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updated test files
1 parent 073bd20 commit b115c6c

11 files changed

+288
-230
lines changed

‎validateFiles/test.36.tst

+1-1
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,7 @@ Total kmers: 157
55
Unique kmers: 61
66
Distinct kmers: 109
77
Missing kmers: 4398046510995
8-
Total edges: 186
8+
Total edges: 184
99
+++Assembly summary+++:
1010
# scaffolds: 0
1111
Total scaffold length: 0

‎validateFiles/test.39.tst

+18-18
Original file line numberDiff line numberDiff line change
@@ -1,11 +1,11 @@
1-
kreeq subgraph -d testFiles/random5.kreeq -f testFiles/random5.fasta
1+
kreeq subgraph -d testFiles/random11.kreeq -f testFiles/random11.fasta --search-depth 32 --traversal-algorithm best-first --no-collapse
22
embedded
33
Subgraph summary statistics:
4-
Total kmers: 158
5-
Unique kmers: 84
6-
Distinct kmers: 121
7-
Missing kmers: 4398046510983
8-
Total edges: 203
4+
Total kmers: 110
5+
Unique kmers: 110
6+
Distinct kmers: 110
7+
Missing kmers: 4398046510994
8+
Total edges: 186
99
+++Assembly summary+++:
1010
# scaffolds: 0
1111
Total scaffold length: 0
@@ -34,25 +34,25 @@ Smallest gap in scaffolds: 0
3434
Base composition (A:C:G:T): 0:0:0:0
3535
GC content %: nan
3636
# soft-masked bases: 0
37-
# segments: 7
38-
Total segment length: 261
39-
Average segment length: 37.29
37+
# segments: 110
38+
Total segment length: 2310
39+
Average segment length: 21.00
4040
# gaps: 0
4141
# paths: 0
42-
# edges: 8
43-
Average degree: 1.14
42+
# edges: 218
43+
Average degree: 1.98
4444
# connected components: 1
45-
Largest connected component length: 261
45+
Largest connected component length: 2310
4646
# dead ends: 2
4747
# disconnected components: 0
4848
Total length disconnected components: 0
4949
# separated components: 1
50-
# bubbles: 2
50+
# bubbles: 0
5151
# circular segments: 0
5252
# circular paths: 0
5353
DBG Summary statistics:
54-
Total kmers: 158
55-
Unique kmers: 84
56-
Distinct kmers: 121
57-
Missing kmers: 4398046510983
58-
Total edges: 203
54+
Total kmers: 79
55+
Unique kmers: 79
56+
Distinct kmers: 79
57+
Missing kmers: 4398046511025
58+
Total edges: 132

‎validateFiles/test.40.tst

+1-1
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
kreeq subgraph -d testFiles/random5.kreeq -f testFiles/random5.fasta --do-not-collapse-nodes
1+
kreeq subgraph -d testFiles/random5.kreeq -f testFiles/random5.fasta
22
embedded
33
Subgraph summary statistics:
44
Total kmers: 158

‎validateFiles/test.41.tst

+17-17
Original file line numberDiff line numberDiff line change
@@ -1,11 +1,11 @@
1-
kreeq subgraph -d testFiles/random6.kreeq -f testFiles/random5.fasta
1+
kreeq subgraph -d testFiles/random5.kreeq -f testFiles/random5.fasta --no-collapse
22
embedded
33
Subgraph summary statistics:
4-
Total kmers: 159
5-
Unique kmers: 41
6-
Distinct kmers: 100
7-
Missing kmers: 4398046511004
8-
Total edges: 173
4+
Total kmers: 158
5+
Unique kmers: 84
6+
Distinct kmers: 121
7+
Missing kmers: 4398046510983
8+
Total edges: 203
99
+++Assembly summary+++:
1010
# scaffolds: 0
1111
Total scaffold length: 0
@@ -34,15 +34,15 @@ Smallest gap in scaffolds: 0
3434
Base composition (A:C:G:T): 0:0:0:0
3535
GC content %: nan
3636
# soft-masked bases: 0
37-
# segments: 4
38-
Total segment length: 180
39-
Average segment length: 45.00
37+
# segments: 121
38+
Total segment length: 2541
39+
Average segment length: 21.00
4040
# gaps: 0
4141
# paths: 0
42-
# edges: 4
43-
Average degree: 1.00
42+
# edges: 244
43+
Average degree: 2.02
4444
# connected components: 1
45-
Largest connected component length: 180
45+
Largest connected component length: 2541
4646
# dead ends: 2
4747
# disconnected components: 0
4848
Total length disconnected components: 0
@@ -51,8 +51,8 @@ Total length disconnected components: 0
5151
# circular segments: 0
5252
# circular paths: 0
5353
DBG Summary statistics:
54-
Total kmers: 159
55-
Unique kmers: 41
56-
Distinct kmers: 100
57-
Missing kmers: 4398046511004
58-
Total edges: 173
54+
Total kmers: 158
55+
Unique kmers: 84
56+
Distinct kmers: 121
57+
Missing kmers: 4398046510983
58+
Total edges: 203

