Add -b option to samtools merge manpage

[SamStudio8]

The manpage for samtools merge is missing documentation on the -b option to provide an input list of BAM files to merge.

Also providing a file to the -b option for samtools merge appears to override any file selection made at the command line, I have added an alternative syntax line in the documentation to try and clarify this.

[SamStudio8]

The manpage version of the usage syntax is also missing descriptions of the following options that are listed in bam_sort.c:

* -l INT   compression level, from 0 to 9 [-1]
* -@ INT   number of BAM compression threads [0]
* -c       combine RG tags with colliding IDs rather than amending them
* -p       combine PG tags with colliding IDs rather than amending them
* -s VALUE override random seed

Should I add these in? I guess the syntax should therefore read something like:

samtools merge [-nur1fcp] [-@ <threads>] [-h <inh.sam>] [-l <compression>] [-R <region>] [-s <seed>] <out.bam> <in1.bam> <in2.bam> [...]
samtools merge [-nur1fcp] [-@ <threads>] [-h <inh.sam>] [-l <compression>] [-R <region>] [-s <seed>] -b <list> <out.bam>

[jrandall]

For what it's worth, I also don't think the [...] is as clear as it could be.
I'd suggest: [<in3.bam> ... <inN.bam>]

Of course, that usage line is getting mighty long. It may at some point make sense to compress the common options:

samtools merge [merge_options] <out.bam> <in1.bam> <in2.bam> [<in3.bam> ... <inN.bam>]
samtools merge [merge_options] -b <bamlist.fofn> <out.bam>

And then list the valid merge_options below (where -b <bamlist.fofn> is not considered an option but rather an argument in the alternate form).

[mp15]

Merged into PR #202