Calculates simple stats for a BAM file


Usage: bamutils stats {options} file1.bam {file2.bam...}

If a region is given, only reads that map to that region will be counted.
Regions should be be in the format: 'ref:start-end' or 'ref:start' using
1-based start coordinates.

Options:
    -all    Show the stats for all fragments (defaults to just the first fragment)

    -nofill Don't fill in missing values when showing stat distributions

    -region chrom:start-end
            Only calculate statistics for this region

    -tags tag_name{:sort_order},tag_name{:sort_order},...

            For each tag that is given, the values for that tag will be
            tallied for all reads. Then a list of the counts will be presented
            along with the mean and maximum values. The optional sort order
            should be either '+' or '-' (defaults to +).

            There are also special case tags that can be used as well:
                MAPQ     - use the mapq score
                LENGTH   - use the length of the read
                MISMATCH - use the mismatch score (# mismatches) + (# indels)
                           where indels count for 1 regardless of length

                           Note: this requires the 'NM' tag (edit distance)
                           to be present

            Common tags:
                AS    Alignment score
                IH    Number of stored alignments in file for a read
                NH    Number of reported alignments for a read
                NM    Edit distance (each indel counts as many as its length)

            For example, to tally the "IH" tag (number of alignments) and the
            read length:
                -tags IH,LENGTH

    -delim char

            If delimiter is given, the reference names are split by this
            delimiter and only the first token is summarized.

    -gtf model.gtf

            If a GTF gene model is given, counts corresponding to exons,
            introns, promoters, junctions, intergenic, and mitochondrial
            regions will be calculated.

            Note: For paired-end reads, only the first fragment is counted
                  regardless of the {-all} option above