‎validateFiles/test.42.tst

+12-12
Original file line numberDiff line numberDiff line change
@@ -1,11 +1,11 @@
1-
kreeq subgraph -d testFiles/random7.kreeq -f testFiles/random5.fasta
1+
kreeq subgraph -d testFiles/random6.kreeq -f testFiles/random5.fasta
22
embedded
33
Subgraph summary statistics:
4-
Total kmers: 157
4+
Total kmers: 159
55
Unique kmers: 41
6-
Distinct kmers: 99
7-
Missing kmers: 4398046511005
8-
Total edges: 170
6+
Distinct kmers: 100
7+
Missing kmers: 4398046511004
8+
Total edges: 173
99
+++Assembly summary+++:
1010
# scaffolds: 0
1111
Total scaffold length: 0
@@ -35,14 +35,14 @@ Base composition (A:C:G:T): 0:0:0:0
3535
GC content %: nan
3636
# soft-masked bases: 0
3737
# segments: 4
38-
Total segment length: 179
39-
Average segment length: 44.75
38+
Total segment length: 180
39+
Average segment length: 45.00
4040
# gaps: 0
4141
# paths: 0
4242
# edges: 4
4343
Average degree: 1.00
4444
# connected components: 1
45-
Largest connected component length: 179
45+
Largest connected component length: 180
4646
# dead ends: 2
4747
# disconnected components: 0
4848
Total length disconnected components: 0
@@ -51,8 +51,8 @@ Total length disconnected components: 0
5151
# circular segments: 0
5252
# circular paths: 0
5353
DBG Summary statistics:
54-
Total kmers: 157
54+
Total kmers: 159
5555
Unique kmers: 41
56-
Distinct kmers: 99
57-
Missing kmers: 4398046511005
58-
Total edges: 170
56+
Distinct kmers: 100
57+
Missing kmers: 4398046511004
58+
Total edges: 173

‎validateFiles/test.43.tst

+14-14
Original file line numberDiff line numberDiff line change
@@ -1,11 +1,11 @@
1-
kreeq subgraph -d testFiles/random8.kreeq -f testFiles/random5.fasta
1+
kreeq subgraph -d testFiles/random7.kreeq -f testFiles/random5.fasta
22
embedded
33
Subgraph summary statistics:
4-
Total kmers: 159
5-
Unique kmers: 35
6-
Distinct kmers: 97
7-
Missing kmers: 4398046511007
8-
Total edges: 165
4+
Total kmers: 157
5+
Unique kmers: 41
6+
Distinct kmers: 99
7+
Missing kmers: 4398046511005
8+
Total edges: 170
99
+++Assembly summary+++:
1010
# scaffolds: 0
1111
Total scaffold length: 0
@@ -35,14 +35,14 @@ Base composition (A:C:G:T): 0:0:0:0
3535
GC content %: nan
3636
# soft-masked bases: 0
3737
# segments: 4
38-
Total segment length: 177
39-
Average segment length: 44.25
38+
Total segment length: 179
39+
Average segment length: 44.75
4040
# gaps: 0
4141
# paths: 0
4242
# edges: 4
4343
Average degree: 1.00
4444
# connected components: 1
45-
Largest connected component length: 177
45+
Largest connected component length: 179
4646
# dead ends: 2
4747
# disconnected components: 0
4848
Total length disconnected components: 0
@@ -51,8 +51,8 @@ Total length disconnected components: 0
5151
# circular segments: 0
5252
# circular paths: 0
5353
DBG Summary statistics:
54-
Total kmers: 159
55-
Unique kmers: 35
56-
Distinct kmers: 97
57-
Missing kmers: 4398046511007
58-
Total edges: 165
54+
Total kmers: 157
55+
Unique kmers: 41
56+
Distinct kmers: 99
57+
Missing kmers: 4398046511005
58+
Total edges: 170

