Writing out to a new bam file

[claudiadast]

I'm trying to use bamnostic to basically read in a BAM, filter out reads where any of the bases have a quality < 10, and then write out the remaining lines to a new BAM file. However, I'm a bit confused as to how you write things out using bamnostic. Here's what I have so far:

import bamnostic as bs
input_bam = bs.AlignmentFile("inputbam.bam", 'rb')
output_bam = bs.AlignmentFile("outputbam.bam", 'wb')

for read in bam:
        qual = read.query_qualities
        if all(q >= 10 for q in qual):
                output_bam.write(read)

But this fails. What's the correct way to write out the lines to a new bam file?

I even tried with the to_bam() method, but it fails as well due to TypeError: to_bam() takes exactly 1 argument (2 given):

out = bs.bam.BamWriter("filteredBam.bam", 'wb')
for read in bam:
        qual = read.query_qualities
        if all(q >= 10 for q in qual):
                   read.to_bam(out)

[betteridiot]

Thank you for bringing this up. This has been an ongoing feature addition for BAMnostic. For transparency's sake, I will shine a light on the issue.

Taking a read from one BAM file and writing it to another is the simplest case of a write function. This is because BAMnostic can just use the read's original unmodified bytes and just "transplant" them.

However, many users may want to create (and/or modify) a read. This is where a write function gets complicated. In this event; the read sequence, quality scores, and CIGAR string have to be re-validated for quality control reasons. Then the whole read has to be recompressed into bytes.

This is why BAMnostic only had very minimal features for writing out to BAM files (#5) and wasn't developed with that in mind.

However, a number of colleagues have asked for this feature set. Due to this new interest, a version should be pushed out within the next 1-2 weeks that will have this feature added.

I apologize for the inconvenience.

[betteridiot]

To be clear, what you wrote should have worked, but BAMnostic has some bugs that are making it not. It's not you, it's me.