hts-specs
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samtools
Specifications of SAM/BAM and related high-throughput sequencing file formats
The SAM specifications does not specify the encoding of the header. S1 states `Unless explicitly specified elsewhere, all fields are encoded using 7-bit US-ASCII` S1 states that alignment lines have...
This is a request to add ELEMENT to the controlled vocabulary for the PL header tag
As proposed in https://github.com/samtools/hts-specs/issues/581#issuecomment-889479244, this PR defines an optional HTTP 426 response that servers can use to tell clients that they should be using htsget: Clients attempting to access a...
Briefly mentioned on https://github.com/igvteam/igv/pull/850#issuecomment-707727642, discussed on some of the htsget meetings, GA4GH's Slack `#fasp` channel (as of today) and possibly on other issues in this repo (please refer to them...
Hello, We would like to add the Ultima Genomics platform to the list of allowed platforms for the PL tag in SAM. Reference [here](https://www.biorxiv.org/content/10.1101/2022.05.29.493900v1). I would appreciate an advice on...
This is a placeholder PR request for the version 2.0.0 bump in refget and a place to accumulate discussion around the changes. To note the major changes are: - Integration...
The `MM` tag describes the modification string relative to the sequencing read as generated by the instrument. For instance, consider this read, where only the 3rd C is modified: ```...
For duplex sequencing technology, we can identify the _strand_ (top or bottom) from which the read was derived relative to the duplex source molecule. This _convention_ or _recommendation_ would allow...
A few somewhat nitty questions on the CRAM spec (section 10.6, Read Features) based on some code cleanup I'm doing in htsjdk. I can make a spec PR based on...
