Count number of alignments per query

[fgvieira]

bamtools count gives the total number of alignments in the BAM file, optionally restricted to some regions.

It would be nice if one could have it grouped by (e.g.) query (i.e. read id) or read group. Even better, if one could restrict the output to groups with a certain number of alignments (e.g. print number of alignments for queries with more than 1000 alignments).