Change description

Author: elarielcl

README.md

@@ -23,7 +23,7 @@ Key parameters:
 - `-a` Output file name. Format .gam or .json.
 
 Parameters related to colinear chaining:
-- `--speed <int>` Use 2 or 3 (or larger values) if you want GraphChainer to be faster, but slightly less accurate (default 1).
+- `--speed <double>` Speed-up factor (default 1). Use >1 (<1, >0) for faster (slower), but less (more) accurate alignments. It increases (decreases) the sampling rate of fragments.
 - `--colinear-split-len <int>` The length of the fragments in which the long read is split to create anchors (default 35).
 - `--colinear-split-gap <int>` The distance between consecutive fragments (default 35). If `--speed` is set, then always `--colinear-split-gap = ceil(--speed * --colinear-split-len`).
 - `--colinear-gap <int>` When converting an optimal chain of anchors into an alignment path, split the path if the distance in the graph between consecutive anchors is greater than this value (default 10000).

src/AlignerMain.cpp

@@ -40,7 +40,7 @@ int main(int argc, char** argv)
 	;
 	boost::program_options::options_description clcparams("Colinear chaining parameters");
 	clcparams.add_options()
-		("speed", boost::program_options::value<long long>(), "Speed-up factor [default 1]. Use >1 (<1) for faster (slower), but less (more) accurate alignments. It increases (decreases) the sampling rate of fragments.")
+		("speed", boost::program_options::value<long long>(), "Speed-up factor [default 1]. Use >1 (<1, >0) for faster (slower), but less (more) accurate alignments. It increases (decreases) the sampling rate of fragments.")
 		("colinear-split-len", boost::program_options::value<long long>(), "The length of the fragments in which the long read is split to create anchors. [default 35]")
 		("colinear-split-gap", boost::program_options::value<long long>(), "The distance between consecutive fragments [default 35]. If --speed is set, then always --colinear-split-gap = ceil(--speed * --colinear-split-len).")
 		("colinear-gap", boost::program_options::value<long long>(), "When converting an optimal chain of anchors into an alignment path, split the path if the distance between consecutive anchors is greater than this value [default 10000].")