Swift access to C HTSLIB

Installation

On OSX with Homebrew

1. brew install homebrew/science/htslib
2. Get to version 1.3 brew switch htslib 1.3

General Unix isntallation

1. Download/compile htslib version 1.3
2. Install htslib with prefix /usr/local/

Usage

See jstjohn/swift-c-htslib-example

Limitations

• No swift wrappers around the C objects returned by htslib functions, they are all of type UnsafeMutablePointer<T>
• No swift support for C macros. Many functions like sam_open are actually macros that call other functions. You need to call the underlying function that the macro calls in swift. The workaround would be to reimplement all htslib macros as swift functions that replicate the behavior of the macro.
• Non-flexible requirement that htslib is installed to /usr/local/[include,lib,share]. The current swift package system does not have a nice way to package c libraries in a portable way Support for Other Build Systems