Michael Macias

I added a simple pileup iterator in acd49bb625bcc23194590006f28a76064923001f that currently just calculates column depths. It piles records over an adaptive window on the reference sequence and is optimized for low...

noodles 0.61.0 / noodles-sam 0.50.0 no longer models optional header fields. Optional fields are now placed as strings in the other fields map ([`Map::other_fields`](https://docs.rs/noodles/0.61.0/noodles/sam/header/record/value/struct.Map.html#method.other_fields)). Here's an example of a header...

The short answer is no; this is currently not supported. Sorry for the delayed response. I originally thought this was doable with the current API and wanted to give an...

With respect to bgzip-compressed formats, you can compose a multithreaded decoder with a format reader. E.g., ```rust let worker_count = thread::available_parallelism().unwrap_or(NonZeroUsize::MIN); let file = File::open(src)?; let decoder = bgzf::MultithreadedReader::with_worker_count(worker_count, file);...

(For reference, this issue was posted in regard to noodles 0.31.1/noodles-bam 0.25.1). noodles 0.35.0/noodles-bam 0.29.0 introduced a change where `Reader::read_header` reads the SAM header and handles the binary reference sequences....

noodles tends to do more record validation and tries to ensure data is spec compliant. However, in your flamegraphs, it seems the DEFLATE implementation htslib linked to is using SIMD...

If you don't need owned records, you can reuse the record buffer. ```rust let mut record = sam::alignment::Record::default(); while bam_reader.read_record(&header, &mut record)? != 0 { // ... } ``` When...

noodles 0.61.0 now allows alignment format records to read and written, but I'm not sure if this will help in a passthrough case like in your tests. Feel free to...

The `tabix_write` example can indeed be applied to create a tabix index for VFC on the fly. [`noodles-vcf/examples/vcf_index.rs`](https://github.com/zaeleus/noodles/blob/bd1098699a5a0ed87dab0c3e6c496ae13faa358d/noodles-vcf/examples/vcf_index.rs) shows how to create one from a file and what record information...

> I am trying to do this with the following code, but the index does not seem to be correct. what do I miss? Thanks for the example. The output...