Add missing SQ tags as per the spec #1238
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nh13
commented
Oct 18, 2023
pysam/libcalignmentfile.pyx
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| @@ -127,7 +128,8 @@ KNOWN_HEADER_FIELDS = {"HD" : {"VN" : str, "SO" : str, "GO" : str}, | |||
| # the end as parsing a CL will ignore any subsequent records. | |||
| VALID_HEADER_ORDER = {"HD" : ("VN", "SO", "GO"), | |||
| "SQ" : ("SN", "LN", "AS", "M5", | |||
| "UR", "SP", "AH"), | |||
| "UR", "SP", "AH", "TP", | |||
| "DS", "AN"), | |||
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These are not in the same order as the spec, so we could take the time to update them?
jmarshall
approved these changes
Oct 20, 2023
|
Thanks. I've added a couple missing from other headers too. No need to reorder them just now, as I think the way forward for this functionality is for these two tables to largely go away — see further comments on #1237. |
|
Thanks @jmarshall ! |
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See #1237