pysam 0.16.0.1 and pysam 0.9.1 give different results

[Jia Zheng]

Hi all,

I used the following code to get the numbers of reads at each position mapped to the reference.

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FileName = sys.argv[1]

samfile = pysam.AlignmentFile(FileName, "rb")

numlist=[]

for pileupcolumn in samfile.pileup("ref",start = 55, stop = 61,truncate=True, max_depth=200000,min_mapping_quality=20):

if pileupcolumn.pos>=starP and pileupcolumn.pos<endP:

numMapped=0

for pileupread in pileupcolumn.pileups:

numMapped+=1

numlist.append(numMapped)

print numlist

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I saved the above code in a file named 'test.py' and then run the script respectively using my laptop (with pysam 0.16.0.1 installed) and office computer (with pysam 0.9.1 installed) as follows:

python test.py input.bam

Then I got different results below. 

the output from pysam 0.16.0.1

 [15481, 15476, 15473, 15473, 15475, 15474]

the output from pysam 0.9.1

 [15486, 15486, 15486, 15486, 15486, 15486]

Anyone knows why? Much appreciated for your help in advance!

Best,

Jia

[Hassan Raza]

Use the latest pysam version, yes there were some updates which corrected and improved the outputs.