Pick up chromium barcode from BX tag about arcs HOT 7 CLOSED

This would be a big improvement for me too. It's also compatible with using bwa mem -pC to copy the BX:Z tag from the FASTQ header to the SAM tags. I'll make it happen later this week. Bump this issue if you don't hear from me.

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Hi guys, there is a new --bx option in ARCS v1.0.2 (just released), or you can also pull it from master. Hope you like it!

from arcs.

Not sure if this was discussed more, but I think this would be a great quality of life improvement. Then you could use the "longranger align" function directly into ARCS from my understanding.

from arcs.

Wonderful! Thanks, Ben! Could that option --bx be the default or auto-detected? If the BX:Z tag is present, use it by default, otherwise resort to the previous behaviour.

from arcs.

@sjackman Yep, you are right, that would be better default behaviour. I will postpone any further fiddling with it until later, though. (Feel free to fix it in the meantime, if you are so inclined.)

from arcs.

I may just. Thanks for the work, Ben!

from arcs.

I've submitted PR #30 which uses the BX:Z tag if present, and otherwise parses the barcode from the read name.

It also makes the -f FASTA file optional. It'll parse the scaffold sizes from the SAM header. If the -f option is specified, it checks that the FASTA sequence lengths and SAM header agree. This makes it really easy to pipe the output of the aligner into ARCS (by setting the SAM file argument to /dev/stdin) without needing to also specify a FASTA file.

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