Region filtering permits samtools cat to produce new CRAMs that only
cover a specified region.  Eg

    samtools cat -o chr1-bit.cram -r chr1:10m-20m in.cram

This is the same as as view command, but considerably faster.

    samtools view -o chr1-bit.cram in.cram chr1:10m-20m

On a similar test the view command took 22.7s while the cat took 0.4s
and the files have the same records.  Unlike view we cannot change
format or do other filtering, however this samtools cat functionality
is designed for rapid read/write based region data extraction for
purposes of distributed processing pipelines.

This can be made faster still with the new -f option which doesn't
precisely filter containers that overlap the start and/or end of the
region, and instead copy out the whole container.

Note breaking up by region in this manner may give some alignment
records in more than one adjacent CRAM file as the record spans both
regions.

As elsewhere, region "*" represents the unmapped data, however we
can't subdivide this easily by position. Hence we can partition a
region, or the entire file, using `-p A/B` for part A of B total
parts.

For example the first tenth of unmapped data would be

    samtools cat -r "*" -p 1/10 -o unmapped_1.cram NA12878_S1.cram

Subdivisions in this manner will never share alignment records between
parts, so the sum of the parts will equal the original input data.

Regions can also be container numbers, using a custom region syntax of
"#:cnum-cnum" for inclusive container numbers, starting at zero.  As
with part numbers, records will not then be in multple output files
unless the same container numbers are shared between files.

We can use `samtools cat -q [-r region]` to query the number of
containers spanning that region and the first/last respectively.
For example, to query the containers for unmapped data.

    samtools cat -q -r "*" NA12878_S1.cram

A more complex usage which breaks a file up into a fixed size number
of containers regardless of part numbers can be implemented using `-q`:

    set -- $(samtools cat -q novaseq.10m.cram)
    nc=$2
    s=0
    while [ $s -lt $nc ]
    do
        e=`expr $s + 123`
        if [ $e -ge $nc ]
        then
            e=$nc
        fi
        r="#:$s-`expr $e - 1`"
        echo Region $r
        samtools cat -o part-`printf "%08d" $s`.cram novaseq.10m.cram -r $r
        s=$e
    done

    # Check with:
    samtools cat part*cram -o full.cram
    samtools view -c full.cram
    samtools view -c novaseq.10m.cram