Michael Macias
Michael Macias
[`Array#map`](https://github.com/ruby/ruby/blob/ruby_1_6/array.c#L1722) was introduced in Ruby 1.6. This was likely because map is [a more common term](http://en.wikipedia.org/wiki/Map_%28higher-order_function%29#Language_comparison) than collect. It would be appropriate to add an `NArray#map` alias for `NArray#collect` to...
Regarding [§ 1.6.1.8 "INFO"](https://github.com/samtools/hts-specs/blob/8a18f34dc88ba7a99bc94dd333bc047b63548367/VCFv4.3.tex#L333-L390), the case where a record INFO field value is missing/unknown seems to be undefined, e.g.,`AF=.`. Is this a valid INFO field, or is it supposed to...
This is a tracking issue for CRAM 3.1 write support. The CRAM 3.1 format is still [a draft](https://github.com/samtools/hts-specs/pull/433), but [there is interest](https://github.com/zaeleus/noodles/issues/78#issuecomment-1220668241) in having noodles-cram demonstrate a second implementation. The...
VCF 4.4 allows setting the first phasing indicitor in a genotype (GT) value, i.e., > The first phasing indicator may be omitted and is implicitly defined as / if any...
In VCF 4.3, the concept of structured and unstructured records was introduced, which requires all structured records to include an ID field (§ 1.4 "[Meta-information lines](https://samtools.github.io/hts-specs/VCFv4.3.pdf#subsection.1.4)" (2022-11-27)). Was this a...
This is in regard to _Sequence Alignment/Map Optional Fields Specification_ (2022-08-17). The base modifications (`MM`) field allows modifications to be either short codes or an ChEBI ID. Short codes are...
In [`test/vcf/4.3/passed/passed_meta_contig.vcf`](https://github.com/samtools/hts-specs/blob/7554e7c7cddacc92e2e467d6f1e0692d626752a0/test/vcf/4.3/passed/passed_meta_contig.vcf), there are two `contig` header records with the same ID. ``` ##contig= ##contig= ``` As per § 1.4 "[Meta-information lines](https://samtools.github.io/hts-specs/VCFv4.3.pdf#subsection.1.4)" (2022-11-27): > All structured lines require an ID...
VCF 4.4 (specifically 008387af8ae39912d7d7a1b03fbd73e26faa2f3f) introduces the new Number value `P` in [§ 1.6.2 "Genotype fields"](https://samtools.github.io/hts-specs/VCFv4.4.pdf#subsubsection.1.6.2) (2023-01-27). Number values are described in [§ 1.4.2 "Information field format"](https://samtools.github.io/hts-specs/VCFv4.4.pdf#subsubsection.1.4.2) but is missing `P`.
As suggested by @jkbonfield in https://github.com/samtools/hts-specs/issues/715#issuecomment-1508097708: > as an aside, I note you're also using MAPQ of 255 for "unavailable". Commendable, but my experience is that everyone just uses 0...
The last record in [`test/vcf/4.3/passed/passed_body_format.vcf`] has a FORMAT key named `G%3AS` (percent-decoded to `G:S`), which is an invalid identifier. From _The Variant Call Format Specification: VCFv4.3 and BCFv2.2_ (2022-08-22) §...