merge public master to my fork #11
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Update CRAM spec section on substitution matrix and codes.
* layed -> laid
Proposal to add Rasko Leinonen as refget maintainer.
#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 #425.
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.)
Update MAINTAINERS.md
Includes barebones authorizationCode Oauth2 flow, which should aid/inform code generation. Uses int64 with minimum 0, unsure if that is really an uint64 though.
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 #431
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