Handle TIDDIT style SV type names #128
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henrikstranneheim
approved these changes
Dec 22, 2023
| @@ -97,7 +97,9 @@ def get_coords(variant): | |||
| end = int(end_pos) if end_pos else int(variant.end) | |||
| coordinates["end"] = end | |||
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| sv_type = variant.INFO.get("SVTYPE").split(":")[0] | |||
| sv_type = variant.INFO.get("SVTYPE") | |||
| @@ -103,7 +103,7 @@ def test_format_tiddit_dup_tandem(duptandem_tiddit_variant, case_obj): | |||
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| def test_format_old_tiddit_dup_tandem(duptandem_old_tiddit_variant, case_obj): | |||
| ## GIVEN a dup with older TIDDIT notation (TDUP, IDUP, ...) | |||
| variant = duptandem_variant | |||
| variant = duptandem_old_tiddit_variant | |||
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Suggested change
| variant = duptandem_old_tiddit_variant | |
| variant: str = duptandem_tiddit_variant_legacy_format |
| @@ -84,7 +84,7 @@ def test_format_dup_tandem(duptandem_variant, case_obj): | |||
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| def test_format_tiddit_dup_tandem(duptandem_tiddit_variant, case_obj): | |||
| ## GIVEN a TIDDIT style notation, ie both SVTYPE info and alt field tag has subtype, eg DUP:TANDEM | |||
| variant = duptandem_variant | |||
| variant = duptandem_tiddit_variant | |||
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Suggested change
| variant = duptandem_tiddit_variant | |
| variant: str = duptandem_tiddit_variant |
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This PR adds | fixes:
How to prepare for test:
sshto ...bash servers/resources/SERVER.scilifelab.se/update-[THIS_TOOL]-stage.sh [THIS-BRANCH-NAME]How to test:
Expected outcome:
Review:
This version is a: