[Biopython] comparing bam files

[Abhishek Pratap]

Hi All

This is my first post to the biopython mailing list. Basically I am
new to both Python and BioP.


So I have two bam files one contains the properly paired reads (file
A) and the other has some of the singeltons (file B) either (read 1 /
read 2).

I have to find the mates of all the singletons from the properly
paired bam file (file A) and then generate a bam file  (file C)which
has all the proper pairs for all the singletons I had.

PS: Also the file A is guaranteed to have all the pairs which might
exist as a singleton in file B.

I want to do this on the binary files and avoid reading in the sam
files. Is that something I can do using some of the bam readers in
biopython ?


Thanks!
-Abhi