-print pysam.pileup.getMessages()
-
-for p in pysam.pileup( "-c", "ex1.bam", raw=True ):
- print str(p),
-
-
-
-print "###########################"
-
-samfile = pysam.Samfile( "ex2.sam.gz", "r" )
-
-print "num targets=", samfile.getNumTargets()
-
-iter = pysam.IteratorRowAll( samfile )
-for x in iter: print str(x)
-
-samfile.close()
-
-print "###########################"
-samfile = pysam.Samfile( "ex2.sam.gz", "r" )
-def my_fetch_callback( alignment ):
- print str(alignment)
-
-try:
- samfile.fetch( "chr1:10-20", my_fetch_callback )
-except AssertionError:
- print "caught fetch exception"
-
-samfile.close()