updated test files

vgl-hub · Jun 29, 2024 · b115c6c · b115c6c
1 parent 073bd20
commit b115c6c
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Showing 11 changed files with 288 additions and 230 deletions.
diff --git a/validateFiles/test.36.tst b/validateFiles/test.36.tst
@@ -5,7 +5,7 @@ Total kmers: 157
 Unique kmers: 61
 Distinct kmers: 109
 Missing kmers: 4398046510995
-Total edges: 186
+Total edges: 184
 +++Assembly summary+++: 
 # scaffolds: 0
 Total scaffold length: 0

diff --git a/validateFiles/test.39.tst b/validateFiles/test.39.tst
@@ -1,11 +1,11 @@
-kreeq subgraph -d testFiles/random5.kreeq -f testFiles/random5.fasta 
+kreeq subgraph -d testFiles/random11.kreeq -f testFiles/random11.fasta --search-depth 32 --traversal-algorithm best-first --no-collapse 
 embedded
 Subgraph summary statistics:
-Total kmers: 158
-Unique kmers: 84
-Distinct kmers: 121
-Missing kmers: 4398046510983
-Total edges: 203
+Total kmers: 110
+Unique kmers: 110
+Distinct kmers: 110
+Missing kmers: 4398046510994
+Total edges: 186
 +++Assembly summary+++: 
 # scaffolds: 0
 Total scaffold length: 0
@@ -34,25 +34,25 @@ Smallest gap in scaffolds: 0
 Base composition (A:C:G:T): 0:0:0:0
 GC content %: nan
 # soft-masked bases: 0
-# segments: 7
-Total segment length: 261
-Average segment length: 37.29
+# segments: 110
+Total segment length: 2310
+Average segment length: 21.00
 # gaps: 0
 # paths: 0
-# edges: 8
-Average degree: 1.14
+# edges: 218
+Average degree: 1.98
 # connected components: 1
-Largest connected component length: 261
+Largest connected component length: 2310
 # dead ends: 2
 # disconnected components: 0
 Total length disconnected components: 0
 # separated components: 1
-# bubbles: 2
+# bubbles: 0
 # circular segments: 0
 # circular paths: 0
 DBG Summary statistics:
-Total kmers: 158
-Unique kmers: 84
-Distinct kmers: 121
-Missing kmers: 4398046510983
-Total edges: 203
+Total kmers: 79
+Unique kmers: 79
+Distinct kmers: 79
+Missing kmers: 4398046511025
+Total edges: 132
diff --git a/validateFiles/test.40.tst b/validateFiles/test.40.tst
@@ -1,4 +1,4 @@
-kreeq subgraph -d testFiles/random5.kreeq -f testFiles/random5.fasta --do-not-collapse-nodes 
+kreeq subgraph -d testFiles/random5.kreeq -f testFiles/random5.fasta 
 embedded
 Subgraph summary statistics:
 Total kmers: 158

