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a-ludi / djunctor

Close assembly gaps using long-reads with focus on correctness.
MIT License
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Weakly anchored alignment chains should not be used for pile ups #43

Closed a-ludi closed 6 years ago

a-ludi commented 6 years ago

There are some alignments that get not filtered correctly. In the screenshot below you can see two examples that lead to misassembly of contig 7 and 9.

2018-06-06-falsy-unfiltered-alignments.png

a-ludi commented 6 years ago

The respective filter is working correctly but two bugs lead to this false behaviour:

  1. transferA2BCandidatesToB2A transferred all read alignments instead of the filtered (commit b25a4a6aee6b04b66f57b2e61870f9f65fc6baa5)
  2. ImproperAlignmentChainsFilter removed all alignment chains (commit 41d2fff7ec0108ec89f701e21aa274e868e36ea6)