Merge branch 'align_lrhq' into 'master'

Align lrhq See merge request machine-learning/bonito!182
nanoporetech · May 20, 2024 · 37a0557 · 37a0557
2 parents e24537a + c15327d
commit 37a0557
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Showing 3 changed files with 4 additions and 3 deletions.
diff --git a/bonito/aligner.py b/bonito/aligner.py
@@ -1,7 +1,6 @@
 """
 Bonito Aligner
 """
-
 from threading import Thread
 from functools import partial
 from mappy import Aligner, ThreadBuffer

diff --git a/bonito/cli/basecaller.py b/bonito/cli/basecaller.py
@@ -82,7 +82,7 @@ def main(args):
 
     if args.reference:
         sys.stderr.write("> loading reference\n")
-        aligner = Aligner(args.reference, preset='map-ont', best_n=1)
+        aligner = Aligner(args.reference, preset=args.mm2_preset)
         if not aligner:
             sys.stderr.write("> failed to load/build index\n")
             exit(1)
@@ -215,5 +215,6 @@ def argparser():
     parser.add_argument("--min-qscore", default=0, type=int)
     parser.add_argument("--min-accuracy-save-ctc", default=0.99, type=float)
     parser.add_argument("--alignment-threads", default=8, type=int)
+    parser.add_argument("--mm2-preset", default='lr:hq', type=str)
     parser.add_argument('-v', '--verbose', action='count', default=0)
     return parser
diff --git a/bonito/cli/duplex.py b/bonito/cli/duplex.py
@@ -347,7 +347,7 @@ def main(args):
 
     if args.reference:
         sys.stderr.write("> loading reference\n")
-        aligner = Aligner(args.reference, preset='map-ont', best_n=1)
+        aligner = Aligner(args.reference, preset=args.mm2_preset)
         if not aligner:
             sys.stderr.write("> failed to load/build index\n")
             exit(1)
@@ -393,4 +393,5 @@ def argparser():
     parser.add_argument("--no-header", action="store_true") # skip-header?
     parser.add_argument("--threads", default=8, type=int)
     parser.add_argument("--alignment-threads", default=8, type=int)
+    parser.add_argument("--mm2-preset", default='lr:hq', type=str)
     return parser