Annotates existing BAM files with UMIs (Unique Molecular Indices, aka Molecular IDs, Molecular barcodes) from a separate FASTQ file. Takes an existing BAM file and a FASTQ file consisting of UMI reads, matches the reads between the files based on read names, and produces an output BAM file where each record is annotated with an optional tag (specified by attribute) that contains the read sequence of the UMI. Trailing read numbers (/1 or /2) are removed from FASTQ read names, as is any text after whitespace, before matching.
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