Generating an onlist by read_id or by region-type generate different product files.

[detrout]

Depending on how you call onlist you can get different multi-round barcode files.

onlist_joined.good.txt contains a version of the product generated barcode list in the right oder.

seqspec onlist -f product -i IGVFFI0790CJXN.fastq.gz -m rna IGVFFI6760GSUG.yaml 
md5sum onlist_joined*.txt 
7f1e51743561883977e5a905bb345ac8  onlist_joined.good.txt
7f1e51743561883977e5a905bb345ac8  onlist_joined.txt

seqspec onlist -f product -s region-type -i barcode -m rna IGVFFI6760GSUG.yaml 
md5sum onlist_joined*.txt 
7f1e51743561883977e5a905bb345ac8  onlist_joined.good.txt
60601ecabfaf49a6b149b3b9c2dc7e9d  onlist_joined.txt

It'd be really nice if the different paths for generating the onlist_joined.txt file made the same output file.

[sbooeshaghi]

Hi @detrout can you confirm this issue persists in the latest commit to devel? If so can you please paste the seqspec file here so that I can diagnose and fix the issue?

[detrout]

Using commit 95d2236 and
python -m seqspec.main onlist -f product -s region-type -i barcode -m rna IGVFFI6760GSUG.yaml -o test-ibarcode.txt
or
python -m seqspec.main onlist -f product -i IGVFFI0790CJXN.fastq.gz -m rna IGVFFI6760GSUG.yaml -o test-iIGVFFI0790CJXN.txt

The output barcodes are still in different orientations

==> test-ibarcode.txt <==
CATTCCTAAACGTGATAACGTGAT
CATTCCTAAACGTGATAAACATCG
CATTCCTAAACGTGATATGCCTAA
CATTCCTAAACGTGATAGTGGTCA
CATTCCTAAACGTGATACCACTGT
CATTCCTAAACGTGATACATTGGC
CATTCCTAAACGTGATCAGATCTG
CATTCCTAAACGTGATCATCAAGT
CATTCCTAAACGTGATCGCTGATC
CATTCCTAAACGTGATACAAGCTA

==> test-iIGVFFI0790CJXN.txt <==
AACGTGATAACGTGATCATTCCTA
AACGTGATAACGTGATCTTCATCA
AACGTGATAACGTGATCCTATATC
AACGTGATAACGTGATACATTTAC
AACGTGATAACGTGATACTTAGCT
AACGTGATAACGTGATCCAATTCT
AACGTGATAACGTGATGCCTATCT
AACGTGATAACGTGATATGCTGCT
AACGTGATAACGTGATCATTTACA
AACGTGATAACGTGATACTCGTAA

[sbooeshaghi]

Ok. Can you try with the most recent commit? Or upload the spec here and I can try.