Very carefully ;) Usually by counting the lines, since there ought to be four lines per record.
Technically FASTQ files can have line wrapping, but this is strongly discouraged. To parse these the code has to track how long the sequence was in order to find the @ marker line and the expected data for the quality scores. It is historical accident that this file format became widely used, despite this and other drawbacks. See also our FASTQ paper https://dx.doi.org/10.1093%2Fnar%2Fgkp1137 Peter On Mon, Nov 28, 2016 at 5:51 PM, Sebastian Gregoricchio <sebastian.gregoricc...@gmail.com> wrote: > Dear all, > I am a student of molecular biology (master degree) and I am studying genome > assembly against a reference genome. > I have a, maybe stupid, question: if i have a quality raw in a fastq file > that starts for symbol @, how can samtools distinguish that raw from the > "description" one? > > Thanks for your attention > > Best regards, > Sebastian Gregoricchio > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > _______________________________________________ > Samtools-help mailing list > Samtools-help@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/samtools-help > ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
