Comments (8)
Yes, it is possible. I updated the doc: https://github.com/medvedevgroup/TwoPaCo#k-mer-size
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In the next release I will make it a parameter for running CMake such that the user will be allowed to specify maximum K directly without editing the code.
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That would be the perfect solution.
Also do you think it would be possible for graphdump to have a regular fasta output option ?
It would be really convenient.
Excellent piece of work by the way !
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Thank you. You mean FASTA file with compressed paths? If so, it is not hard to do, I will add in the next release.
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Yes it would be great. Thank you for your answers
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Added in 0.9.2.
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I just tested it
graphdump -f fasta test.bin -s seq51.fa
PARSE ERROR: Argument: -f (--format)
Value 'fasta' does not meet constraint: seq|group|dot|gfa1|gfa2
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That is interesting. Are you sure you pulled the latest revision? What is the output of --help, does fasta appear in the formats list?
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Related Issues (20)
- Question about GFA format HOT 3
- Redundant k-mer in contigs HOT 8
- Problem building TwoPaCo in BioLinux HOT 4
- Linking twopaco to TBB fails HOT 4
- Replace deprecated auto_ptr
- MAC OS compilation failed HOT 3
- target not created
- Undefined symbol HOT 2
- undefined reference to `__cxa_init_primary_exception@CXXABI_1.3.11' HOT 3
- `twopaco` and `graphdump` functions not found HOT 1
- typo?
- Creation of many temporary files (of considerable size) when there are many references. HOT 4
- meaning of software name HOT 3
- Confused about + and - stranded nodes in GFA HOT 5
- Is it stuck when there is really low CPU usage? HOT 3
- Cause of input corrupted error? HOT 1
- Fails to build with TBB 2021.5.0 HOT 4
- Present API for pufferfish HOT 1
- Fail to install TwoPaCo HOT 1
- Fix error handling
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