This structure inherits from CDBG_Build_opt and introduces only a few new members which are color-related. More...
Inherits CDBG_Build_opt.
Data Fields | |
| string | filename_colors_in |
| String containing the name of a Bifrost color file to read in ColoredCDBG<U>::read(). More... | |
| bool | outputColors |
| Boolean indicating if the graph should be colored or not. More... | |
 Data Fields inherited from CDBG_Build_opt | |
| 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... | |
Detailed Description
This structure inherits from CDBG_Build_opt and introduces only a few new members which are color-related.
See the documentation of CDBG_Build_opt for the inherited members. An example of using such a structure is shown in src/Bifrost.cpp.
Field Documentation
◆ filename_colors_in
| CCDBG_Build_opt::filename_colors_in |
String containing the name of a Bifrost color file to read in ColoredCDBG<U>::read().
Default is an empty string (no file specified).
◆ outputColors
| CCDBG_Build_opt::outputColors |
Boolean indicating if the graph should be colored or not.
This member is not used by any function of ColoredCDBG or CompactedDBG<U, T>. It is used by the Bifrost CLI. Default is true.
The documentation for this struct was generated from the following file:
- src/ColoredCDBG.hpp
