Is a patch to original sff_extract implementation still applicable to current code?

[mmokrejs]

Hi, in the past I found an error in sff_extract distributed through mira_3rdparty_06-07-2012.tar.bz2 , see https://www.freelists.org/post/mira_talk/sff-extract-fix-broken-handling-of-overlapped-trim-points-leaking-adapters-into-supposedly-clean-output .

The code in seq_crumbs is rewritten a lot but I wonder whether you would like to check whether the logic contain the same bug or not. Here is the patch: sff_extract.patch.txt

There used to be bug in biopython around 1.62 to 1.64 exploited by overlapped trimpoints which made the slicing go wrong. Test your seq_crumbs-based sff_extract with biopython-1.65 or newer.