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Make sequence field optional in odgi bin when output via --json #86

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subwaystation opened this issue Mar 9, 2020 · 1 comment · Fixed by #87
Closed

Make sequence field optional in odgi bin when output via --json #86

subwaystation opened this issue Mar 9, 2020 · 1 comment · Fixed by #87
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@subwaystation
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@josiahseaman
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josiahseaman commented Mar 13, 2020

Code added on component_segmentation should match header variable names:

            if "odgi_version" in path:
                # this is the header
                assert path["odgi_version"] == ODGI_VERSION, f"Expecting version {ODGI_VERSION}." \
                    f"This version added the header with pangenome nucleotide count."
                print(f"Found file with {path['pangenome_length']} nucleotides in the pangenome and"
                      f" a bin size of {path['bin_width']}bp Bin width.")

I'm starting with ODGI_VERSION 10. But these numbers will likely diverge since not every update in one requires and update in the other.

josiahseaman added a commit to graph-genome/component_segmentation that referenced this issue Mar 13, 2020
subwaystation added a commit that referenced this issue Mar 16, 2020
added parameter --no-seqs to bin and header for JSON output
fixes #86
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