running samtools view command produces no output

[robertwhbaldwin]

greetings,

I was using the samtools view command as follows:
samtools view -@ 10 -O BAM -o paired.bam -f 1 fixed.bam
and it worked fine the output bam is there.

But when I use the same command in pysam:
pysam.view("-@",str(threads), "-o", "test2.bam", "-O", "BAM", "-f","1","fixed.bam")

There's no output. Even when I remove the -o there's nothing to the terminal window. This is true even if I change the command to just convert a sam to bam. Running other samtools commands inside pysam like sort and index do work however.

[jmarshall]

By default, pysam.view() captures the output and returns it as the function's value. So you would see the output with print(pysam.view(…)).

You can prevent this by adding …, catch_stdout=False to enable your -o option to take effect. See also #1096.

At present pysam.samtools.*(…) and pysam.bcftools.*(…) are a bit too clever with I/O redirection. In particular, pysam.view()/pysam.samtools.view() will add its own -o output to effect the default redirection, which overrides your -o option and filename — hence why you need catch_stdout=False explicitly. In future I plan to change this to use more straightforward descriptor dup(2)-ing, which will make this more reliable and remove the need for this extra argument.