Slice and Container ref seq IDs must match #401
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jkbonfield
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jmarshall
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thefferon
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* Update CRAM spec section on substitution matrix and codes. * Respond to review comments. * CRAM Slice and Container ref seq IDs must match (samtools#401) * Code review part 2. * Fix minor typo in the predecessors of BCF2 (samtools#427) * layed -> laid * Update MAINTAINERS.md (samtools#432) Proposal to add Rasko Leinonen as refget maintainer. * add jmmut to MAINTAINERS.md and move Cristina to "Past Members" * change order of maintainers * Clarify that INFO/END is used to form a CHROM:POS-END region (PR samtools#436) (samtools#436) INFO/END (when present) provides the size of the interval that the variant is located in, along with the CHROM and POS fields. This is also used when indexing VCF/BCF files, as can be gleaned from §6.3.1's description of BCF's rlen field. The implications of INFO/END have not previously been clear. In the absence of clear documentation, some SV tools have been using INFO/END fields for their own semi-related purposes (using INFO/CHR2:INFO/END as the other side's position in an interchromosomal rearrangement), leading to broken .csi indexes and region queries that don't work. Fixes samtools#425. * Allow C and Java native text spellings of NaN and infinities (samtools#409) C's printf doesn't output mixed case, while Java's Double.valueOf and Double.toString parse/output only `Infinity`, not `Inf`. Rather than requiring special-case code for both input and output in both languages, relax the VCF specification to allow NAN/INF/INFINITY case-insensitively. (Add "IEEE-754" to be specific and to improve the line breaks.) * Adding a note about <NON_REF> (samtools#380) * Update PDFs (CRAM and VCF additions; others cosmetic) CRAMv3 PRs samtools#401 and samtools#412. VCFv4.3 PRs samtools#380 (<NON_REF>), samtools#409 (infinity/NaN), and samtools#436 (INFO/END). All: Minor typo and whitespace formatting fixes. * Add htsget 1.2.0 OpenAPI v3.0.2 spec (PR samtools#385) Includes barebones authorizationCode Oauth2 flow, which should aid/inform code generation. Uses int64 with minimum 0, unsure if that is really an uint64 though. * Codify the existing policy of generally squashing PRs (PR samtools#444) * Permit AP_Delta in multi-ref slices. This means AP_delta can become negative. I have validated this decodes fine in both htsjdk and htslib. This is because AP is ITF8 and hence signed, like all other integers, so it would need explicit code to forbid this (which obviously isn't in the implementations). Hence the limitation is primarily one of an over-zealous specification. The impact of this is for position-sorted multi-ref slices AP can legally be stored efficiently. Also clarified fields in the container compression header when in multi-ref mode. Fixes samtools#431
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Resolves the remaining piece of #370