Fixup

eaasna · Sep 13, 2023 · 2e062bd · 2e062bd
1 parent f418fc2
commit 2e062bd
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Showing 2 changed files with 39 additions and 39 deletions.
diff --git a/src/consolidate/io.cpp b/src/consolidate/io.cpp
@@ -45,4 +45,4 @@ void write_stellar_output(std::filesystem::path const & out_path,
     fout.close();
 }
 
-}
+} // namespace valik
diff --git a/test/data/dream/4bins15window1error.gff.out b/test/data/dream/4bins15window1error.gff.out
@@ -1,8 +1,8 @@
 I/O options:
   database file   : ref.fasta
-  query file      : tmp/valik/my_dir/query_0_0.fasta
+  query file      : tmp/valik/my_dir/query_1_0.fasta
   alphabet        : dna
-  output file     : tmp/valik/my_dir/query_0_0.fasta.gff
+  output file     : tmp/valik/my_dir/query_1_0.fasta.gff
   output format   : gff
 
 User specified parameters:
@@ -25,22 +25,22 @@ Calculated parameters:
   overlap      : 0
 
 Loaded 3 query sequences.
-Loaded sequence chr1.
+Loaded sequence chr2.
 
 Constructing index...
 
 Aligning all query sequences to database sequence...
-  chr1
-  chr1, complement
+  chr2
+  chr2, complement
 
 # Eps-matches     : 3
 
 
 I/O options:
   database file   : ref.fasta
-  query file      : tmp/valik/my_dir/query_1_0.fasta
+  query file      : tmp/valik/my_dir/query_1_1.fasta
   alphabet        : dna
-  output file     : tmp/valik/my_dir/query_1_0.fasta.gff
+  output file     : tmp/valik/my_dir/query_1_1.fasta.gff
   output format   : gff
 
 User specified parameters:
@@ -76,9 +76,9 @@ Aligning all query sequences to database sequence...
 
 I/O options:
   database file   : ref.fasta
-  query file      : tmp/valik/my_dir/query_0_1.fasta
+  query file      : tmp/valik/my_dir/query_0_0.fasta
   alphabet        : dna
-  output file     : tmp/valik/my_dir/query_0_1.fasta.gff
+  output file     : tmp/valik/my_dir/query_0_0.fasta.gff
   output format   : gff
 
 User specified parameters:
@@ -152,9 +152,9 @@ Aligning all query sequences to database sequence...
 
 I/O options:
   database file   : ref.fasta
-  query file      : tmp/valik/my_dir/query_1_1.fasta
+  query file      : tmp/valik/my_dir/query_1_2.fasta
   alphabet        : dna
-  output file     : tmp/valik/my_dir/query_1_1.fasta.gff
+  output file     : tmp/valik/my_dir/query_1_2.fasta.gff
   output format   : gff
 
 User specified parameters:
@@ -190,9 +190,9 @@ Aligning all query sequences to database sequence...
 
 I/O options:
   database file   : ref.fasta
-  query file      : tmp/valik/my_dir/query_1_2.fasta
+  query file      : tmp/valik/my_dir/query_1_3.fasta
   alphabet        : dna
-  output file     : tmp/valik/my_dir/query_1_2.fasta.gff
+  output file     : tmp/valik/my_dir/query_1_3.fasta.gff
   output format   : gff
 
 User specified parameters:
@@ -266,9 +266,9 @@ Aligning all query sequences to database sequence...
 
 I/O options:
   database file   : ref.fasta
-  query file      : tmp/valik/my_dir/query_0_2.fasta
+  query file      : tmp/valik/my_dir/query_0_1.fasta
   alphabet        : dna
-  output file     : tmp/valik/my_dir/query_0_2.fasta.gff
+  output file     : tmp/valik/my_dir/query_0_1.fasta.gff
   output format   : gff
 
 User specified parameters:
@@ -304,9 +304,9 @@ Aligning all query sequences to database sequence...
 
 I/O options:
   database file   : ref.fasta
-  query file      : tmp/valik/my_dir/query_1_3.fasta
+  query file      : tmp/valik/my_dir/query_1_4.fasta
   alphabet        : dna
-  output file     : tmp/valik/my_dir/query_1_3.fasta.gff
+  output file     : tmp/valik/my_dir/query_1_4.fasta.gff
   output format   : gff
 
 User specified parameters:
@@ -380,9 +380,9 @@ Aligning all query sequences to database sequence...
 
 I/O options:
   database file   : ref.fasta
-  query file      : tmp/valik/my_dir/query_1_4.fasta
+  query file      : tmp/valik/my_dir/query_1_5.fasta
   alphabet        : dna
-  output file     : tmp/valik/my_dir/query_1_4.fasta.gff
+  output file     : tmp/valik/my_dir/query_1_5.fasta.gff
   output format   : gff
 
 User specified parameters:
@@ -456,9 +456,9 @@ Aligning all query sequences to database sequence...
 
