Opened 4 years ago

Closed 3 years ago

#913 closed request (fixed)

BamPairIterator sorted wrt first read

Reported by: Peter Owned by: Peter
Priority: major Milestone: yat 0.18
Component: omic Version:
Keywords: Cc:

Description

BamPairIterator? iterates over read pairs such that sorted with respect to the second read. Here, instead we want the same thing but sorted with respect to the first read.

It's dangerous in the general case as iterator has to store virtually everything between current ::first and ::second (its mate), so if read pairs with large \c isize are included this is not feasible (in contrast to the current BamPairIterator)

Change History (2)

comment:1 Changed 3 years ago by Peter

Milestone: yat 0.x+yat 0.18
Status: newaccepted

comment:2 Changed 3 years ago by Peter

Resolution: fixed
Status: acceptedclosed

In 3878:

New class BamPairIterator2 that takes a sort range of bam reads as
input and behaves as iterating through bam read pairs sorted with
respect to the second read. Also fixed an error in
test::Suite::trivial_iterator and apply that test on BamPairIterator?

closes #913
fixes #838

Note: See TracTickets for help on using tickets.