diff --git a/validateFiles/test.41.tst b/validateFiles/test.41.tst
@@ -1,11 +1,11 @@
-kreeq subgraph -d testFiles/random6.kreeq -f testFiles/random5.fasta 
+kreeq subgraph -d testFiles/random5.kreeq -f testFiles/random5.fasta --no-collapse 
 embedded
 Subgraph summary statistics:
-Total kmers: 159
-Unique kmers: 41
-Distinct kmers: 100
-Missing kmers: 4398046511004
-Total edges: 173
+Total kmers: 158
+Unique kmers: 84
+Distinct kmers: 121
+Missing kmers: 4398046510983
+Total edges: 203
 +++Assembly summary+++: 
 # scaffolds: 0
 Total scaffold length: 0
@@ -34,15 +34,15 @@ Smallest gap in scaffolds: 0
 Base composition (A:C:G:T): 0:0:0:0
 GC content %: nan
 # soft-masked bases: 0
-# segments: 4
-Total segment length: 180
-Average segment length: 45.00
+# segments: 121
+Total segment length: 2541
+Average segment length: 21.00
 # gaps: 0
 # paths: 0
-# edges: 4
-Average degree: 1.00
+# edges: 244
+Average degree: 2.02
 # connected components: 1
-Largest connected component length: 180
+Largest connected component length: 2541
 # dead ends: 2
 # disconnected components: 0
 Total length disconnected components: 0
@@ -51,8 +51,8 @@ Total length disconnected components: 0
 # circular segments: 0
 # circular paths: 0
 DBG Summary statistics:
-Total kmers: 159
-Unique kmers: 41
-Distinct kmers: 100
-Missing kmers: 4398046511004
-Total edges: 173
+Total kmers: 158
+Unique kmers: 84
+Distinct kmers: 121
+Missing kmers: 4398046510983
+Total edges: 203
diff --git a/validateFiles/test.42.tst b/validateFiles/test.42.tst
@@ -1,11 +1,11 @@
-kreeq subgraph -d testFiles/random7.kreeq -f testFiles/random5.fasta 
+kreeq subgraph -d testFiles/random6.kreeq -f testFiles/random5.fasta 
 embedded
 Subgraph summary statistics:
-Total kmers: 157
+Total kmers: 159
 Unique kmers: 41
-Distinct kmers: 99
-Missing kmers: 4398046511005
-Total edges: 170
+Distinct kmers: 100
+Missing kmers: 4398046511004
+Total edges: 173
 +++Assembly summary+++: 
 # scaffolds: 0
 Total scaffold length: 0
@@ -35,14 +35,14 @@ Base composition (A:C:G:T): 0:0:0:0
 GC content %: nan
 # soft-masked bases: 0
 # segments: 4
-Total segment length: 179
-Average segment length: 44.75
+Total segment length: 180
+Average segment length: 45.00
 # gaps: 0
 # paths: 0
 # edges: 4
 Average degree: 1.00
 # connected components: 1
-Largest connected component length: 179
+Largest connected component length: 180
 # dead ends: 2
 # disconnected components: 0
 Total length disconnected components: 0
@@ -51,8 +51,8 @@ Total length disconnected components: 0
 # circular segments: 0
 # circular paths: 0
 DBG Summary statistics:
-Total kmers: 157
+Total kmers: 159
 Unique kmers: 41
-Distinct kmers: 99
-Missing kmers: 4398046511005
-Total edges: 170
+Distinct kmers: 100
+Missing kmers: 4398046511004
+Total edges: 173
diff --git a/validateFiles/test.43.tst b/validateFiles/test.43.tst
@@ -1,11 +1,11 @@
-kreeq subgraph -d testFiles/random8.kreeq -f testFiles/random5.fasta 
+kreeq subgraph -d testFiles/random7.kreeq -f testFiles/random5.fasta 
 embedded
 Subgraph summary statistics:
-Total kmers: 159
-Unique kmers: 35
-Distinct kmers: 97
-Missing kmers: 4398046511007
-Total edges: 165
+Total kmers: 157
+Unique kmers: 41
+Distinct kmers: 99
+Missing kmers: 4398046511005
+Total edges: 170
 +++Assembly summary+++: 
 # scaffolds: 0
 Total scaffold length: 0
@@ -35,14 +35,14 @@ Base composition (A:C:G:T): 0:0:0:0
 GC content %: nan
 # soft-masked bases: 0
 # segments: 4
-Total segment length: 177
-Average segment length: 44.25
+Total segment length: 179
+Average segment length: 44.75
 # gaps: 0
 # paths: 0
 # edges: 4
 Average degree: 1.00
 # connected components: 1
-Largest connected component length: 177
+Largest connected component length: 179
 # dead ends: 2
 # disconnected components: 0
 Total length disconnected components: 0
@@ -51,8 +51,8 @@ Total length disconnected components: 0
 # circular segments: 0
 # circular paths: 0
 DBG Summary statistics:
-Total kmers: 159
-Unique kmers: 35
-Distinct kmers: 97
-Missing kmers: 4398046511007
-Total edges: 165
+Total kmers: 157
+Unique kmers: 41
+Distinct kmers: 99
+Missing kmers: 4398046511005
+Total edges: 170
diff --git a/validateFiles/test.44.tst b/validateFiles/test.44.tst
@@ -1,11 +1,11 @@
-kreeq subgraph -d testFiles/random9.kreeq -f testFiles/random5.fasta 
+kreeq subgraph -d testFiles/random8.kreeq -f testFiles/random5.fasta 
 embedded
 Subgraph summary statistics:
-Total kmers: 157
-Unique kmers: 37
+Total kmers: 159
+Unique kmers: 35
 Distinct kmers: 97
 Missing kmers: 4398046511007
-Total edges: 166
+Total edges: 165
 +++Assembly summary+++: 
 # scaffolds: 0
 Total scaffold length: 0
@@ -51,8 +51,8 @@ Total length disconnected components: 0
 # circular segments: 0
 # circular paths: 0
 DBG Summary statistics:
-Total kmers: 157
-Unique kmers: 37
+Total kmers: 159
+Unique kmers: 35
 Distinct kmers: 97
 Missing kmers: 4398046511007
-Total edges: 166
+Total edges: 165
diff --git a/validateFiles/test.45.tst b/validateFiles/test.45.tst
@@ -1,11 +1,11 @@
-kreeq subgraph -d testFiles/test1.kreeq -f testFiles/random1.fasta --search-depth 0 --no-collapse
+kreeq subgraph -d testFiles/random9.kreeq -f testFiles/random5.fasta 
 embedded
 Subgraph summary statistics:
-Total kmers: 1156
-Unique kmers: 168
-Distinct kmers: 260
-Missing kmers: 4398046510844
-Total edges: 448
+Total kmers: 157
+Unique kmers: 37
+Distinct kmers: 97
+Missing kmers: 4398046511007
+Total edges: 166
 +++Assembly summary+++: 
 # scaffolds: 0
 Total scaffold length: 0
@@ -34,15 +34,15 @@ Smallest gap in scaffolds: 0
 Base composition (A:C:G:T): 0:0:0:0
 GC content %: nan
 # soft-masked bases: 0
-# segments: 260
-Total segment length: 5460
-Average segment length: 21.00
+# segments: 4
+Total segment length: 177
+Average segment length: 44.25
 # gaps: 0
 # paths: 0
-# edges: 520
-Average degree: 2.00
+# edges: 4
+Average degree: 1.00
 # connected components: 1
-Largest connected component length: 5460
+Largest connected component length: 177
 # dead ends: 2
 # disconnected components: 0
 Total length disconnected components: 0
@@ -51,8 +51,8 @@ Total length disconnected components: 0
 # circular segments: 0
 # circular paths: 0
 DBG Summary statistics:
-Total kmers: 172
-Unique kmers: 25
-Distinct kmers: 96
-Missing kmers: 4398046511008
-Total edges: 160
+Total kmers: 157
+Unique kmers: 37
+Distinct kmers: 97
+Missing kmers: 4398046511007
+Total edges: 166