Closed karel-brinda closed 1 week ago
Btw. if kseq is used for parsing fasta files, this imho supports gzip, so don't understand the error messages:
$ ./kmercamel -k 13 -p node.fa.gz
Path 'node.fa.gz' contains no k-mers.
KmerCamel v0.2
Accepted arguments:
-p path_to_fasta - required; valid path to fasta file
-k k_value - required; integer value for k
-a algorithm - the algorithm to be run [global (default), globalAC, local, localAC, streaming]
-o output_path - if not specified, the output is printed to stdout
-d d_value - integer value for d_max; default 5
-c - treat k-mer and its reverse complement as equal
-h - print help
Example usage: ./kmers -p path_to_fasta -k 13 -d 5 -a global
Possible algorithms: global globalAC local localAC streaming
Btw. if kseq is used for parsing fasta files, this imho supports gzip, so don't understand the error messages:
$ ./kmercamel -k 13 -p node.fa.gz Path 'node.fa.gz' contains no k-mers. KmerCamel v0.2 Accepted arguments: -p path_to_fasta - required; valid path to fasta file -k k_value - required; integer value for k -a algorithm - the algorithm to be run [global (default), globalAC, local, localAC, streaming] -o output_path - if not specified, the output is printed to stdout -d d_value - integer value for d_max; default 5 -c - treat k-mer and its reverse complement as equal -h - print help Example usage: ./kmers -p path_to_fasta -k 13 -d 5 -a global Possible algorithms: global globalAC local localAC streaming
At this point, global does not use kseq as I found it easier to implement it efficiently without kseq than try to find an usage of kseq that won't consume more memory than my current approach.
It's ok but should be documented how to use, can be solved by process substitution:
./kmercamel -k 13 -p <(gzcat node.fa.gz)
Added to README
It's ok but should be documented how to use, can be solved by process substitution: