|
Bifrost
|
Most members of this structure are parameters for CompactedDBG<U, G>::build(), except for: More...
Inherited by CCDBG_Build_opt.
Data Fields | |
| bool | verbose |
| Print information messages during execution if true. More... | |
| size_t | nb_threads |
| Number of threads to use for building the graph. More... | |
| size_t | nb_bits_kmers_bf |
| Number of Bloom filter bits per k-mer occurring in the FASTA/FASTQ/GFA files of CDBG_Build_opt::filename_in. More... | |
| string | inFilenameBBF |
| String containing the name of a Bloom filter file that is generated by CompactedDBG<U, G>::filter. More... | |
| string | outFilenameBBF |
| String containing the name of a Bloom filter file that will be generated by CompactedDBG<U, G>::filter. More... | |
| vector< string > | filename_seq_in |
| Vector of strings, each string is the name of a FASTA/FASTQ/GFA file to use for the graph construction. More... | |
| vector< string > | filename_ref_in |
| Vector of strings, each string is the name of a FASTA/FASTQ/GFA file to use for the graph construction. More... | |
| int | k |
| Length of k-mers (not used by CompactedDBG<U, G>::build). More... | |
| int | g |
| Length of g-mers, the minimizers, such that g < k (not used by CompactedDBG<U, G>::build). More... | |
| bool | build |
| Boolean indicating if the graph must be built. More... | |
| bool | update |
| Boolean indicating if the graph must be updated. More... | |
| bool | clipTips |
| Clip short tips (length < 2k) of the graph (not used by CompactedDBG<U, G>::build). More... | |
| bool | deleteIsolated |
| Remove short isolated unitigs (length < 2k) of the graph (not used by CompactedDBG<U, G>::build). More... | |
| bool | useMercyKmers |
| Keep in the graph low coverage k-mers (cov=1) connecting tips of the graph. More... | |
| bool | outputGFA |
| Boolean indicating if the graph is written to a GFA file. More... | |
| bool | outputFASTA |
| Boolean indicating if the graph is written to a FASTA file. More... | |
| bool | outputBFG |
| Boolean indicating if the graph is written to a BFG/BFI file. More... | |
| string | prefixFilenameOut |
| Prefix for the name of the file to which the graph must be written. More... | |
| string | filename_graph_in |
| String containing the name of a GFA file to read using CompactedDBG<U, G>::read. More... | |
Most members of this structure are parameters for CompactedDBG<U, G>::build(), except for:
| CDBG_Build_opt::build |
Boolean indicating if the graph must be built.
This parameter is not used by any function of CompactedDBG<U, G> but is used by the Bifrost CLI. Default is false.
| CDBG_Build_opt::clipTips |
Clip short tips (length < 2k) of the graph (not used by CompactedDBG<U, G>::build).
Default is false.
| CDBG_Build_opt::deleteIsolated |
Remove short isolated unitigs (length < 2k) of the graph (not used by CompactedDBG<U, G>::build).
Default is false.
| CDBG_Build_opt::filename_graph_in |
String containing the name of a GFA file to read using CompactedDBG<U, G>::read.
Default is empty string (no input file).
| CDBG_Build_opt::filename_ref_in |
Vector of strings, each string is the name of a FASTA/FASTQ/GFA file to use for the graph construction.
Each such file will NOT be filtered before construction such that all k-mers in those files will be used. Mandatory parameter.
| CDBG_Build_opt::filename_seq_in |
Vector of strings, each string is the name of a FASTA/FASTQ/GFA file to use for the graph construction.
Each such file will be filtered before construction such that k-mers with exactly one occurrence in those files will be discarded. Mandatory parameter.
| CDBG_Build_opt::g |
Length of g-mers, the minimizers, such that g < k (not used by CompactedDBG<U, G>::build).
Default is 23.
| CDBG_Build_opt::inFilenameBBF |
String containing the name of a Bloom filter file that is generated by CompactedDBG<U, G>::filter.
If empty, CompactedDBG<U, G>::filter is called. Otherwise, the Bloom filter is loaded from this file and CompactedDBG<U, G>::filter is not called. Note that you need such a Bloom filter even in reference mode. Default is empty string (no input file).
| CDBG_Build_opt::k |
Length of k-mers (not used by CompactedDBG<U, G>::build).
Default is 31.
| CDBG_Build_opt::nb_bits_kmers_bf |
Number of Bloom filter bits per k-mer occurring in the FASTA/FASTQ/GFA files of CDBG_Build_opt::filename_in.
Default is 14.
| CDBG_Build_opt::nb_threads |
Number of threads to use for building the graph.
Default is 1.
| CDBG_Build_opt::outFilenameBBF |
String containing the name of a Bloom filter file that will be generated by CompactedDBG<U, G>::filter.
If empty, the file is not created. Otherwise, the Bloom filter is written to this file. Default is empty string (no output file).
| CDBG_Build_opt::outputBFG |
Boolean indicating if the graph is written to a BFG/BFI file.
Default is false.
| CDBG_Build_opt::outputFASTA |
Boolean indicating if the graph is written to a FASTA file.
Default is false.
| CDBG_Build_opt::outputGFA |
Boolean indicating if the graph is written to a GFA file.
Default is true.
| CDBG_Build_opt::prefixFilenameOut |
Prefix for the name of the file to which the graph must be written.
Mandatory parameter.
| CDBG_Build_opt::update |
Boolean indicating if the graph must be updated.
This parameter is not used by any function of CompactedDBG<U, G> but is used by the Bifrost CLI. Default is false.
| CDBG_Build_opt::useMercyKmers |
Keep in the graph low coverage k-mers (cov=1) connecting tips of the graph.
Default is false.
| CDBG_Build_opt::verbose |
Print information messages during execution if true.
Default is false.
1.8.20