feat(hmnrandomread): add local dependency

Makefile

@@ -3,12 +3,13 @@ TARGET = HmnRandomRead
 DIRINC = ./include
 DIRSRC = ./src
 DIROBJ = ./obj
+DIRLIB=./lib
 
 SRC = $(wildcard $(DIRSRC)/*.cpp)
 OBJ = $(patsubst %.cpp,$(DIROBJ)/%.o,$(notdir $(SRC)))
 
 CXX = g++
-LIBS = -I $(DIRINC)
+LIBS = -I $(DIRINC) -I lib/htslib-1.16
 CXXFLAGS = -std=c++14 -Wall -Wextra -O3 -g3 -lhts
 
 # Rules

lib/htslib-1.16/INSTALL

@@ -0,0 +1,293 @@
+                    Building and Installing HTSlib
+                    ==============================
+
+Requirements
+============
+
+Building HTSlib requires a few programs and libraries to be present.
+See the "System Specific Details" below for guidance on how to install
+these.
+
+At least the following are required:
+
+    GNU make
+    C compiler (e.g. gcc or clang)
+
+In addition, building the configure script requires:
+
+    autoheader
+    autoconf
+    autoreconf
+
+Running the configure script uses awk, along with a number of
+standard UNIX tools (cat, cp, grep, mv, rm, sed, among others).  Almost
+all installations will have these already.
+
+Running the test harness (make test) uses:
+
+    bash
+    perl
+
+HTSlib uses the following external libraries.  Building requires both the
+library itself, and include files needed to compile code that uses functions
+from the library.  Note that some Linux distributions put include files in
+a development ('-dev' or '-devel') package separate from the main library.
+
+    zlib       (required)
+    libbz2     (required, unless configured with --disable-bz2)
+    liblzma    (required, unless configured with --disable-lzma)
+    libcurl    (optional, but strongly recommended)
+    libcrypto  (optional for Amazon S3 support; not needed on MacOS)
+
+Disabling libbzip2 and liblzma will make some CRAM files unreadable, so
+is not recommended.
+
+Using libcurl provides HTSlib with network protocol support, for
+example it enables the use of ftp://, http://, and https:// URLs.
+It is also required if direct access to Amazon S3 or Google Cloud
+Storage is enabled.
+
+Amazon S3 support requires an HMAC function to calculate a message
+authentication code.  On MacOS, the CCHmac function from the standard
+library is used.  Systems that do not have CCHmac will get this from
+libcrypto.  libcrypto is part of OpenSSL or one of its derivatives (LibreSSL
+or BoringSSL).
+
+On Microsoft Windows we recommend use of Mingw64/Msys2.  Whilst the
+code may work on Windows with other environments, these have not been
+verified.  Use of the configure script is a requirement too.
+
+Update htscodecs submodule
+==========================
+
+Note that this section only applies to git checkouts.  If you're building
+from a release tar file, you can skip this section.
+
+Some parts of HTSlib are provided by the external "htscodecs" project.  This
+is included as a submodule.  When building from the git repository,
+either clone the project using "git clone --recurse-submodules", or run:
+
+    git submodule update --init --recursive
+
+to ensure the correct version of the submodule is present.
+
+It is also possible to link against an external libhtscodecs library
+by using the '--with-external-htscodecs' configure option.  When
+this is used, the submodule files will be ignored.
+
+Building Configure
+==================
+
+This step is only needed if configure.ac has been changed, or if configure
+does not exist (for example, when building from a git clone).  The
+configure script and config.h.in can be built by running:
+
+    autoreconf -i
+
+Basic Installation
+==================
+
+To build and install HTSlib, 'cd' to the htslib-1.x directory containing
+the package's source and type the following commands:
+
+    ./configure
+    make
+    make install
+
+The './configure' command checks your build environment and allows various
+optional functionality to be enabled (see Configuration below).  If you
+don't want to select any optional functionality, you may wish to omit
+configure and just type 'make; make install' as for previous versions
+of HTSlib.  However if the build fails you should run './configure' as
+it can diagnose the common reasons for build failures.
+
+The 'make' command builds the HTSlib library and various useful
+utilities: bgzip, htsfile, and tabix.  If compilation fails you should
+run './configure' as it can diagnose problems with your build environment
+that cause build failures.
+
+The 'make install' command installs the libraries, library header files,
+utilities, several manual pages, and a pkgconfig file to /usr/local.
+The installation location can be changed by configuring with --prefix=DIR
+or via 'make prefix=DIR install' (see Installation Locations below).
+
+
+Configuration
+=============
+
+By default, './configure' examines your build environment, checking for
+requirements such as the zlib development files, and arranges for a plain
+HTSlib build.  The following configure options can be used to enable
+various features and specify further optional external requirements:
+
+--enable-plugins
+    Use plugins to implement exotic file access protocols and other
+    specialised facilities.  This enables such facilities to be developed
+    and packaged outwith HTSlib, and somewhat isolates HTSlib-using programs
+    from their library dependencies.  By default (or with --disable-plugins),
+    any enabled pluggable facilities (such as libcurl file access) are built
+    directly within HTSlib.
+
+    The <https://github.com/samtools/htslib-plugins> repository contains
+    several additional plugins, including the iRODS (<http://irods.org/>)
+    file access plugin previously distributed with HTSlib.
+
+--with-plugin-dir=DIR
+    Specifies the directory into which plugins built while building HTSlib
+    should be installed; by default, LIBEXECDIR/htslib.
+
+--with-plugin-path=DIR:DIR:DIR...
+    Specifies the list of directories that HTSlib will search for plugins.
+    By default, only the directory specified via --with-plugin-dir will be
+    searched; you can use --with-plugin-path='DIR:$(plugindir):DIR' and so
+    on to cause additional directories to be searched.
+
+--with-external-htscodecs
