-package main
+// Copyright (C) The Lightning Authors. All rights reserved.
+//
+// SPDX-License-Identifier: AGPL-3.0
+
+package lightning
import (
"bufio"
- "bytes"
"fmt"
"io"
)
return taglib.setTags(seqs)
}
-func (taglib *tagLibrary) FindAll(buf []byte, fn func(id tagID, pos, taglen int)) {
+func (taglib *tagLibrary) FindAll(in *bufio.Reader, passthrough io.Writer, fn func(id tagID, pos, taglen int)) error {
+ var window = make([]byte, 0, taglib.keylen*1000)
var key tagmapKey
- valid := 0 // if valid < taglib.keylen, key has "no data" zeroes that are otherwise indistinguishable from "A"
- for i, base := range buf {
+ for offset := 0; ; {
+ base, err := in.ReadByte()
+ if err == io.EOF {
+ return nil
+ } else if err != nil {
+ return err
+ } else if base == '\r' || base == '\n' {
+ if buf, err := in.Peek(1); err == nil && len(buf) > 0 && buf[0] == '>' {
+ return nil
+ } else if err == io.EOF {
+ return nil
+ }
+ continue
+ } else if base == '>' || base == ' ' {
+ return fmt.Errorf("unexpected char %q at offset %d in fasta data", base, offset)
+ }
+
+ if passthrough != nil {
+ if base >= 'A' && base <= 'Z' {
+ // lowercase for passthrough
+ base += 'a' - 'A'
+ }
+ _, err = passthrough.Write([]byte{base})
+ if err != nil {
+ return err
+ }
+ }
+ offset++
if !isbase[int(base)] {
- valid = 0
+ // 'N' or various other chars meaning exact
+ // base not known
+ window = window[:0]
continue
- } else {
- valid++
+ }
+ window = append(window, base)
+ if len(window) == cap(window) {
+ copy(window, window[len(window)-taglib.keylen:])
+ window = window[:taglib.keylen]
}
key = ((key << 2) | twobit[int(base)]) & taglib.keymask
- if valid < taglib.keylen {
+
+ if len(window) < taglib.keylen {
continue
} else if taginfo, ok := taglib.tagmap[key]; !ok {
continue
- } else if tagstart := i - taglib.keylen + 1; len(taginfo.tagseq) > taglib.keylen && (len(buf) < i+len(taginfo.tagseq) || !bytes.Equal(taginfo.tagseq, buf[i:i+len(taginfo.tagseq)])) {
- // key portion matches, but not the entire tag
- continue
+ } else if len(taginfo.tagseq) != taglib.keylen {
+ return fmt.Errorf("assertion failed: len(%q) != keylen %d", taginfo.tagseq, taglib.keylen)
} else {
- fn(taginfo.id, tagstart, len(taginfo.tagseq))
- valid = 0 // don't try to match overlapping tags
+ fn(taginfo.id, offset-taglib.keylen, len(taginfo.tagseq))
+ window = window[:0] // don't try to match overlapping tags
}
}
+ return nil
}
func (taglib *tagLibrary) Len() int {
return len(taglib.tagmap)
}
+func (taglib *tagLibrary) TagLen() int {
+ return taglib.keylen
+}
+
var (
twobit = func() []tagmapKey {
r := make([]tagmapKey, 256)
}
return nil
}
+
+func (taglib *tagLibrary) Tags() [][]byte {
+ out := make([][]byte, len(taglib.tagmap))
+ untwobit := []byte{'a', 'c', 'g', 't'}
+ for key, info := range taglib.tagmap {
+ seq := make([]byte, taglib.keylen)
+ for i := len(seq) - 1; i >= 0; i-- {
+ seq[i] = untwobit[int(key)&3]
+ key = key >> 2
+ }
+ out[int(info.id)] = seq
+ }
+ return out
+}