v0.8.0

CHANGES.md

@@ -1,6 +1,6 @@
 - v0.8.0
     - `unikmer`:
-         - do not ignore files from cli arugments when given flag `-i/--infile-list`.
+         - new option `-i/--infile-list`, if given, files in the list file are appended to files from cli arguments.
          - improve performance of binary file reading and writing.
     - `unikmer sort/split/merge`: safer forcing deletion of existed outdir, and better log.
     - `unikmer split`: performance improvement for single sorted input file.

README.md

@@ -1,7 +1,7 @@
 # unikmer
 
 unikmer (unique-kmer) is a golang package and a command-line toolkit for
-manipulating unique small [k-mers](https://en.wikipedia.org/wiki/K-mer) (k <= 32)
+manipulating small [k-mers](https://en.wikipedia.org/wiki/K-mer) (k <= 32)
 without frequency information.
 
 K-mers (k <= 32) are encoded into `uint64`, stored in builtin `map` of golang in RAM,
@@ -29,7 +29,7 @@ and serialized in binary format.
 [![GoDoc](https://godoc.org/github.com/shenwei356/unikmer?status.svg)](https://godoc.org/github.com/shenwei356/unikmer)
 [![Go Report Card](https://goreportcard.com/badge/github.com/shenwei356/unikmer)](https://goreportcard.com/report/github.com/shenwei356/unikmer)
 
-The unikmer package provides basic manipulations of unique small K-mers 
+The unikmer package provides basic manipulations of small K-mers
 (without frequency information) and also provides serialization methods.
 
 ### Installation
@@ -56,7 +56,7 @@ CPU: AMD Ryzen 7 2700X Eight-Core Processor, 3.7 GHz
 ## The toolkit
 
 `unikmer` is a command-line toolkit providing functions including counting,
-format convertion, set operations and searching on unique small k-mers (k <= 32)
+format convertion, set operations and searching on small k-mers (k <= 32)
 without frequency information.
 
 ### Installation

unikmer/cmd/diff.go

@@ -277,6 +277,10 @@ Tips:
 		}
 		// -----------------------------------------------------------------------
 
+		if threads > len(files)-1 {
+			threads = len(files) - 1
+		}
+
 		done := make(chan int)
 
 		toStop := make(chan int, threads+2)
@@ -338,13 +342,11 @@ Tips:
 		}
 
 		// -----------------------------------------------------------------------
+		log.Infof("%d workers in position", threads)
+
 		hasDiff := true
 		var wgWorkers sync.WaitGroup
-		nWorkers := opt.NumCPUs
-		if len(files) == 2 { // only need one worker
-			nWorkers = 1
-		}
-		for i := 0; i < nWorkers; i++ { // workers
+		for i := 0; i < threads; i++ { // workers
 			wgWorkers.Add(1)
 
 			go func(i int) {

unikmer/cmd/root.go

@@ -36,7 +36,7 @@ var RootCmd = &cobra.Command{
 	Long: fmt.Sprintf(`unikmer - Unique-Kmer Toolkit
 
 A command-line toolkit providing functions including counting, format
-convertion, set operations and searching on unique small k-mers (k <= 32)
+convertion, set operations and searching on small k-mers (k <= 32)
 without frequency information.
 
 K-mers (k <= 32) are encoded into 'uint64', stored in builtin 'map' of golang