Concatenate reads with linked-read barcodes

If you want to combine linked-read data, you run into an immediate issue: barcode clashing. Different samples will likely share barcodes by chance. A single sample that was made into multiple linked-read libraries will have barcode clashing across libraries for the same reason. Therefore, concatenating needs to happen with barcode recoding to make sure barcodes are completely unique between all things being merged.

SAM

djinn sam concat INPUT...

Concatenate records from linked-read SAM/BAM files while making sure molecule identification tags (MI or BX) remain unique for every sample. This is a means of accomplishing the same as 'samtools cat', except all MI/BX tags are updated so individuals don't have overlapping tags (which would mess up all the linked-read info). The default ignores existing MI tags and writes new ones that correspond to unique BX tags. Using --mi is the opposite, where it ignores existing BX tags and writes new ones that correspond with the MI tags in the barcode style of your choice.

djinn sam concat sample1.bam sample1.lib2.bam sample1.lib3.bam > sample1.bam

djinn sam concat sample*.bam > pop_A.bam