rm nasty bug in weird fasta processing

cobilab · Oct 18, 2023 · 1f09c60 · 1f09c60
1 parent af29e1b
commit 1f09c60
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Showing 3 changed files with 7 additions and 34 deletions.
diff --git a/bin/gto b/bin/gto
diff --git a/bin/gto_fasta_rand_extra_chars b/bin/gto_fasta_rand_extra_chars
diff --git a/src/FastaRandExtraChars.c b/src/FastaRandExtraChars.c
@@ -64,46 +64,19 @@ int main(int argc, char *argv[])
 
  Buffer = CreateBuffer(BUF_SIZE);
 
+ uint8_t header = 0, sym;
  while((streamSize = fread(Buffer->buf, 1, Buffer->size, stdin)))
  {
  for(index = 0 ; index < streamSize ; ++index)
  {
- value = Buffer->buf[index];
- switch(line)
- {
- case 0: 
- if(value == '\n')
- { 
- line = 1;
- putchar(value);
- break;
- }
+ sym = Buffer->buf[index];
 
- if(position == 0 && value != '>')
- {
- RandIfExtra(value, bases);
- line = 1;
- break;
- }
+ if(sym == '>'){ header = 1; putchar(sym); continue; }
+ if(sym == '\n' && header == 1){ header = 0; putchar(sym); continue; }
+ if(sym == '\n'){ putchar(sym); continue; }
+ if(header == 1){ putchar(sym); continue; }
 
- if(position++ == 0 && value == '>')
- {
- putchar(value);
- break;
- }
- putchar(value);
- break;
- case 1: 
- if(value == '\n')
- { 
- line = 0; 
- position = 0;
- putchar(value);
- break; 
- }
- RandIfExtra(value, bases);
- break;
- } 
+ RandIfExtra(sym, bases);
  }
  }