diff options
author | Daniel Baumann <daniel.baumann@progress-linux.org> | 2024-04-28 12:36:04 +0000 |
---|---|---|
committer | Daniel Baumann <daniel.baumann@progress-linux.org> | 2024-04-28 12:36:04 +0000 |
commit | b09c6d56832eb1718c07d74abf3bc6ae3fe4e030 (patch) | |
tree | d2caec2610d4ea887803ec9e9c3cd77136c448ba /dependencies/pkg/mod/golang.org/x/exp@v0.0.0-20220613132600-b0d781184e0d/shootout/reverse-complement.go | |
parent | Initial commit. (diff) | |
download | icingadb-upstream.tar.xz icingadb-upstream.zip |
Adding upstream version 1.1.0.upstream/1.1.0upstream
Signed-off-by: Daniel Baumann <daniel.baumann@progress-linux.org>
Diffstat (limited to 'dependencies/pkg/mod/golang.org/x/exp@v0.0.0-20220613132600-b0d781184e0d/shootout/reverse-complement.go')
-rw-r--r-- | dependencies/pkg/mod/golang.org/x/exp@v0.0.0-20220613132600-b0d781184e0d/shootout/reverse-complement.go | 108 |
1 files changed, 108 insertions, 0 deletions
diff --git a/dependencies/pkg/mod/golang.org/x/exp@v0.0.0-20220613132600-b0d781184e0d/shootout/reverse-complement.go b/dependencies/pkg/mod/golang.org/x/exp@v0.0.0-20220613132600-b0d781184e0d/shootout/reverse-complement.go new file mode 100644 index 0000000..11b59d2 --- /dev/null +++ b/dependencies/pkg/mod/golang.org/x/exp@v0.0.0-20220613132600-b0d781184e0d/shootout/reverse-complement.go @@ -0,0 +1,108 @@ +//go:build ignore +// +build ignore + +/* +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + * Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. + + * Redistributions in binary form must reproduce the above copyright + notice, this list of conditions and the following disclaimer in the + documentation and/or other materials provided with the distribution. + + * Neither the name of "The Computer Language Benchmarks Game" nor the + name of "The Computer Language Shootout Benchmarks" nor the names of + its contributors may be used to endorse or promote products derived + from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE +LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR +CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF +SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS +INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN +CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) +ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE +POSSIBILITY OF SUCH DAMAGE. +*/ + +/* The Computer Language Benchmarks Game + * http://shootout.alioth.debian.org/ + * + * contributed by The Go Authors. + */ + +package main + +import ( + "bufio" + "os" +) + +const lineSize = 60 + +var complement = [256]uint8{ + 'A': 'T', 'a': 'T', + 'C': 'G', 'c': 'G', + 'G': 'C', 'g': 'C', + 'T': 'A', 't': 'A', + 'U': 'A', 'u': 'A', + 'M': 'K', 'm': 'K', + 'R': 'Y', 'r': 'Y', + 'W': 'W', 'w': 'W', + 'S': 'S', 's': 'S', + 'Y': 'R', 'y': 'R', + 'K': 'M', 'k': 'M', + 'V': 'B', 'v': 'B', + 'H': 'D', 'h': 'D', + 'D': 'H', 'd': 'H', + 'B': 'V', 'b': 'V', + 'N': 'N', 'n': 'N', +} + +func main() { + in := bufio.NewReader(os.Stdin) + buf := make([]byte, 1024*1024) + line, err := in.ReadSlice('\n') + for err == nil { + os.Stdout.Write(line) + + // Accumulate reversed complement in buf[w:] + nchar := 0 + w := len(buf) + for { + line, err = in.ReadSlice('\n') + if err != nil || line[0] == '>' { + break + } + line = line[0 : len(line)-1] + nchar += len(line) + if len(line)+nchar/60+128 >= w { + nbuf := make([]byte, len(buf)*5) + copy(nbuf[len(nbuf)-len(buf):], buf) + w += len(nbuf) - len(buf) + buf = nbuf + } + + // This loop is the bottleneck. + for _, c := range line { + w-- + buf[w] = complement[c] + } + } + + // Copy down to beginning of buffer, inserting newlines. + // The loop left room for the newlines and 128 bytes of padding. + i := 0 + for j := w; j < len(buf); j += 60 { + n := copy(buf[i:i+60], buf[j:]) + buf[i+n] = '\n' + i += n + 1 + } + os.Stdout.Write(buf[0:i]) + } +} |