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Fix for 2 bugs in the fastq reader: #497

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@wdu wdu commented Jun 15, 2023

  • \r\n handling may cause reading a byte past end of buffer, parser fails
  • checking end-of-file condition can only be reliably done after a call to getLine() returns NULL. One particular case is that some gzip files contain empty gzip blocks at the end of the file, which can´t be predicted by the current eof() code Tested with files provided in issue ERROR: Read name line should start with '@' #491.

This reverts commit 0ee1b3b, "fix a regression bug of FASTQ reader"

- \r\n handling may cause reading a byte past end of buffer, parser fails
- checking end-of-file condition can only be reliably done
  after a call to getLine() returns NULL. One particular case
  is that some gzip files contain empty gzip blocks at the end
  of the file, which can´t be predicted by the current eof() code
  Tested with files provided in issue OpenGene#491.

This reverts commit 0ee1b3b, "fix a regression bug of FASTQ reader"
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