Mon Nov 26 13:16:47 2018


Input:
../stage_c/singles.fastq


../contig_overlaps.txt

Output directory: 
Maximum number of overlaps: 100000000
Threads: 1
Minimum clique size: 2
Minimal overlap percentage: 0
Minimal overlap length: 100
Edge threshold: 0.995
Overlap threshold (to be reconsidered): 0.9
First it: 0
Add duplicates: 0
Resolve read orientations: 1
Keep singletons of length at least: 100
Enumerate cliques: 0
Error correction: 0
Ignore inclusions: 1
Graph only: 0
FNO: 1
Mismatch prob: 0
Original readcount: 2200
Optimize: 0
No inclusion overlaps: 0
Merge contigs: 0
Remove_multi_occ: 0
Remove transitive edges: 1
Minimal read length: 100
Remove branches: 1
Remove backedges: 1


Output:
Vertex count: 4
Edge count: 2
Duplicate overlaps: 0
Self-overlaps: 0
Inclusions: 0
Conflicting edges removed: 0
Number of backedges (DFS): 0

Total clique count: 0
Superread (singles) count: 1
Superread (paired) count: 0
Superread (trivials) count: 2
Next overlaps count: 1

*****************************************

Mon Nov 26 13:16:47 2018


Input:
singles.fastq
None
None
overlaps.txt

Output directory: 
Maximum number of overlaps: 100000000
Threads: 1
Minimum clique size: 2
Minimal overlap percentage: 0
Minimal overlap length: 100
Edge threshold: 0.995
Overlap threshold (to be reconsidered): 0.9
First it: 0
Add duplicates: 0
Resolve read orientations: 1
Keep singletons of length at least: 100
Enumerate cliques: 0
Error correction: 0
Ignore inclusions: 1
Graph only: 0
FNO: 1
Mismatch prob: 0
Original readcount: 2200
Optimize: 0
No inclusion overlaps: 0
Merge contigs: 0
Remove_multi_occ: 0
Remove transitive edges: 1
Minimal read length: 100
Remove branches: 1
Remove backedges: 1


Output:
Vertex count: 3
Edge count: 1
Duplicate overlaps: 0
Self-overlaps: 0
Inclusions: 0
Conflicting edges removed: 0
Number of backedges (DFS): 0

Total clique count: 0
Superread (singles) count: 1
Superread (paired) count: 0
Superread (trivials) count: 1
Next overlaps count: 0

*****************************************