+    Build and link against an external copy of the htscodecs library
+    instead of using the source files in the htscodecs directory.
+
+--enable-libcurl
+    Use libcurl (<http://curl.se/>) to implement network access to
+    remote files via FTP, HTTP, HTTPS, etc.  By default or with
+    --enable-libcurl=check, configure will probe for libcurl and include
+    this functionality if libcurl is available.  Use --disable-libcurl
+    to prevent this.
+
+--enable-gcs
+    Implement network access to Google Cloud Storage.  By default or with
+    --enable-gcs=check, this is enabled when libcurl is enabled.
+
+--enable-s3
+    Implement network access to Amazon AWS S3.  By default or with
+    --enable-s3=check, this is enabled when libcurl is enabled.
+
+--disable-bz2
+    Bzip2 is an optional compression codec format for CRAM, included
+    in HTSlib by default.  It can be disabled with --disable-bz2, but
+    be aware that not all CRAM files may be possible to decode.
+
+--disable-lzma
+    LZMA is an optional compression codec for CRAM, included in HTSlib
+    by default.  It can be disabled with --disable-lzma, but be aware
+    that not all CRAM files may be possible to decode.
+
+--with-libdeflate
+    Libdeflate is a heavily optimized library for DEFLATE-based compression
+    and decompression.  It also includes a fast crc32 implementation.
+    By default, ./configure will probe for libdeflate and use it if
+    available.  To prevent this, use --without-libdeflate.
+
+Each --enable-FEATURE/--disable-FEATURE/--with-PACKAGE/--without-PACKAGE
+option listed also has an opposite, e.g., --without-external-htscodecs
+or --disable-plugins.  However, apart from those options for which the
+default is to probe for related facilities, using these opposite options
+is mostly unnecessary as they just select the default configure behaviour.
+
+The configure script also accepts the usual options and environment variables
+for tuning installation locations and compilers: type './configure --help'
+for details.  For example,
+
+    ./configure CC=icc --prefix=/opt/icc-compiled
+
+would specify that HTSlib is to be built with icc and installed into bin,
+lib, etc subdirectories under /opt/icc-compiled.
+
+If dependencies have been installed in non-standard locations (i.e. not on
+the normal include and library search paths) then the CPPFLAGS and LDFLAGS
+environment variables can be used to set the options needed to find them.
+For example, NetBSD users may use:
+
+    ./configure CPPFLAGS=-I/usr/pkg/include \
+                LDFLAGS='-L/usr/pkg/lib -Wl,-R/usr/pkg/lib'
+
+to allow compiling and linking against dependencies installed via the ports
+collection.
+
+Installation Locations
+======================
+
+By default, 'make install' installs HTSlib libraries under /usr/local/lib,
+HTSlib header files under /usr/local/include, utility programs under
+/usr/local/bin, etc.  (To be precise, the header files are installed within
+a fixed 'htslib' subdirectory under the specified .../include location.)
+
+You can specify a different location to install HTSlib by configuring
+with --prefix=DIR or specify locations for particular parts of HTSlib by
+configuring with --libdir=DIR and so on.  Type './configure --help' for
+the full list of such install directory options.
+
+Alternatively you can specify different locations at install time by
+typing 'make prefix=DIR install' or 'make libdir=DIR install' and so on.
+Consult the list of prefix/exec_prefix/etc variables near the top of the
+Makefile for the full list of such variables that can be overridden.
+
+You can also specify a staging area by typing 'make DESTDIR=DIR install',
+possibly in conjunction with other --prefix or prefix=DIR settings.
+For example,
+
+    make DESTDIR=/tmp/staging prefix=/opt
+
+would install into bin, lib, etc subdirectories under /tmp/staging/opt.
+
+
+System Specific Details
+=======================
+
+Installing the prerequisites is system dependent and there is more
+than one correct way of satisfying these, including downloading them
+from source, compiling and installing them yourself.
+
+For people with super-user access, we provide an example set of commands
+below for installing the dependencies on a variety of operating system
+distributions.  Note these are not specific recommendations on distribution,
+compiler or SSL implementation.  It is assumed you already have the core set
+of packages for the given distribution - the lists may be incomplete if
+this is not the case.
+
+Debian / Ubuntu
+---------------
+
+sudo apt-get update  # Ensure the package list is up to date
+sudo apt-get install autoconf automake make gcc perl zlib1g-dev libbz2-dev liblzma-dev libcurl4-gnutls-dev libssl-dev
+
+Note: libcurl4-openssl-dev can be used as an alternative to libcurl4-gnutls-dev.
+
+RedHat / CentOS
+---------------
+
+sudo yum install autoconf automake make gcc perl-Data-Dumper zlib-devel bzip2 bzip2-devel xz-devel curl-devel openssl-devel
+
+Note: On some versions perl FindBin will need to be installed to make the tests work.
+
+sudo yum install perl-FindBin
+
+Alpine Linux
+------------
+
+doas apk update  # Ensure the package list is up to date
+doas apk add autoconf automake make gcc musl-dev perl bash zlib-dev bzip2-dev xz-dev curl-dev libressl-dev
+
+OpenSUSE
+--------
+
+sudo zypper install autoconf automake make gcc perl zlib-devel libbz2-devel xz-devel libcurl-devel libopenssl-devel
+
+Windows MSYS2/MINGW64
+---------------------
+
+The configure script must be used as without it the compilation will
+likely fail.
+
+Follow MSYS2 installation instructions at
+https://www.msys2.org/wiki/MSYS2-installation/
+
+Then relaunch to MSYS2 shell using the "MSYS2 MinGW x64" executable.
+Once in that environment (check $MSYSTEM equals "MINGW64") install the
+compilers using pacman -S and the following package list:
+
+base-devel mingw-w64-x86_64-toolchain
+mingw-w64-x86_64-libdeflate mingw-w64-x86_64-zlib mingw-w64-x86_64-bzip2
+mingw-w64-x86_64-xz mingw-w64-x86_64-curl mingw-w64-x86_64-autotools
+mingw-w64-x86_64-tools-git
+
+(The last is only needed for building libraries compatible with MSVC.)

