Various bug fixes.
Added code to generate logs when a crash occurs. Must upgrade to LispWorks 6.1.1 to use this.
Split/Merge tools:
- Missed duplicate marking of fragments that are potential duplicates because they match with pairs  where reads map to different chromosomes. Such pairs were separated into the spread reads file. elPrep now duplicates the information by duplicating reads of such pairs in their “chromosome” file. We also added a filter that removes these reads again when outputting result files. All of this is possible through elPrep’s standard filter architecture.
- Verification issues for split/merge results. The order in which pairs are processed may impact which reads are marked as duplicates. This is because pairs may have identical scores compared to their duplicate pairs. So depending on distribution, parallelism, the order in which pairs are checked varies hence it varies which pair is marked duplicate. Added a test where we always mark the pair with the longest qname. Only use this for verifying results.
Merge tool:
- added check for non-existing “chromosome” files which can happen after replacing the reference sequence dictionary.
- fixed bug in merge loop that occurred when merging empty chromosome file to an empty spread reads file.
Utils:
- tree-reduce on empty input returns empty list instead of t.