Add support for (1) interleaved reads & (2) reading from pipes #213
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luispedro
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Cool, this would be nice to have! I’ll review the code as soon as I can. I’m happy you were able to get rid of some code duplication as well. Just a note: I usually prefer smaller, self-contained commits (max. one refactoring, bug fix, added feature per commit), but it’s ok now. (No need to change anything now.) |
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I also generally prefer small contained commits, but these were hard to do such that each individual commit is still correct and passing all the tests, which I also try to do (the PR does contain 3 separate commits, which makes it seem bigger than a single one). I do have another improvement on my side, which I was waiting for this to be merged, but that is a purely micro-optimization commit to make things just a tiny bit faster. |
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Otherwise, the close function gets called multiple times
This also adds support for mixing paired and single end reads in the input mix It requires more complexity in reading in records, but it results in overall simpler code
This enables inputs to be piped into strobealign It requires keeping in memory some of the data that has been read in so that it can be processed twice (once for estimating the read length and then the actual read alignment)
luispedro
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Okay, I resolved the conflicts and cleaned up the history now. The design is cleaner too: there is a single |
CHANGES.md
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| @@ -35,6 +35,8 @@ | |||
| * Suppress some logging output by default. | |||
| * Added option `-v` for showing full logging output. | |||
| * Issue #206: Added option `-U` for suppressing output of unaligned reads. Thanks @sjaenick. | |||
| * Add support for interleaved reads | |||
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Feel free to add a "Thanks @luispedro" on these two bullet points.
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Thank you for this PR @luispedro ! Yes @marcelm, I am happy to merge this.
Yes, I think its time to properly add credits to contributors in this repo (and elsewhere). |
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Thanks again! |
I was exploring adding support for strobealign in NGLess and it would enable some optimizations if (1) it supports the interleaved reads format, including mixing paired and single-end reads and (2) reads can be piped in.
Adding support for the former is actually quite easy and I feel the result is slightly cleaner (less repeated code)
Adding support for piping in reads is a bit more complex because of the read length estimation. But the complexity is all hidden inside the InputBuffer/RewindableFile classes.