lib/htslib-1.16/LICENSE

@@ -0,0 +1,69 @@
+[Files in this distribution outwith the cram/ subdirectory are distributed
+according to the terms of the following MIT/Expat license.]
+
+The MIT/Expat License
+
+Copyright (C) 2012-2022 Genome Research Ltd.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.
+
+
+[Files within the cram/ subdirectory in this distribution are distributed
+according to the terms of the following Modified 3-Clause BSD license.]
+
+The Modified-BSD License
+
+Copyright (C) 2012-2022 Genome Research Ltd.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice,
+   this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the names Genome Research Ltd and Wellcome Trust Sanger Institute
+   nor the names of its contributors may be used to endorse or promote products
+   derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR ITS CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+
+[The use of a range of years within a copyright notice in this distribution
+should be interpreted as being equivalent to a list of years including the
+first and last year specified and all consecutive years between them.
+
+For example, a copyright notice that reads "Copyright (C) 2005, 2007-2009,
+2011-2012" should be interpreted as being identical to a notice that reads
+"Copyright (C) 2005, 2007, 2008, 2009, 2011, 2012" and a copyright notice
+that reads "Copyright (C) 2005-2012" should be interpreted as being identical
+to a notice that reads "Copyright (C) 2005, 2006, 2007, 2008, 2009, 2010,
+2011, 2012".]