Make count_tab compatible with umi_tools extract
#654
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…o longer writing out byte-encoded strings Remove count_tab test fixing script
TomSmithCGAT
reviewed
Aug 1, 2024
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This is a direct copy of the previous tests/chr19_gene_assigned_cell.tsv, right? No need to keep a copy from my perspective, so this file can be removed
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Yes, with some manipulations to get the cell barcode and UMI in the correct (new) order.
TomSmithCGAT
requested changes
Aug 1, 2024
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Thank you very much for this @eachanjohnson! Could you please remove the copy of the previous test file and then I'll merge
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OK, previous copy of the file has been removed. |
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Provides a fix for #651.
I've updated the
get_cell_umi_read_string()function in umi_tools/sam_methods.py so that the UMI and cell barcode are extracted in the same order thatumi_tools extractcreates them. I've also updated the docstring of umi_tools/count_tab.py to reflect this.Since I had to update the test input file tests/count_tab_cell.tsv, I thought I would also fix the issue where
count_tabwrites out byte-encoded strings for the cell barcode. It was a small change but makes using downstream bash tools much easier.Let me know what you think!