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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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