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Updates including fix for roi on counts-nano output and move to strict SAM as assumed in format command #62

	name: DNMTools build (macOS)

	on:
	workflow_dispatch:
	push:
	branches: [ "master" ]
	pull_request:
	branches: [ "master" ]

	jobs:
	build-with-gcc-on-x86:
	runs-on: macos-13
	steps:
	- uses: actions/checkout@v4
	with:
	submodules: recursive
	- name: Update Homebrew
	run: brew update
	- name: Install autotools
	run: brew install automake
	- name: Install dependencies
	run: brew install htslib gsl
	- name: Generate configure script
	run: ./autogen.sh
	- name: configure with g++-14
	run: ./configure CXX="g++-14" CPPFLAGS="-I$(brew --prefix)/include" LDFLAGS="-L$(brew --prefix)/lib"
	- name: make
	run: make -j4
	build-with-gcc-on-arm64:
	runs-on: macos-15
	steps:
	- uses: actions/checkout@v4
	with:
	submodules: recursive
	- name: Update Homebrew
	run: brew update
	- name: Install autotools
	run: brew install automake
	- name: Install dependencies
	run: brew install htslib gsl
	- name: Generate configure script
	run: ./autogen.sh
	- name: configure with g++-14
	run: ./configure CXX="g++-14" CPPFLAGS="-I$(brew --prefix)/include" LDFLAGS="-L$(brew --prefix)/lib"
	- name: make
	run: make -j4
	build-with-clang-on-arm64:
	runs-on: macos-15
	steps:
	- uses: actions/checkout@v4
	with:
	submodules: recursive
	- name: Update Homebrew
	run: brew update
	- name: Install autotools
	run: brew install automake
	- name: Install dependencies
	run: brew install htslib gsl
	- name: Generate configure script
	run: ./autogen.sh
	- name: configure with clang++
	run: ./configure CXX="clang++" CPPFLAGS="-I$(brew --prefix)/include" LDFLAGS="-L$(brew --prefix)/lib"
	- name: make
	run: make -j4