Add general support for parsing .gz files

[karel-brinda]

It's ok but should be documented how to use, can be solved by process substitution:

./kmercamel -k 13 -p <(gzcat node.fa.gz)

[karel-brinda]

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

[OndrejSladky]

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.

[OndrejSladky]

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