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Provide more informative error message when encountering unexpected n… #689

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cinquin
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@cinquin cinquin commented Apr 22, 2018

…ewline character in SAM header.

@daviesrob
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This could print lots of lines if the problem happens at the start of a long header. There's also no way of limiting the output if the header doesn't include a terminating NUL character, which could be a security problem.

It would be best to keep track of the start of the last line so that the dump always begins at a sensible place. Then use memchr() to find out where the current line ends and use an output format of the form "%.*s", len, last_start to restrict the amount of data that gets printed. Or even better might be an extra function that prints a few lines of header with some extra checks to ensure that the output characters are actually printable, as outputting binary nonsense is generally not a good idea.

@jkbonfield
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It's also incorrect to say "unexpected newline" because this error will be triggered on a header that has zero newlines (and also doesn't start with an @).

Not that we can (legally) create such things, but the whole point of this is to spot illegal / corrupted data.

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