Updated README with integrated large camel.

README.md

@@ -20,8 +20,7 @@ They come in two different implementations (their results may differ due to the
 Note that at this point only the implementations with hash table are optimized and that the Aho-Corasick automaton
 based versions of the algorithms are only experimental.
 
-The hashing based implementations of the default KmerCamel🐫 (`./kmercamel`) support $k$-mer with $k$ at most 31,
-whereas the larger KmerCamel🐫 (`./kmercamel-large`) supports $k$-mers with $k$ at most 63 (at the cost of slight slowdown).
+The hashing based implementations of KmerCamel🐫 support $k$-mer with $k$ at most 63,
 
 All algorithms can be used to either work in the unidirectional model or in the bidirectional model
 (i.e. treat $k$-mer and its reverse complement as the same; in this case either of them appears in the result).
@@ -62,8 +61,8 @@ on macOS.
 
 The program has the following arguments:
 
-- `-p path_to_fasta` - the path to fasta file. This is a required argument.
-- `-k value_of_k` - the size of one k-mer. This is a required argument.
+- `-p path_to_fasta` - the path to fasta file (can be `gzip`ed). This is a required argument.
+- `-k value_of_k` - the size of one k-mer (up to 63). This is a required argument.
 - `-a algorithm` - the algorithm which should be run. Either `global` or `globalAC` for Global Greedy, `local` or `localAC` for Local Greedy.
 The versions with AC use Aho-Corasick automaton. Default `global`.
 - `-o output_path` - the path to output file. If not specified, output is printed to stdout.
@@ -79,27 +78,18 @@ The output contains the resulting superstring - capital letters indicate that at
 For example:
 
 ```
-./kmercamel -p ./spneumoniae.fa -a local -k 12 -d 7 -c
+./kmercamel -p ./spneumoniae.fa -a local -k 31 -d 5 -c
 ```
 
-runs the Local Greedy in the bidirectional model on the streptococcus fasta file with `k=12` and `d=7`.
+runs the Local Greedy in the bidirectional model on the streptococcus fasta file with `k=31` and `d=5`.
 
 Alternatively, if your operating system supports it, you can run `./🐫` instead of `./kmercamel`.
 
-Currently, KmerCamel🐫 does not support gziped files as an input.
-A possible workaround is to use `gzcat` and process substitution.
-
-```
-./kmercamel -k 13 -p <(gzcat fasta_file.fa.gz)
-```
-
-Note: on some systems you might need to use the name `zcat` instead of `gzcat`.
-
 ### Mask optimization
 
 For mask optimization, run the subcommand `optimize` with the following arguments:
 
-- `p path_to_fasta` - the path to fasta file. This is a required argument.
+- `p path_to_fasta` - the path to fasta file (can be `gzip`ed). This is a required argument.
 - `k k_value` - the size of one k-mer. This is a required argument.
 - `a algorithm` - the algorithm for mask optimization. Either `ones` for maximizing the number of 1s, `runs` for minimizing the number of runs of 1s, `runsapprox` for approximately minimizing the number of runs of 1s, or `zeros` for maximizing the number of 0s. Default `ones`.
 - `o output_path` - the path to output file. If not specified, output is printed to stdout.
@@ -110,26 +100,11 @@ For mask optimization, run the subcommand `optimize` with the following argument
 For example:
 
 ```
-./kmercamel optimize -p ./global-spneumoniae.fa -k 12 -a runs -c
+./kmercamel optimize -p ./global-spneumoniae.fa -k 31 -a runs -c
 ```
 
 minimizes the number of runs of 1s in the mask of the superstring computed by Global Greedy in the bidirectional model on the streptococcus fasta file with `k=12`.
 
-Note: currently mask optimization cannot read gziped files, nor can the proccess substititution be used.
-
-### Large $k$-mers
-
-The default version of KmerCamel🐫 does not support $k > 31$. For those values, use the large KmerCamel🐫,
-which supports $k < 64$.
-
-For example:
-
-```
-./kmercamel-large -p ./spneumoniae.fa -a global -k 63 -c
-```
-
-Note: for smaller $k$ it is recommended to use default KmerCamel🐫 as it is faster.
-
 ### Turn off memory optimizations for Global
 
 In order to reduce the memory footprint of hash-table based Global Greedy,

src/main.cpp

@@ -16,22 +16,22 @@
 int Help() {
     std::cerr << "KmerCamel version " << VERSION << std::endl;
     std::cerr << "Accepted arguments:" << std::endl;
-    std::cerr << "  -p path_to_fasta - required; valid path to fasta file" << std::endl;
-    std::cerr << "  -k k_value       - required; integer value for k" << std::endl;
+    std::cerr << "  -p path_to_fasta - required; valid path to fasta file (can be gziped)" << std::endl;
+    std::cerr << "  -k k_value       - required; integer value for k (up to 63)" << std::endl;
     std::cerr << "  -a algorithm     - the algorithm to be run [global (default), globalAC, local, localAC, streaming]" << std::endl;
     std::cerr << "  -o output_path   - if not specified, the output is printed to stdout" << std::endl;
     std::cerr << "  -d d_value       - integer value for d_max; default 5" << std::endl;
     std::cerr << "  -c               - treat k-mer and its reverse complement as equal" << std::endl;
     std::cerr << "  -m               - turn off the memory optimizations for global" << std::endl;
     std::cerr << "  -h               - print help" << std::endl;
     std::cerr << "  -v               - print version" << std::endl;
-    std::cerr << "Example usage:       ./kmercamel -p path_to_fasta -k 13 -d 5 -a local" << std::endl;
+    std::cerr << "Example usage:       ./kmercamel -p path_to_fasta -k 31 -d 5 -a local -c" << std::endl;
     std::cerr << "Possible algorithms: global globalAC local localAC streaming" << std::endl;
     std::cerr << std::endl;
     std::cerr << "For optimization of masks use `kmercamel optimize`."  << std::endl;
     std::cerr << "Accepted arguments:" << std::endl;
-    std::cerr << "  -p path_to_fasta - required; valid path to fasta file" << std::endl;
-    std::cerr << "  -k k_value       - required; integer value for k" << std::endl;
+    std::cerr << "  -p path_to_fasta - required; valid path to fasta file (can be gziped)" << std::endl;
+    std::cerr << "  -k k_value       - required; integer value for k (up to 63)" << std::endl;
     std::cerr << "  -a algorithm     - the algorithm to be run [ones (default), runs, runsapprox, zeros]" << std::endl;
     std::cerr << "  -o output_path   - if not specified, the output is printed to stdout" << std::endl;
     std::cerr << "  -c               - treat k-mer and its reverse complement as equal" << std::endl;
@@ -184,7 +184,7 @@ int main(int argc, char **argv) {
         std::cerr << "d must be non-negative." << std::endl;
         return Help();
     } else if (k > MAX_K && (algorithm == "local" || algorithm == "global")) {
-        std::cerr << "k > " << MAX_K << " not supported for the algorithm '" + algorithm + "'. Use the 128bit version of KmerCamel or the AC version of the algorithm instead." << std::endl;
+        std::cerr << "k > " << MAX_K << " not supported for the algorithm '" + algorithm + "'. Use the  AC version of the algorithm instead." << std::endl;
         return Help();
     } else if (d_set && (algorithm == "globalAC" || algorithm == "global" || algorithm == "streaming")) {
         std::cerr << "Unsupported argument d for algorithm '" + algorithm + "'." << std::endl;