I was wondering if it is possible to merge two separate BAM files into one paired-end BAM using packages from bioconductor.
I know how to do it using external algorithms, but I am writing a package and I need to do it with bioconductor packages.
I have two separate BAM files were pair information in each file is in its Qnames. For example for bam1, read1 has name: name1/1 and for bam2, read1 has name: name1/2.
I know there are functions for reading or testing pair-end bam files, so I thought it would be strange if there isnt any for writing pair-end bam files.