How to trim after, instead of before, extraction

[clintval]

I am trying to extract UMIs from the beginning of paired reads and put those UMI sequences into the RX SAM tag as is convention.

This works, but the UMI sequence remains in the reads afterwards:

$ splitcode \
    --nFastqs 2 \
    --select '0,1' \
    --extract '0:0<umi1[2]>,1:0<umi2[2]>' \
    --x-names \
    --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	ACGTAA	,:FF	RX:Z:AC-GG
A01000:460:XXXXXX:1:2101:10004:10081	141	*	0	0	*	*     	0	0	GGTCAA	,:ff	RX:Z:AC-GG

If I try to trim the UMI sequence away, trimming occurs before extraction.

$ splitcode \
    --nFastqs 2 \
    --select '0,1' \
    --extract '0:0<umi1[2]>,1:0<umi2[2]>' \
    --trim-5 '2,2' \
    --x-names \
    --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	GTAA	,:FF	RX:Z:GT-TC
A01000:460:XXXXXX:1:2101:10004:10081	141	*	0	0	*	*     	0	0	TCAA	,:ff	RX:Z:GT-TC

Could there be a way to trim after extraction?

I notice that the quality trimming operations can be optionally triggered after extraction.

Or am I thinking about how to use splitcode incorrectly?