‎validateFiles/test.44.tst

+7-7
Original file line numberDiff line numberDiff line change
@@ -1,11 +1,11 @@
1-
kreeq subgraph -d testFiles/random9.kreeq -f testFiles/random5.fasta
1+
kreeq subgraph -d testFiles/random8.kreeq -f testFiles/random5.fasta
22
embedded
33
Subgraph summary statistics:
4-
Total kmers: 157
5-
Unique kmers: 37
4+
Total kmers: 159
5+
Unique kmers: 35
66
Distinct kmers: 97
77
Missing kmers: 4398046511007
8-
Total edges: 166
8+
Total edges: 165
99
+++Assembly summary+++:
1010
# scaffolds: 0
1111
Total scaffold length: 0
@@ -51,8 +51,8 @@ Total length disconnected components: 0
5151
# circular segments: 0
5252
# circular paths: 0
5353
DBG Summary statistics:
54-
Total kmers: 157
55-
Unique kmers: 37
54+
Total kmers: 159
55+
Unique kmers: 35
5656
Distinct kmers: 97
5757
Missing kmers: 4398046511007
58-
Total edges: 166
58+
Total edges: 165

‎validateFiles/test.45.tst

+17-17
Original file line numberDiff line numberDiff line change
@@ -1,11 +1,11 @@
1-
kreeq subgraph -d testFiles/test1.kreeq -f testFiles/random1.fasta --search-depth 0 --no-collapse
1+
kreeq subgraph -d testFiles/random9.kreeq -f testFiles/random5.fasta
22
embedded
33
Subgraph summary statistics:
4-
Total kmers: 1156
5-
Unique kmers: 168
6-
Distinct kmers: 260
7-
Missing kmers: 4398046510844
8-
Total edges: 448
4+
Total kmers: 157
5+
Unique kmers: 37
6+
Distinct kmers: 97
7+
Missing kmers: 4398046511007
8+
Total edges: 166
99
+++Assembly summary+++:
1010
# scaffolds: 0
1111
Total scaffold length: 0
@@ -34,15 +34,15 @@ Smallest gap in scaffolds: 0
3434
Base composition (A:C:G:T): 0:0:0:0
3535
GC content %: nan
3636
# soft-masked bases: 0
37-
# segments: 260
38-
Total segment length: 5460
39-
Average segment length: 21.00
37+
# segments: 4
38+
Total segment length: 177
39+
Average segment length: 44.25
4040
# gaps: 0
4141
# paths: 0
42-
# edges: 520
43-
Average degree: 2.00
42+
# edges: 4
43+
Average degree: 1.00
4444
# connected components: 1
45-
Largest connected component length: 5460
45+
Largest connected component length: 177
4646
# dead ends: 2
4747
# disconnected components: 0
4848
Total length disconnected components: 0
@@ -51,8 +51,8 @@ Total length disconnected components: 0
5151
# circular segments: 0
5252
# circular paths: 0
5353
DBG Summary statistics:
54-
Total kmers: 172
55-
Unique kmers: 25
56-
Distinct kmers: 96
57-
Missing kmers: 4398046511008
58-
Total edges: 160
54+
Total kmers: 157
55+
Unique kmers: 37
56+
Distinct kmers: 97
57+
Missing kmers: 4398046511007
58+
Total edges: 166

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