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This should be relatively easy (except for autodetection). Basically, copy the FASTA parsing code and add an additional step to parse the "sequence" from a bitstring (that contains a mask too) into a Vec of nucleotides and add a impl<'a> From<TwoBit<'a>> for SeqRecord<'a>. Note we can't use our existing bitkmer code because 2bit decodes 0 to 3 as GACT instead of ACGT as we do.
Autodetection can probably rely upon the first line(s) matching something like >...:\d+-\d+\r?\nP? We probably don't want this as an actual regex though. There's an actual magic header sequence in the details from UCSC.
This should be relatively easy (except for autodetection). Basically, copy the FASTA parsing code and add an additional step to parse the "sequence" from a bitstring (that contains a mask too) into a Vec of nucleotides and add a
impl<'a> From<TwoBit<'a>> for SeqRecord<'a>
. Note we can't use our existing bitkmer code because 2bit decodes 0 to 3 as GACT instead of ACGT as we do.Format details: http://jcomeau.freeshell.org/www/genome/2bitformat.html(this seems to be a format someone just made up and doesn't match the output offaToTwoBit
at all)Format details: http://genome.ucsc.edu/FAQ/FAQformat.html#format7
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