extract method to get the reads_mapped data from a flagstat file

code-deduplication: abrummet
extract method to open and initialize the output file

code-deduplication: abrummet
proper scoping on the subroutine

code-deduplication: abrummet
whitespace

code-deduplication: abrummet
extract method to get the right bam file

code-deduplication: abrummet
extract method to get the right input flagstat file

code-deduplication: abrummet
Simplify variable names

Make these variables less specific to this module.  Its execute() will
take over for Genome::Model::Tools::Synthesizer::StatsGenerator::execute()
which is functionally the same.

code-deduplication: abrummet
Defer to the other class' execute()

Genome::Model::SmallRns::Command::StatsGenerator::execute() has been
refactored to be generic enough for GMT::Synthesizer::StatsGenerator::execute(),
as long as the latter defines functions for output_file_headers(),
resolve_bam_file() and resolve_input_flagstat_file().

The main differences were output file headers and command-line parameter
names.  Also, the GMT version fabbed up its own command lines for running
mergeBed and intersectBed.  The former uses another GMT module to accomplish
the same thign.

code-deduplication: abrummet