To facilitate reprocessing data, it would be helpful if the pairtools suite permitted filtering an existing .pairs file using the same filters available in the parse and parse2 commands, such as --max-insert-size or max-inter-align-gap.
One way to do this might be to permit parse/parse2 to accept .pairs as input. Another way might be to split the filtering features into a separate command, and have the parse/parse2 commands bundle sam/bam -> pairs parsing with the separate filtering command.
I have an alternative solution which would be to reverse-parse .pairs to a .sam format, then stream it into parse/parse2. That's pretty hackish, so please let me know if you're seriously considering implementing this feature. Thanks for making this suite of useful tools!
To facilitate reprocessing data, it would be helpful if the pairtools suite permitted filtering an existing .pairs file using the same filters available in the parse and parse2 commands, such as
--max-insert-sizeormax-inter-align-gap.One way to do this might be to permit parse/parse2 to accept .pairs as input. Another way might be to split the filtering features into a separate command, and have the parse/parse2 commands bundle sam/bam -> pairs parsing with the separate filtering command.
I have an alternative solution which would be to reverse-parse .pairs to a .sam format, then stream it into parse/parse2. That's pretty hackish, so please let me know if you're seriously considering implementing this feature. Thanks for making this suite of useful tools!