How can I get the number of mapped reads for a particular region?

`samtools view -c -F 4 my.bam` gives me count in the entire bam file but I can't just add `-r Chr1:0:1000` to get reads in that region only.
    samtools view in.bam chr1:0-1000 | wc -l

but better way is to do it with <a href="http://bedtools.readthedocs.org/en/latest/content/tools/multicov.html">bedtools</a> if you have many regions, for e.g like exon coordinates or peak coordinates, which is more efficient way for counting purpose.

    bedtools multicov -bams aln1.bam [ aln2.bam aln3.bam . . ] -bed ivls-of-interest.bed