Remove inconsistant mutation error #1233
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Codecov Report
@@ Coverage Diff @@
## main #1233 +/- ##
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- Coverage 93.71% 93.70% -0.02%
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Files 26 26
Lines 21618 21599 -19
Branches 909 909
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- Hits 20260 20239 -21
- Misses 1319 1321 +2
Partials 39 39
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Adding silent mutations has made some tests error, looking into it |
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Good, that's a sign it's working! Let me know if you have any questions/would like me to take a look at anything. |
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Ah, the issue is that a site with only silent mutations has a blank vcf |
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Last failure is due to this change exposing #1225 to the test suite. Will fix that in seperate PR and merge before this one. |
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Oh dear, this means I should finish up #1226 |
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What's the status here @benjeffery? Should we skip some tests here in this PR so we can merge it, then rebase #1226 and fix there? |
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This only needs #1225, which I'm working on. Should be done in soon, so will just wait and rebase. |
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#1225 is getting more complicated than I realised so have added a skip here. |
| pos = self.transformed_positions[variant.index] | ||
| ref = variant.alleles[0] | ||
| alt = ",".join(variant.alleles[1:]) | ||
| alt = ",".join(variant.alleles[1:]) if len(variant.alleles) > 1 else "." |
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Can confirm this is the correct behaviour.
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Fixes #1180
WIP, needs stats tests