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Number of reads in bam file

How to count the number of mapped reads in a BAM or SAM file?

# get the total number of reads of a BAM file (may include unmapped and duplicated multi-aligned reads)
samtools view -c SAMPLE.bam
568345

# counting only mapped (primary aligned) reads
samtools view -c -F 260 SAMPLE.bam
345623

options
  -c  count reads and print the total number
  -f bitcode  output reads that fulfill the checked 'bitcode' criteria, see SAM bitcode fields
  -F bitcode  exclude reads that match one or more checked 'bitcode' criteria, see SAM bitcode fields
  -F 260  output primary aligned mapped reads
                       read unmapped & not primary alignment criteria 3 & 9 are selected for exclusion
                       bit 3 + bit 9 = 4 + 256 = 260



decode SAM bitcode flag number (meaning of flag bits)
http://broadinstitute.github.io/picard/explain-flags.html