How to update htslib.cr when htslib is upgraded ?

[kojix2]

Here, let's consider how to update htslib.cr when htslib is updated.

(1) Install crystal_lib and make sure it works.
(2) Next, use crystal_lib to automatically generate the bindings. (llvm needed)

The created htslib bindings are in a single file.
This can lead to poor readability, becuse, htslib consists of various files formats such as sam, bam, vcf, bcf, tabix, etc.

(3) Format file

(4) Problems with generated C bindings

1. bit-fields
2. duplicate definition: alias / type

This is a serious problem. crystal_lib cannot parse bitfields. htslib structures often contain bitfields. Therefore, the bitfields need to be commented out. This fix currently needs to be done manually.

Perform automatic code formatting with the crystal command.
Other than automatic formatting, manual code formatting may not be recommended here. It certainly makes the code more readable, but it is best to avoid doing that every time htslib is upgraded.

[kojix2]

Structs

    struct Bgzf

    struct KstringT

    struct SamHdrT

    struct HtsOpt
    struct HtsFile
    struct HtsFormat
    struct HtsFormatVersion
    struct HtsThreadPool
    struct HtsPairPosT
    struct HtsPair64T
    struct HtsPair64MaxT
    struct HtsReglistT
    struct HtsItrT
    struct HtsItrTBins

    struct Bam1T
    struct Bam1CoreT
    struct BamPileup1T

    struct HtsBaseMod

    struct TbxConfT
    struct TbxT

    struct BcfHdrT
    struct BcfIdpairT
    struct BcfIdinfoT
    struct BcfHrecT
    struct Bcf1T
    struct BcfDecT
    struct BcfInfoT
    struct BcfFmtT
    struct BcfVariantT

Enums

    enum HtsLogLevel
    enum HtsFmtOption
    enum HtsFormatCategory
    enum HtsExactFormat
    enum HtsCompression
    enum CramContentType