Sort linked-read data by barcode

Sometimes you want/need linked-read data to be sorted by barcode. In order to accomplish this with Djinn, the barcode must be in a SAM tag (e.g. BX, BC) FASTQ or SAM/BAM format. If your barcodes aren't in a SAM tag, consider using fastq convert or standardize to convert it into a compliant format.

FASTQ

usage
djinn fastq sort SAMTAG PREFIX INPUT...

example | sort fastq with barcodes in BC tag
djinn fastq sort BC pebbles_sorted data/pebbles.R1.fq.gz data/pebbles.R2.fq.gz

Running Options

argument	description
`SAMTAG`	required 2-letter name of the SAM tag storing the barcode (e.g. `BC` or `BX`)
`PREFIX`	required output filename prefix
`INPUT`	required FASTQ file or file pair
`-t` `--threads`	Number of threads to use (default: 4)

SAM

usage
djinn sam sort SAMTAG INPUT

example | sort fastq with barcodes in BC tag
djinn sam sort BC data/pebbles.bam

Running Options

argument	description
`SAMTAG`	required 2-letter name of the SAM tag storing the barcode (e.g. `BC` or `BX`)
`INPUT`	required SAM/BAM file
`-t` `--threads`	Number of threads to use (default: 4)