feat: allow parsing single ended RA files #247
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src/read_pair_iter.rs
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| @@ -352,6 +382,7 @@ impl ReadPairIter { | |||
| if self.buffer.remaining_mut() < 512 { | |||
| self.buffer = BytesMut::with_capacity(BUF_SIZE) | |||
| } | |||
| let is_single_ended = self.is_single_ended()?; | |||
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This function is inside the "inner loop" of FASTQ processing, so you can't be re-running the fairly heavy-weight is_single_ended function here -- it's too slow because it's opening files and parsing reads.
I thinkis_single_ended should be a pre-computed flag that is set when you construct the ReadPairIter.
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Fixed. This had made the iterations 100x slower on testing (DETECT_CHEMISTRY that usually takes <5 min had run overnight for something like 8hours when I was testing).
src/read_pair_iter.rs
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| @@ -322,6 +322,36 @@ impl ReadPairIter { | |||
| }) | |||
| } | |||
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| pub fn is_single_ended(&self) -> Result<bool, FastqError> { | |||
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This should return the value of a flag stored in the struct. THere should probably be a non-public method that computes this once at the time you create the ReadPairIter
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