Tipp3

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. Removed additional temp files that are generated when merging
classifications.

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. Added a missing check for input file existence.
. Adjusted scripts for customizing a TIPP3 reference package.
. Restructured some of the Job classes to be more flexible with customized
parameters from ``main.config`` or ``-c custom.config``. E.g., now that you
can change any supported parameters of BSCAMPP in a customized config file.
See ``custom.config`` on the GitHub page for an example.
. Fixed an issue that overrides user-defined placement and alignment methods.
. Changed from using ``lz4`` to ``gzip`` on compressing intermediate files
for better compatibility.

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. Removed standalone code for BSCAMPP that was previously included under
``tipp3/tools/bscampp``. Now ``bscampp`` is a requirement that will be
installed when TIPP3 is installed.

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. Added the full pipeline to create a customized TIPP reference package. Please
refer to the Wiki page and the Jupyter notebook in ``refpkg_scripts``.
. Added subcommands: "abundance" and "download_refpkg".
``run_tipp3.py abundance`` has the original TIPP3 behavior for abundance
profiling. ``run_tipp3.py download_refpkg`` can be used to download the
latest TIPP3 reference package to a designated directory. For adjustment,
The other two installed binaries ``tipp3`` and ``tipp3-fast`` now function
only for the subcommand "abundance".
. Fixed help text typos and adjusted exception logging to exit with
return code 1.

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. Fixed a missing exit command for function ``tipp3_stop()``.
. Minor help text fixes.

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. Fixed a bug in code that prevented BLASTN from reading in fasta/fa files
correctly.
. Added new output file ``query_classifications.tsv`` that aggregates all
mapped query reads with their taxonomic identifications.
. Included other minor bug fixes and code updates.