bam2fastq - extract raw sequence from BAM alignment files

http://www.hudsonalpha.org/gsl/software/bam2fastq.php

samtools idxstats
Retrieve and print stats in the index file. The output is TAB delimited with each line consisting of reference sequence name, sequence length, # mapped reads and # unmapped reads.

http://samtools.sourceforge.net/samtools.shtml