diff --git a/validateFiles/test.36.tst b/validateFiles/test.36.tst index af96fa0..303f315 100644 --- 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 index 2241980..99a62ee 100644 --- 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 index 2df594a..2241980 100644 --- 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 index 2698adf..fb70ce4 100644 --- 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 index 59606cc..2698adf 100644 --- 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 index bebfef1..59606cc 100644 --- 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 index e16c873..bebfef1 100644 --- 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 index 4fb6bef..e16c873 100644 --- 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 diff --git a/validateFiles/test.46.tst b/validateFiles/test.46.tst index d788d22..836e04d 100644 --- a/validateFiles/test.46.tst +++ b/validateFiles/test.46.tst @@ -1,112 +1,58 @@ -kreeq-decompressor lookup -i testFiles/decompressor1.bkwig -c testFiles/decompressor1.bed +kreeq subgraph -d testFiles/test1.kreeq -f testFiles/random1.fasta --search-depth 0 --no-collapse embedded -21 -sequence1:20-30 -3,2,2 -2,2,2 -2,2,2 -2,2,2 -2,2,2 -2,2,2 -2,2,2 -2,2,2 -2,2,2 -4,1,2 - -sequence1:40-43 -2,2,1 -2,2,2 -2,2,2 - -sequence2:15-70 -0,0,0 -0,0,0 -0,0,0 -0,0,0 -0,0,0 -0,0,0 -0,0,0 -0,0,0 -0,0,0 -0,0,0 -0,0,0 -2,2,0 -2,2,2 -2,2,2 -4,1,2 -2,2,1 -2,2,2 -2,2,2 -2,2,2 -2,2,2 -2,2,2 -2,2,2 -2,2,2 -2,2,2 -2,1,2 -2,2,1 -2,2,2 -2,2,2 -2,2,2 -2,0,2 -0,0,0 -0,0,0 -0,0,0 -0,0,0 -0,0,0 -0,0,0 -0,0,0 -0,0,0 -0,0,0 -0,0,0 -0,0,0 -0,0,0 -0,0,0 -0,0,0 -0,0,0 -0,0,0 -0,0,0 -0,0,0 -0,0,0 -0,0,0 -0,0,0 -2,2,0 -2,2,2 -2,2,2 -2,1,2 - -sequence2:30-39 -2,2,1 -2,2,2 -2,2,2 -2,2,2 -2,2,2 -2,2,2 -2,2,2 -2,2,2 -2,2,2 - -sequence3:20-30 -3,2,2 -2,2,2 -2,2,2 -2,2,2 -2,2,2 -2,2,2 -2,0,2 -0,0,0 -0,0,0 -0,0,0 - -sequence3:60-70 -2,2,1 -2,2,2 -2,2,2 -2,2,2 -2,2,2 -2,2,2 -2,2,2 -2,2,2 -2,2,2 -2,1,2 - +Subgraph summary statistics: +Total kmers: 1156 +Unique kmers: 168 +Distinct kmers: 260 +Missing kmers: 4398046510844 +Total edges: 446 ++++Assembly summary+++: +# scaffolds: 0 +Total scaffold length: 0 +Average scaffold length: nan +Scaffold N50: 0 +Scaffold auN: 0.00 +Scaffold L50: 0 +Largest scaffold: 0 +Smallest scaffold: 0 +# contigs: 0 +Total contig length: 0 +Average contig length: nan +Contig N50: 0 +Contig auN: 0.00 +Contig L50: 0 +Largest contig: 0 +Smallest contig: 0 +# gaps in scaffolds: 0 +Total gap length in scaffolds: 0 +Average gap length in scaffolds: 0.00 +Gap N50 in scaffolds: 0 +Gap auN in scaffolds: 0.00 +Gap L50 in scaffolds: 0 +Largest gap in scaffolds: 0 +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 +# gaps: 0 +# paths: 0 +# edges: 520 +Average degree: 2.00 +# connected components: 1 +Largest connected component length: 5460 +# dead ends: 2 +# disconnected components: 0 +Total length disconnected components: 0 +# separated components: 1 +# bubbles: 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 diff --git a/validateFiles/test.47.tst b/validateFiles/test.47.tst index 8a041a0..d788d22 100644 --- a/validateFiles/test.47.tst +++ b/validateFiles/test.47.tst @@ -1,37 +1,24 @@ -kreeq-decompressor inflate -i testFiles/decompressor2.bkwig +kreeq-decompressor lookup -i testFiles/decompressor1.bkwig -c testFiles/decompressor1.bed embedded 21 -fixedStep chrom=sequence1 start=0 step=1 -480,479,0 -480,479,479 -480,479,479 -480,479,479 -480,479,479 -480,479,479 -480,479,479 -480,479,479 -480,479,479 -480,479,479 -480,479,479 -480,479,479 -480,479,479 -480,479,479 -480,479,479 -480,479,479 -480,479,479 -480,479,479 -480,479,479 -480,479,479 -480,479,479 -480,479,479 -480,479,479 -480,479,479 -480,479,479 -480,479,479 -480,479,479 -480,479,479 -480,479,479 -480,0,479 +sequence1:20-30 +3,2,2 +2,2,2 +2,2,2 +2,2,2 +2,2,2 +2,2,2 +2,2,2 +2,2,2 +2,2,2 +4,1,2 + +sequence1:40-43 +2,2,1 +2,2,2 +2,2,2 + +sequence2:15-70 0,0,0 0,0,0 0,0,0 @@ -43,6 +30,25 @@ fixedStep chrom=sequence1 start=0 step=1 0,0,0 0,0,0 0,0,0 +2,2,0 +2,2,2 +2,2,2 +4,1,2 +2,2,1 +2,2,2 +2,2,2 +2,2,2 +2,2,2 +2,2,2 +2,2,2 +2,2,2 +2,2,2 +2,1,2 +2,2,1 +2,2,2 +2,2,2 +2,2,2 +2,0,2 0,0,0 0,0,0 0,0,0 @@ -52,3 +58,55 @@ fixedStep chrom=sequence1 start=0 step=1 0,0,0 0,0,0 0,0,0 +0,0,0 +0,0,0 +0,0,0 +0,0,0 +0,0,0 +0,0,0 +0,0,0 +0,0,0 +0,0,0 +0,0,0 +0,0,0 +0,0,0 +2,2,0 +2,2,2 +2,2,2 +2,1,2 + +sequence2:30-39 +2,2,1 +2,2,2 +2,2,2 +2,2,2 +2,2,2 +2,2,2 +2,2,2 +2,2,2 +2,2,2 + +sequence3:20-30 +3,2,2 +2,2,2 +2,2,2 +2,2,2 +2,2,2 +2,2,2 +2,0,2 +0,0,0 +0,0,0 +0,0,0 + +sequence3:60-70 +2,2,1 +2,2,2 +2,2,2 +2,2,2 +2,2,2 +2,2,2 +2,2,2 +2,2,2 +2,2,2 +2,1,2 + diff --git a/validateFiles/test.48.tst b/validateFiles/test.48.tst new file mode 100644 index 0000000..8a041a0 --- /dev/null +++ b/validateFiles/test.48.tst @@ -0,0 +1,54 @@ +kreeq-decompressor inflate -i testFiles/decompressor2.bkwig +embedded +21 +fixedStep chrom=sequence1 start=0 step=1 +480,479,0 +480,479,479 +480,479,479 +480,479,479 +480,479,479 +480,479,479 +480,479,479 +480,479,479 +480,479,479 +480,479,479 +480,479,479 +480,479,479 +480,479,479 +480,479,479 +480,479,479 +480,479,479 +480,479,479 +480,479,479 +480,479,479 +480,479,479 +480,479,479 +480,479,479 +480,479,479 +480,479,479 +480,479,479 +480,479,479 +480,479,479 +480,479,479 +480,479,479 +480,0,479 +0,0,0 +0,0,0 +0,0,0 +0,0,0 +0,0,0 +0,0,0 +0,0,0 +0,0,0 +0,0,0 +0,0,0 +0,0,0 +0,0,0 +0,0,0 +0,0,0 +0,0,0 +0,0,0 +0,0,0 +0,0,0 +0,0,0 +0,0,0