 I/O options:
   database file   : ref.fasta
-  query file      : tmp/valik/my_dir/query_1_5.fasta
+  query file      : tmp/valik/my_dir/query_1_6.fasta
   alphabet        : dna
-  output file     : tmp/valik/my_dir/query_1_5.fasta.gff
+  output file     : tmp/valik/my_dir/query_1_6.fasta.gff
   output format   : gff
 
 User specified parameters:
@@ -570,9 +570,9 @@ Aligning all query sequences to database sequence...
 
 I/O options:
   database file   : ref.fasta
-  query file      : tmp/valik/my_dir/query_1_6.fasta
+  query file      : tmp/valik/my_dir/query_1_7.fasta
   alphabet        : dna
-  output file     : tmp/valik/my_dir/query_1_6.fasta.gff
+  output file     : tmp/valik/my_dir/query_1_7.fasta.gff
   output format   : gff
 
 User specified parameters:
@@ -608,9 +608,9 @@ Aligning all query sequences to database sequence...
 
 I/O options:
   database file   : ref.fasta
-  query file      : tmp/valik/my_dir/query_0_3.fasta
+  query file      : tmp/valik/my_dir/query_0_2.fasta
   alphabet        : dna
-  output file     : tmp/valik/my_dir/query_0_3.fasta.gff
+  output file     : tmp/valik/my_dir/query_0_2.fasta.gff
   output format   : gff
 
 User specified parameters:
@@ -722,9 +722,9 @@ Aligning all query sequences to database sequence...
 
 I/O options:
   database file   : ref.fasta
-  query file      : tmp/valik/my_dir/query_0_4.fasta
+  query file      : tmp/valik/my_dir/query_0_3.fasta
   alphabet        : dna
-  output file     : tmp/valik/my_dir/query_0_4.fasta.gff
+  output file     : tmp/valik/my_dir/query_0_3.fasta.gff
   output format   : gff
 
 User specified parameters:
@@ -760,9 +760,9 @@ Aligning all query sequences to database sequence...
 
 I/O options:
   database file   : ref.fasta
-  query file      : tmp/valik/my_dir/query_1_7.fasta
+  query file      : tmp/valik/my_dir/query_1_8.fasta
   alphabet        : dna
-  output file     : tmp/valik/my_dir/query_1_7.fasta.gff
+  output file     : tmp/valik/my_dir/query_1_8.fasta.gff
   output format   : gff
 
 User specified parameters:
@@ -836,9 +836,9 @@ Aligning all query sequences to database sequence...
 
 I/O options:
   database file   : ref.fasta
-  query file      : tmp/valik/my_dir/query_0_5.fasta
+  query file      : tmp/valik/my_dir/query_0_4.fasta
   alphabet        : dna
-  output file     : tmp/valik/my_dir/query_0_5.fasta.gff
+  output file     : tmp/valik/my_dir/query_0_4.fasta.gff
   output format   : gff
 
 User specified parameters:
@@ -874,9 +874,9 @@ Aligning all query sequences to database sequence...
 
 I/O options:
   database file   : ref.fasta
-  query file      : tmp/valik/my_dir/query_1_8.fasta
+  query file      : tmp/valik/my_dir/query_1_9.fasta
   alphabet        : dna
-  output file     : tmp/valik/my_dir/query_1_8.fasta.gff
+  output file     : tmp/valik/my_dir/query_1_9.fasta.gff
   output format   : gff
 
 User specified parameters:
@@ -950,9 +950,9 @@ Aligning all query sequences to database sequence...
 
 I/O options:
   database file   : ref.fasta
-  query file      : tmp/valik/my_dir/query_1_9.fasta
+  query file      : tmp/valik/my_dir/query_0_5.fasta
   alphabet        : dna
-  output file     : tmp/valik/my_dir/query_1_9.fasta.gff
+  output file     : tmp/valik/my_dir/query_0_5.fasta.gff
   output format   : gff
 
 User specified parameters:
@@ -975,13 +975,13 @@ Calculated parameters:
   overlap      : 0
 
 Loaded 3 query sequences.
-Loaded sequence chr2.
+Loaded sequence chr1.
 
 Constructing index...
 
 Aligning all query sequences to database sequence...
-  chr2
-  chr2, complement
+  chr1
+  chr1, complement
 
 # Eps-matches     : 3
-Original file line number
+Diff line change
@@ Expand Up @@
         fout.close();
     }
-    }
+    } // namespace valik