I have a bam file produces by BWA-MEM. It has some unmapped reads, e.g.

    D00733:389:CD1T7ANXX:3:1101:1572:2235	77	*	0	0	*	*	0	0	CAGTTTCACTGTATAAATTGCTTATACTTAGACATGCATGGCTTAATCTT	AAB=AFGDGCFFGGGGGGGGGCGGGGGGGGGGGGGGGGGGGGGGGGGGGF	AS:i:0	XS:i:0
    D00733:389:CD1T7ANXX:3:1101:1572:2235	141	*	0	0	*	*	0	0	GTATCTTCTAGAGAGAGGGAATGGGCGAGAGAAAAAGAGATTTCGGTTTC	BBB@BGGGGGGGGFGGGGGGGGEGGGGGGDGFGGGGGGGGEGGGGGFGGG	AS:i:0	XS:i:0
    D00733:389:CD1T7ANXX:3:1101:6797:2243	77	*	0	0	*	*	0	0	TGTCTGGACCTGGTGAGTTTCCCCGTGTTGAGTCAAATTAAGCCGCAGGC	3A<0BDGGGGGGGGGGGGGFGGGGGFGGGGGGGGGGGGGGGGGGGGGGGG	AS:i:0	XS:i:0


I use pysam to count some stats on the bam file, but for some reason pysam does not find these unmapped reads.

    bam=pysam.AlignmentFile(file,"rb")
    for line in bam.fetch():
        line=line.tostring(bam)
	    line=line.split("\t")
	    if  line[2]=="*":
		    print(line)

The code does not return anything

Any ideas how to fix this?

Thanks

you should add `until_eof=True` in the `fetch()`