Add UMI support to FASTQ input/output.#1960
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vasudeva8 merged 1 commit intosamtools:developfrom Oct 21, 2025
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The fastq_umi option (FASTQ_OPT_UMI enum) is used to enable UMI parsing in read names. When reading FASTQ it converts the 8th Illumina field to an aux tag (default to RX). We may need to amend this if people require it to work on earlier Illumina naming systems, but for now we target the current software. When writing FASTQ we hunt for a series of tags and choose the first one found. RX is the usual one, but users may wish to also use OX if they potentially have error corrected data in RX and want to regenerate fastq from the original uncorrect tag. Complexities arrive when dealing with /1 or /2 and #num multi-plexing strings, meaning we have to use temporary buffers rather than simply truncating the read names. Note we convert dual-index UMIs of SEQ+SEQ to RX:Z:SEQ-SEQ as per the SAMtags recommendation. However it's a bit wild west out there and not everyone does this. (I've seen 10X outputs with CR using underscores for example.) This is a best efforts approach to reduce the likelihood of incompatibility with downstream pipelines.
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The fastq_umi option (FASTQ_OPT_UMI enum) is used to enable UMI parsing in read names.
When reading FASTQ it converts the 8th Illumina field to an aux tag (default to RX). We may need to amend this if people require it to work on earlier Illumina naming systems, but for now we target the current software.
When writing FASTQ we hunt for a series of tags and choose the first one found. RX is the usual one, but users may wish to also use OX if they potentially have error corrected data in RX and want to regenerate fastq from the original uncorrect tag.
Complexities arrive when dealing with /1 or /2 and #num multi-plexing strings, meaning we have to use temporary buffers rather than simply truncating the read names.