pysam.view method silently fails to write BAM file when --output is used

[sbslee]

Dear pysam team,

Thanks always for your hard work!

Today I'd like to report a potential bug in the pysam.view method. Basically, it appears that the method silently fails to write BAM file when --output is used.

For example, it correctly works if I simply print the output of the method:

(test) sbslee@Seung-beens-Mac-mini Desktop % cat test1.py 
import pysam
input_bam = 'HG00276_PyPGx.sorted.markdup.recal.bam'
region = 'chr22:42513500-42513510'
print(pysam.view(input_bam, region))
(test) sbslee@Seung-beens-Mac-mini Desktop % python test1.py | head -n 1
[W::hts_idx_load3] The index file is older than the data file: HG00276_PyPGx.sorted.markdup.recal.bai
HNMY2CCXX:3:1108:1832082:0	163	chr22	42513351	60	150M	=	42513555	354	TTTTTAATTCCACAGTGTTTGAAGGACATACTTGAAATAAATTTAAAATCCATTGAGATTTGTTTCGTGGTCCAGAATATGGCCTATCTTGGTGAATGTTTCATGTGTATGTGAAACTGAGGCATCCATCCCTCAGTTTCAACCACCCAT	?EEEEFIGHFFIEGFDGGIHHIKGGIEJIHFJHHILJHFDKIIIHKKKIGGDIJHCFDIIIHHIIG?HHGIGGDGIIDHIHGFGEGHGKIGGIHDKIHHII;KIHDGHB?:HHCD??J@DGFFJIGHJD<@1EFJ@DII@D4@=D@@;<D	MC:Z:150M	MD:Z:150	PG:Z:MarkDuplicates	RG:Z:2117	NM:i:0	AS:i:150	XS:i:27

However, if I try to write the output to a new BAM file using --output, it does nothing without producing any errors:

(test) sbslee@Seung-beens-Mac-mini Desktop % cat test2.py
import pysam
input_bam = 'HG00276_PyPGx.sorted.markdup.recal.bam'
output_bam = 'HG00276_PyPGx_CYP2D6.bam'
region = 'chr22:42513500-42513510'
pysam.view(input_bam, region, '--output', output_bam)
(test) sbslee@Seung-beens-Mac-mini Desktop % python test2.py 
[W::hts_idx_load3] The index file is older than the data file: HG00276_PyPGx.sorted.markdup.recal.bai

Link to test BAM file: https://1drv.ms/u/s!Apgoq3uQ2gCqgrsQmcNbCDYyw9rzsg?e=c86K1u
Link to test index file: https://1drv.ms/u/s!Apgoq3uQ2gCqgrsPD0TSk-2Kx1yDUg?e=TUYAUK

I'm using the latest version of pysam (0.19.0):

(test) sbslee@Seung-beens-Mac-mini Desktop % conda list | grep "pysam"
pysam                     0.19.0           py39h7ab3854_0    bioconda

I installed pysam using conda:

conda create -n test pysam=0.19.0

Thanks for your time!

[jmarshall]

If you wrapped print(…) around the call in test2.py, you would see that the output is captured as the return value of pysam.view() — just as in test1.py.

If you are using -o or --output or etc options to redirect the output yourself within the pysam.view() etc call, you need to use pysam.view(…, catch_stdout=False) as per #677 (comment) and #958 (comment) et al.

To be sure, this is not clearly documented.

[sbslee]

@jmarshall

Thanks for the prompt answer. I missed those issues when I was searching through the repository. Will close this as it's a duplicated question.