Check FASTQ fields 1 and 3 #18
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According to the spec, field 1 must begin with `@` and field 3 must begin with `+`. Checking for these helps prevent users from accidentally deconvoluting files that have been corrupted or improperly concatenated.
tmgreen
reviewed
Apr 27, 2023
| if (line3 == null) { | ||
| throw InvalidFileException(file, "File contains an incomplete FASTQ read") | ||
| } else Read(line0, line1) | ||
| if (line0.charAt(0) != '@') { throw InvalidFileException(file, "Corrupt or incorrect FASTQ") } |
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very minor suggestion but helpful nonetheless: maybe you could augment these msgs to say, e.g. "no '@' prefix in line 1" or something.
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🦅 🐦 |
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According to the spec, field 1 must begin with
@and field 3 mustbegin with
+. Checking for these helps prevent users from accidentallydeconvoluting files that have been corrupted or improperly concatenated.