tree: Handle compressed alignment when excluding sites #786
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Use `read_sequences` to read compressed or uncompressed alignments during tree building when excluded sites are provided. Fixes #782
Codecov Report
@@ Coverage Diff @@
## master #786 +/- ##
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+ Coverage 33.76% 33.77% +0.01%
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Files 41 41
Lines 5896 5897 +1
Branches 1426 1426
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+ Hits 1991 1992 +1
Misses 3819 3819
Partials 86 86
Continue to review full report at Codecov.
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Note for posterity that I worked on this PR as part of a co-coding session with @joverlee521, @victorlin, and @j23414 who acted as reviewers-at-the-time-of-coding. :) |
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Description of proposed changes
Use
read_sequencesto read compressed or uncompressed alignments during tree building when excluded sites are provided.Related issue(s)
Fixes #782
Testing
Adds a functional test to
tree.tto confirm the expected behavior.