import HTSeq
bamfile = HTSeq.BAM_Reader("SRR001432_head.bam")
gtffile = HTSeq.GFF_Reader("Homo_sapiens.GRCh37.56_chrom1.gtf")
coverage = HTSeq.GenomicArray("auto", stranded=False, typecode="i")
for almnt in bamfile:
   if almnt.aligned:
      coverage[almnt.iv] += 1