A bug: pysam.pileup will not work if all the reads per base qualities are 10 (+)

[dolittle007]

An interesting bug,
If reads per base qualities are all 10, (+++++++++), the pysam.pileup will not work properly.

[jmarshall]

In what way did it did not work properly? Please add an example program that demonstrates the problem.

[dolittle007]

I attached a small SAM file and codes to demonstrate this weird bug.
I've tested it using pysam 0.16.0.1 and 0.15.3, they both have this bug.
I also tried using different steppers ('all' and 'nofilter') in pysam.pileup. The bug is still there.

@HD	VN:1.6	SO:coordinate
@SQ	SN:chr1	LN:248956422
@RG	ID:XX	SM:hs	LB:ga	PL:PacBio
@PG	ID:minimap2	PN:minimap2	VN:2.17-r941	CL:minimap2 -t 8 -R @RG\tID:XX\tSM:hs\tLB:ga\tPL:PacBio --MD -ax splice:hq -uf --secondary=no hg38.fa XX.fastq
ccs	16	chr1	169691400	60	10M	*	0	0	ATCAAATTTG	++++++++++	RG:Z:XX	NM:i:0	ms:i:1705	AS:i:1581	nn:i:0	ts:A:+	tp:A:P	cm:i:544	s1:i:1604	s2:i:0	de:f:0	MD:Z:1705	rl:i:0

############################

sam =  pysam.AlignmentFile('example.sam','r')
for i in sam.pileup():
    for pileupread in i.pileups:
        print(pileupread)
    

The output will be empty.

But after changing the reads quality to "+++++~++++" (keep the rest part unchanged).
The output will be as expected.

ccs	16	0	169691399	60	10M	-1	-1	10	ATCAAATTTG	array('B', [10, 10, 93, 10, 10, 10, 10, 10, 10, 10])	[('RG', 'XX'), ('NM', 0), ('ms', 1705), ('AS', 1581), ('nn', 0), ('ts', '+'), ('tp', 'P'), ('cm', 544), ('s1', 1604), ('s2', 0), ('de', 0.0), ('MD', '1705'), ('rl', 0)]	2	0	1313935984	0	0	0	0

example.sam

Please fix it.
Thank you.

[jmarshall]

pileup() can omit bases with low quality scores. The default is to omit < 13, which means all your base quality 10s (+) are dropped. If you lower the quality threshold via e.g. sam.pileup(min_base_quality = 5) you will see all these bases in the output.