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[WIP] Update minimap version #1027

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[WIP] Update minimap version #1027

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2609208
[WIP] Update minimap version
Donaim Oct 23, 2023
86fb348
Adjust unimportant parameter in test
Donaim Oct 23, 2023
3cc0614
Merge branch 'master' into update-minimap
Donaim Oct 21, 2024
16ef7c0
save
Donaim Oct 21, 2024
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2 changes: 1 addition & 1 deletion micall/tests/test_consensus_aligner.py
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Original file line number Diff line number Diff line change
Expand Up @@ -515,7 +515,7 @@ def test_start_contig_insertion_minimap2(projects):
r_en=2060,
q_st=0,
q_en=63,
mapq=9,
mapq=8,
cigar=[[30, CigarActions.MATCH],
[3, CigarActions.INSERT],
[30, CigarActions.MATCH]],
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4 changes: 2 additions & 2 deletions micall/utils/consensus_aligner.py
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Expand Up @@ -269,7 +269,7 @@ def start_contig(self,
coordinate_seq = self.projects.getGenotypeReference(coordinate_name)
except KeyError:
coordinate_seq = self.projects.getReference(coordinate_name)
aligner = Aligner(seq=coordinate_seq, preset='map-ont')
aligner = Aligner(seq=coordinate_seq, bw=500, bw_long=500, preset='map-ont')
self.alignments = list(aligner.map(self.consensus))
if self.alignments or 10_000 < len(self.consensus):
self.algorithm = 'minimap2'
Expand Down Expand Up @@ -896,7 +896,7 @@ def seed_concordance(self, seed_name, projects, seed_coordinates, excluded_regio
if self.seed_concordance_writer is None:
return
seed_ref = self.projects.getReference(seed_name)
seed_aligner = Aligner(seq=seed_ref, preset='map-ont')
seed_aligner = Aligner(seq=seed_ref, bw=500, bw_long=500, preset='map-ont')
seed_alignments = list(seed_aligner.map(self.consensus))

regions = projects.getCoordinateReferences(seed_name)
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2 changes: 1 addition & 1 deletion pyproject.toml
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Expand Up @@ -37,7 +37,7 @@ dependencies = [
"reportlab==4.2.0",
"pysam==0.22.1",
"genetracks @ git+https://github.com/cfe-lab/genetracks.git@v0.4",
"mappy==2.17",
"mappy==2.28",
"drawsvg==2.3.0",
"cairosvg==2.7.1",
"aligntools",
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