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@ahl27 ahl27 commented Dec 20, 2024

writeXStringSet and writeQualityScaledXStringSet previously restricted inputs based on the width of sequences due to limitations in the internal I/O buffer. Now arbitrarily long sequences can be written, resulting in support for width > 200003 for XStringSet objects and also support for writing QualityScaledXStringSet objects with sequences longer than 200kbp.

More specific changes:

  • writeXStringSet now supports any integer value for width
  • writeXStringSet called with zero or negative values for width will now using unbounded width (i.e., each sequence written on a single line)
  • writeQualityScaledXStringSet now functions for sequences of arbitrary length, fixing Issue 177 (Error writing long reads with writeQualityScaledXStringSet #117)
  • Unit test cases added to cover new functionality. Could consider adding more tests to cover other SolexaQuality and IlluminaQuality, as well as verifying that the output widths are the correct number of characters.

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