Add back -w window size setting

hivdb · Mar 10, 2024 · eb27e54 · eb27e54
1 parent f2890cf
commit eb27e54
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Showing 2 changed files with 4 additions and 3 deletions.
diff --git a/data/alignment-config_hiv1.json b/data/alignment-config_hiv1.json
@@ -44,7 +44,7 @@
         "8797",
         "9417"
       ],
-      "minimap2Opts": "-k 10 --score-N 0 --secondary no"
+      "minimap2Opts": "-k 10 -w 5 --score-N 0 --secondary no"
     },
     {
       "fragmentName": "HIV1gag",

diff --git a/data/alignment-config_hiv1.yml b/data/alignment-config_hiv1.yml
@@ -101,10 +101,11 @@ fragmentConfig:
       codon-alignment, '--min-gap-distance=15', '8797', '9417'   # nef
     ]
     # 1. use smaller k-mer (default: 15) for increasing alignment sensitivity
-    # 2. no penalty for N base is recommended in several MiniMap2 issues:
+    # 2. use smaller window size (default: 10) for increasing alignment sensitivity
+    # 3. no penalty for N base is recommended in several MiniMap2 issues:
     #    https://github.com/lh3/minimap2/issues/354 and
     #    https://github.com/lh3/minimap2/issues/720
-    minimap2Opts: "-k 10 --score-N 0 --secondary no"
+    minimap2Opts: "-k 10 -w 5 --score-N 0 --secondary no"
   - fragmentName: HIV1gag
     fromFragment: HXB2_x_ConsensusB
     geneName: HIV1gag
-Original file line number
+Diff line change
@@ Expand Up / @@ -44,7 +44,7 @@ @@
             "8797",
             "9417"
           ],
-          "minimap2Opts": "-k 10 --score-N 0 --secondary no"
+          "minimap2Opts": "-k 10 -w 5 --score-N 0 --secondary no"
         },
         {
           "fragmentName": "HIV1gag",
@@ Expand Down @@