sum of products of mapq and mapped bases for each read in a from a BAM file Given a BAM file, I'd like to calculate the sum, over all reads, of the mapping quality and the number of mapped bases (i.e. number of M's in the CIGAR string).

For example, given two reads like this:

read1: mapq=40, mapped_bases=10
read2: mapq=20, mapped_bases=50


The number I'm looking for is: 

(40*10) + (20*50) = 1400


One option here is to stream the file and get the two quantities line-by-line. But this seems likely to be slow. Thoughts welcome.
BAM files are stored line by line, so your only option is to process it that way. In python with pysam:

import pysam

bam = pysam.AlignmentFile("something.bam")
tot = 0
for read in bam.fetch():
    if read.is_unmapped:
        continue
    tl = 0
    for op, l in read.cigartuples:
        if op in [0, 7, 8]:
            tl += l
    tot += tl * read.mapping_quality
bam.close()
print("the total is {}".format(tot))