A01000:460:XXXXXX:1:2101:10004:10081	141	*	0	0	*	*     	0	0	GGTC	,:ff

Notice 77 and 141 SAM flags which indicate first and second of pair.

But when I want to use information stored in one of the index FASTQs, I cannot keep the first two paired:

$ splitcode \
    --nFastqs 3 \
    --select '0,1' \
    --out-bam \
    --pipe \
    r1.fastq.gz \
    r2.fastq.gz \
    index_1.fastq.gz \
    | samtools view | head -n2
A01000:460:XXXXXX:1:2101:10004:10081	12	*	0	0	*	*     	0	0	ACGT	,:FF
A01000:460:XXXXXX:1:2101:10004:10081	12	*	0	0	*	*     	0	0	GGTC	,:ff

Notice 12 and 12 SAM flags which are not first or second of pair.

What I'm trying to do is find and extract a variety of cell barcodes, UMIs, linkers, and other complex information from R1, R2, and a single index file while writing the R1 and R2 template sequences to a correctly formatted unmapped SAM/BAM file. I was hoping --select 0,1 might indicate to splitcode I want to retain a pair of reads from only those FASTQ files.

[Yenaled]

Thanks, it doesn’t keep that information but you’re right that it should. I’ll tag this as a “bug” and will try to fix this for the next release.

[Yenaled]

New release should cover this