bug in ext/htslib/configure.ac

[nadyawilliams]

The configuration file configure.ac is problematic due to the use of "make" on the AC_INIT line.
This works only in limited number of cases, specifically, when one runs configure by hand
outside of the automated build system. I need to run compilation automatically which involves
a few levels of instructions and executing make, cmake etc. For this, a verbose option of make
is enabled and is passed to sub-makes, which means lines "make1: Entering directory..." and
"make1: Leaving directory" and printed on stdout at each level of make.

When per your cmake configuration one gets to executing "autoeader && autoconf"" for htslib
the result of "make print-version" is not an expected string for version but 3 lines as below (directory name shortened for readability):

make7: Entering directory /export/...cut...//kallisto-0.46.2/ext/htslib' 1.4.1 make7: Leaving directory /export/...cut.../kallisto-0.46.2/ext/htslib'.

This happens because the output of "make print-version" is wrapped with entering/leaving
directory lines per top level Makefile because the stdout for target print-version is combined
now with the top level makes verbosity output.

The fix:
To prevent the erroneous stdout to be inserted in the output of autoconf one would need
to change AC_INIT line to use a command other than make. One can put PACKAGE_VERSION
definition from Makefile into the shell script and call the execution of this shell script in
place of "make print-version":
m4_esyscmd_s([./getVersion.sh 2>/dev/null])

This would avoid any verbosity from the makefiles.