Fix build issues by updating alignment-writer to v0.4.0.

Added a more descriptive error message when attempting to read from files that are in an unsupported format (see #10).

Changelog

Usage changes

• Require the number of pseudoalignment targets as the --n-refs parameter when calling telescope. This is because the number cannot be determined from the themisto plaintext file format.

Added features

• Added the --cin toggle to read the last alignment file from cin (default: false).
• Added the --merge toggle for merging two or more Themisto pseudoalignments into a single file (rather than writing the kallisto style output) (default: false).
• Added the --write-compact toggle for writing the pseudoalignments from --merge in the alignment-writer format (default: true).

Removed features

• Removed the --index argument since it is no longer supported with Themisto >=v2.0.0.
• Removed the unpaired mode which concatenated two or more alignments into a single alignment.
• Removed many unused methods and methods that modified class member variables in unintuitive ways.

Internal changes

• Extensive rewrite of the entire codebase to approach a state that can be released as a stable version.

Build pipeline

• C++17 is now required to build telescope.
• Added more verbose flags for Debug builds.
• Added some optimization flags for Release builds.
• Include the headers in a smarter way to help providing them when building as part of other projects.
• Rename log.hpp and version.h with the telescope_ prefix to avoid name clashes with other projects.

Reimplement input reading functions using the BitMagic library.

• Speed up reading in alignments.
• Reduced memory footprint on large problems.

Housekeeping and major rewrites.

New features

• New 'ThemistoGrouped()' function for reading in Themisto alignments and returning the alignment counts per some user-defined grouping.

Code structure

• Wrapped everything in namespace 'telescope'.
• Wrapped functions that read input to namespace 'telescope::read', and functions that write output to namespace 'telescope::write'.
• Better naming for all functions.
• Cleaned up the header files so that everything can be used in external projects by simply including the 'telescope.hpp' header.

Build pipeline

• Download cxxio instead of shipping with telescope.
• Add download option for the googletest framework with -DCMAKE_BUILD_TESTS=1.

Changes to build pipeline and dependencies:

Dependencies

• Swap zstr to bxzstr.
• Download bxzstr and cxxargs from GitHub when building instead of shipping with telescope.
• ...but also allow providing predownloaded bxzstr and cxxargs headers via the CMAKE_BXZSTR_HEADERS and CMAKE_CXXARGS_HEADERS options to the cmake call.

Build pipeline

• Support slightly older versions of cmake (minimum v2.8.12 instead of v3.0).
• Remove the -Wno-sign-compare flag when building in Debug mode.
• Add the -Wpedantic flag when building in Debug mode.

v0.2.0 of telescope

• Add (faster) functions for reading in kallisto alignments.
• Better error checking for input directories and files.
• Require Themisto alignment index directory as input (replaces giving --n-refs through command line).
• Add support for working with Themisto-style pseudoalignments.
• Add data structures for pseudoalignment, kallisto-style pseudoalignment, and Themisto-style pseudoalignment.

Fix build issues on GCC and on Linux.